Index

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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

$

$(String) - Static method in class org.jmol.i18n.GT
 

A

a - Variable in class javajs.util.Matrix
 
a - Variable in class org.jmol.g3d.PrecisionRenderer
 
a - Variable in class org.jmol.util.SimpleUnitCell
 
a_ - Variable in class org.jmol.util.SimpleUnitCell
 
A4 - Class in javajs.util
A 4 element axis angle represented by single precision floating point x,y,z,angle components.
A4() - Constructor for class javajs.util.A4
Constructs and initializes a AxisAngle4f to (0,0,1,0).
aaTest1 - Variable in class org.jmol.viewer.TransformManager
 
aatoken - Variable in class org.jmol.script.ScriptEval
 
AB - Enum constant in enum class jspecview.common.PanelData.LinkMode
 
ABC - Enum constant in enum class jspecview.common.PanelData.LinkMode
 
ABI_IJ - Static variable in class org.jmol.minimize.forcefield.ForceField
 
ABI_JK - Static variable in class org.jmol.minimize.forcefield.ForceField
 
AbinitReader - Class in org.jmol.adapter.readers.xtal
 
AbinitReader() - Constructor for class org.jmol.adapter.readers.xtal.AbinitReader
 
aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
 
AboutDialog - Class in jspecview.application
The About Dialog class is the help | about window for JSpecView.
AboutDialog - Class in org.openscience.jmol.app.jmolpanel
 
AboutDialog(Frame) - Constructor for class jspecview.application.AboutDialog
Constructor that initalises the Dialog a parent frame, no title and modality to true
AboutDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
 
abs - Static variable in class org.jmol.script.T
 
absolute - Static variable in class org.jmol.script.T
 
ABSOLUTE - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
 
AbstractButton - Class in org.jmol.awtjs.swing
 
AbstractButton(String) - Constructor for class org.jmol.awtjs.swing.AbstractButton
 
AbstractTableModel - Interface in org.jmol.awtjs.swing
 
ac - Variable in class org.jmol.adapter.readers.cif.CifReader
 
ac - Variable in class org.jmol.adapter.readers.simple.InputReader
 
ac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
ac - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ac - Variable in class org.jmol.atomdata.AtomData
 
ac - Variable in class org.jmol.jvxl.readers.JvxlReader
 
ac - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
ac - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
ac - Variable in class org.jmol.modelset.AtomCollection
 
ac - Variable in class org.jmol.util.JmolMolecule
 
accept(File) - Method in class jspecview.java.AwtDialogFileFilter
Implementation of method from interface FileFilter.
accept(File) - Method in class org.jmol.dialog.Dialog.TypeFilter
 
accept(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
 
ACCEPTOR - Enum constant in enum class org.jmol.c.HB
 
acm - Variable in class org.jmol.viewer.Viewer
 
acos - Static variable in class org.jmol.script.T
 
act - Variable in class org.jmol.modelset.Model
atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
action(String) - Method in interface org.jmol.api.JmolAudioPlayer
 
action(String) - Method in class org.jmol.util.JmolAudio
Execute an action from load audio "xxxxx.wav" filter "id=a1 action=xxx"
ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_center - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_count - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_select - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
 
ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
actionCommand - Variable in class org.jmol.awtjs.swing.JComponent
 
actionListener - Variable in class org.jmol.awtjs.swing.JComponent
 
actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
ActionManager - Class in org.jmol.viewer
 
ActionManager() - Constructor for class org.jmol.viewer.ActionManager
 
ActionManagerMT - Class in org.jmol.multitouch
 
ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
 
actionPerformed(ActionEvent) - Method in class jspecview.application.PreferencesDialog
Sets the color of the selected element on the current color button
actionPerformed(ActionEvent) - Method in class jspecview.java.AwtDialogManager
ActionListener callback
actionPerformed(ActionEvent) - Method in class org.jmol.awt.AwtPopupHelper
 
actionPerformed(ActionEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.ImageDialog
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
 
actionPerformed(String) - Method in class jspecview.js2d.JsDialogManager
Jmol.Swing.click() callback (via SwingController)
actionRotateBond(int, int, int, int, boolean) - Method in class org.jmol.modelkit.ModelKit
Actually rotate the bond.
activate() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
activate() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
activateQuery() - Method in class jme.JME
 
add - Static variable in class org.jmol.script.T
 
add(float) - Method in class javajs.util.Quat
 
add(int, V) - Method in class javajs.util.Lst
 
add(String) - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
add(Map<String, Object>, NucleicMonomer, NucleicMonomer) - Static method in class org.jmol.modelsetbio.BasePair
 
add(M3) - Method in class javajs.util.M3
Sets the value of this matrix to sum of itself and matrix m1.
add(Matrix) - Method in class javajs.util.Matrix
add two matrices
add(T3) - Method in class javajs.util.M4
add to translation
add(T3) - Method in class javajs.util.T3
Sets the value of this tuple to the vector sum of itself and tuple t1.
add(T3d) - Method in class javajs.util.T3d
Sets the value of this tuple to the vector sum of itself and tuple t1.
add(T3i) - Method in class javajs.util.T3i
Sets the value of this tuple to the sum of itself and t1.
add(SC) - Method in interface org.jmol.api.SC
 
add(SC) - Method in class org.jmol.awt.AwtSwingComponent
 
add(SC) - Method in class org.jmol.awtjs.swing.AbstractButton
 
add(SC) - Method in class org.jmol.awtjs.swing.ButtonGroup
 
add(Component) - Method in class org.jmol.awtjs.swing.Container
 
add(JComponent, Object) - Method in class org.jmol.awtjs.swing.JPanel
 
add(JComponent, GridBagConstraints) - Method in class org.jmol.awtjs.swing.Grid
 
add(V) - Method in class javajs.util.Lst
Deprecated.
ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JC
 
add2(T3d, T3d) - Method in class javajs.util.T3d
Sets the value of this tuple to the vector sum of tuples t1 and t2.
add2(T3, T3) - Method in class javajs.util.T3
Sets the value of this tuple to the vector sum of tuples t1 and t2.
add3(float, float, float) - Method in class javajs.util.T3
Add {a b c}
add33(M34) - Method in class javajs.util.M34
 
addActionListener(Object) - Method in interface org.jmol.api.SC
 
addActionListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
 
addActionListener(Object) - Method in class org.jmol.awtjs.swing.JComponent
Note that it will be the job of the JavaScript on the page to do with actionListener what is desired.
addActions(List<Action>) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
 
addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
addAnnotation(Lst<String>) - Method in class jspecview.common.PanelData
 
addApplyBtn - Variable in class jspecview.dialog.JSVDialog
 
addAssembly(String[]) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
addAtom(double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
add a proton to the atom list
addAtom(int, Group, int, String, String, int, int, int, P3, float, V3, int, float, float, float, Lst<Object>, boolean, byte, BS, float) - Method in class org.jmol.modelset.ModelSet
 
addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtoms(int) - Method in class org.jmol.modelset.Group
 
addAtoms(BS) - Method in interface org.jmol.api.AtomIndexIterator
 
addAtoms(BS) - Method in class org.jmol.modelset.AtomIteratorWithinModel
turns this into a SPHERICAL iterator for "within Distance" measures
addAtoms(BS) - Method in class org.jmol.symmetry.UnitCellIterator
 
addAtomSet(String) - Method in class org.jmol.modelkit.ModelKit
 
addAtomstoMatrix() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
Generate noeMatrix and map fields for DistanceJMolecule.
addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtomXYZSymName(String[], int, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addAttribute(SB, String, String) - Static method in class org.jmol.adapter.writers.CMLWriter
 
addAttributes(SB, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
 
addBasePair(BasePair) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
addBioMoleculeOperation(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
addBioMoleculeOperation(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
 
addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addBond(MinBond, int) - Method in class org.jmol.minimize.MinAtom
 
addBondNoCheck(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addBonds - Variable in class org.jmol.adapter.writers.CMLWriter
 
addBoundBoxPoint(T3) - Method in class org.jmol.util.BoxInfo
 
addButton(String, String) - Method in interface jspecview.api.PlatformDialog
 
addButton(String, String) - Method in class jspecview.java.AwtDialog
 
addButton(String, String) - Method in class jspecview.js2d.JsDialog
 
addButton(JmolAbstractButton, String) - Method in class org.jmol.console.GenericConsole
 
addBytes(byte[], int, int) - Method in class javajs.util.ZipData
 
addCheckBox(String, String, int, boolean) - Method in interface jspecview.api.PlatformDialog
 
addCheckBox(String, String, int, boolean) - Method in class jspecview.java.AwtDialog
 
addCheckBox(String, String, int, boolean) - Method in class jspecview.js2d.JsDialog
 
addCifAtom(Atom, String, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
addCoef(Map<String, Object>, float[], String, float, float, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
addCommand(int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
addCommand(String) - Method in class org.jmol.util.CommandHistory
Adds any number of lines to the command history
addCommand(String) - Method in class org.jmol.viewer.Viewer
Adds one or more commands to the command history
addComponent(Component) - Method in class org.jmol.awtjs.swing.Container
 
addConnectedHAtoms(Atom, BS) - Method in class org.jmol.modelset.BondCollection
 
addConsoleListener(Object) - Method in interface org.jmol.api.JmolAbstractButton
 
addConsoleListener(Object) - Method in class org.jmol.console.JmolButton
 
addConsoleListener(Object) - Method in class org.jmol.console.JmolLabel
 
addConsoleListener(Object) - Method in class org.jmol.console.JmolToggleButton
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBox
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBoxMenuItem
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenu
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenuItem
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJRadioButtonMenuItem
 
addContourPoints(Lst<Object>, BS, int, SB, T3[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
addContourVertex(P3, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addCouple(int, int, int, int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
addCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
addData(MOCalculation, boolean) - Method in interface org.jmol.quantum.mo.DataAdder
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder11H
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder13I
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder7F
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder9G
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderF
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderG
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderH
 
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderI
 
addDialog(int, Annotation.AType, AnnotationData) - Method in class jspecview.common.PanelData
 
addDisplayedBackbone(Atom, boolean) - Method in class org.jmol.shapebio.Backbone
 
addedData - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addedDataKey - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addEquiv(double[], double[], double[]) - Method in class org.jmol.quantum.NMRNoeMatrix
 
addExplicitLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addExtension(String) - Method in class jspecview.java.AwtDialogFileFilter
Adds an extension to the JSpecViewFileFilter
addFunction(JmolScriptFunction) - Method in class org.jmol.viewer.Viewer
 
addFunction(ScriptFunction) - Method in class org.jmol.script.ScriptEval
 
addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
 
addHeader() - Method in class org.jmol.adapter.readers.cif.CifReader
 
addHeader() - Method in class org.jmol.adapter.readers.cif.MMTFReader
 
addHeader(Lst<String[]>, String, String) - Static method in class jspecview.source.JDXReader
 
addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addHetero(String, String, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
addHighlight(double, double, int, int, int, int) - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a JSVPanel
addHighlight(double, double, int, int, int, int) - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that adds a highlight to a portion of the plot area of a JSVPanel
addHighlight(double, double, int, int, int, int) - Method in class jspecview.appletjs.JSVApplet
 
addHighlight(double, double, int, int, int, int) - Method in class jspecview.application.MainFrame
 
addHighlight(GraphSet, double, double, Spectrum, int, int, int, int) - Method in class jspecview.common.PanelData
Add information about a region of the displayed spectrum to be highlighted applet only right now
addHistoryWindowDimInfo(String, Component, Dimension) - Method in interface org.jmol.api.JmolAppAPI
 
addHistoryWindowDimInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.JmolApp
 
addHistoryWindowInfo(String, Component, Point) - Method in interface org.jmol.api.JmolAppAPI
 
addHistoryWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.JmolApp
 
addHydrogenBond(Lst<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
 
addhydrogens - Static variable in class org.jmol.script.T
 
addHydrogens(BS, int) - Method in class org.jmol.viewer.Viewer
 
addHydrogens(Lst<Atom>, P3[]) - Method in class org.jmol.modelset.ModelSet
these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW
addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in interface org.jmol.api.JmolScriptManager
 
addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.script.ScriptManager
Add hydrogens to a model
addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
addImageResource(Object, int, int, int[], boolean) - Method in class javajs.export.PDFCreator
 
addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in class org.jmol.modelsetbio.BioResolver
Get bonding info for double bonds and add implicit hydrogen atoms, if needed.
addInfo(Map<String, String>) - Method in class javajs.export.PDFCreator
 
addIntegralRegion(double, double) - Method in class jspecview.common.IntegralData
 
addItemListener(Object) - Method in interface org.jmol.api.SC
 
addItemListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
 
addItemListener(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
 
addItems(String[][]) - Method in class org.jmol.popup.PopupResource
 
addJDXSpectrum(String, Spectrum, boolean) - Method in class jspecview.source.JDXSource
Adds a Spectrum to the list
addJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
addJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
Add using Jmol atom index
addJmolProperties(Properties) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addJmolWindowInfo(String, Component, Point) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Deprecated.
addJmolWindowInnerInfo(String, Component, Dimension) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addLast(V) - Method in class javajs.util.Lst
 
addLatticeVector(Lst<float[]>, String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
addLatticeVector(Lst<float[]>, String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
addLatticeVectors(Lst<float[]>) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.SpaceGroup
 
addListener(PanelListener) - Method in class jspecview.common.PanelData
 
addListSelectionListener(Object) - Method in class org.jmol.awtjs.swing.JTable
It will be the function of the JavaScript on the page to do with selectionListener what is desired.
addListSelectionListener(Object) - Method in interface org.jmol.awtjs.swing.ListSelectionModel
 
addLockedAtoms(SymmetryInterface, BS) - Method in class org.jmol.modelkit.ModelKit
Only for the current model
addMacrosMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addMarks(String) - Method in class jspecview.common.IntegralData
INTEGRATION MARK list where list is a comma-separated list of ppm1-ppm2 with :x.x added to normalize one of them and starting with 0-0 clears the integration
addMatrix(String, M4, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtJmolPopup
 
addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtModelKitPopup
 
addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.popup.GenericPopup
 
addMenuItem(JMenu, String, char, ActionListener) - Static method in class jspecview.application.ApplicationMenu
 
addMenuItem(SC, String) - Method in class org.jmol.popup.GenericPopup
 
addMenuItems(String, String, SC, PopupResource) - Method in class org.jmol.popup.GenericPopup
 
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
 
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
 
addMethyl(double, double, double, double, double, double, double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
Add a methyl group to the atom list
addMo(String, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
addMOData(int, Lst<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
addModulation(Map<String, double[]>, String, double[], int) - Method in class org.jmol.adapter.readers.cif.MSRdr
Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description
addModulation(Map<String, double[]>, String, double[], int) - Method in interface org.jmol.adapter.smarter.MSInterface
 
addMol() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
addMol() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
addMolAtom(int, int, String, int, float, float, float) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
addMolBond(String, String, int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
addMolecule(JmolMolecule[], int, Node[], int, BS, int, int, BS) - Static method in class org.jmol.util.JmolMolecule
 
addMolFile(String, int, SB, BS, BS, boolean, boolean, boolean, Quat, boolean) - Method in class org.jmol.adapter.writers.MOLWriter
 
addMouseListener(Object) - Method in interface org.jmol.api.SC
 
addMouseListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
 
addMouseListener(Object) - Method in class org.jmol.awtjs.swing.Component
 
addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBondFromNames(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBondWithOrder(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBondWithOrderA(Atom, Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNOE(int, int, String, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addOp(T) - Method in class org.jmol.script.ScriptMathProcessor
addOp The primary driver of the Reverse Polish Notation evaluation engine.
addPeakData(String) - Method in class jspecview.source.JDXReader
 
addPeakData(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
addPeakData(String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
addPeakHighlight(PeakInfo) - Method in class jspecview.common.PanelData
 
addPluginMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
 
addPoint(T3, T3, T3, float) - Static method in class org.jmol.util.BoxInfo
 
addPointXYZ(float, float, float, P3, P3, float) - Static method in class org.jmol.util.BoxInfo
 
addPolygon(int[], BS) - Method in class org.jmol.util.MeshSurface
 
addPolygonC(int[], int, BS, boolean) - Method in class org.jmol.util.MeshSurface
 
addPopulation(double[]) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
 
addProcess(String, ScriptContext) - Method in interface org.jmol.api.JmolParallelProcessor
 
addProcess(String, ScriptContext) - Method in class org.jmol.script.ScriptParallelProcessor
 
addProperties(Properties) - Method in class org.openscience.jmol.app.HistoryFile
Adds the given properties to the history.
addProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
Adds the given property to the history.
addPropertyChangeListener(PropertyChangeListener) - Method in class jspecview.java.FileDropperJmol
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
 
addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
 
addRenderer(int) - Method in interface org.jmol.api.JmolRendererInterface
 
addRenderer(int) - Method in class org.jmol.export.Export3D
 
addRenderer(int) - Method in class org.jmol.g3d.Graphics3D
allows core JavaScript loading to not involve these classes
addRenderer(int) - Method in class org.jmol.util.GData
 
addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
 
addRotatedTensor(Atom, Tensor, int, boolean, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
addSelectOption(String, String, String[], int, boolean) - Method in interface jspecview.api.PlatformDialog
 
addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.java.AwtDialog
 
addSelectOption(String, String, String[], int, boolean) - Method in class jspecview.js2d.JsDialog
 
addSGTransform(SymmetryInterface, String, M4, M4) - Static method in class org.jmol.modelkit.ModelKit
 
addSites(Map<String, Map<String, Object>>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
 
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.AdfReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.AmsReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.CsfReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.DgridReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(int, int, int, int, int, double, double) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.AmsReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
 
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.CsfReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MOReader
See MopacSlaterReader
addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
 
addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
 
addSpecShift(double) - Method in class jspecview.common.Measurement
 
addSpecShift(double) - Method in class jspecview.common.Spectrum
 
addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addStateScript(String, BS, BS, BS, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addStructure(STR, String, String, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addStructureProtected(STR, String, String, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addStructureSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
We must add groups to the proper bsStructure element
addSubSpectrum(Spectrum, boolean) - Method in class jspecview.common.Spectrum
adds an nD subspectrum and titles it "Subspectrum " These spectra can be iterated over using the UP and DOWN keys.
addSubsystem(String, Matrix) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
addSubsystem(String, Matrix) - Method in interface org.jmol.adapter.smarter.MSInterface
 
addSubSystemOp(String, Matrix, Matrix, Matrix) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
addSymmetry(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
addTensor(Tensor, String) - Method in class org.jmol.modelset.AtomCollection
 
addTensor(Tensor, String, boolean) - Method in class org.jmol.adapter.smarter.Atom
 
addTextField(String, String, String, String, String, boolean) - Method in interface jspecview.api.PlatformDialog
 
addTextField(String, String, String, String, String, boolean) - Method in class jspecview.java.AwtDialog
 
addTextField(String, String, String, String, String, boolean) - Method in class jspecview.js2d.JsDialog
 
addTo(GenericZipTools, SB) - Method in class javajs.util.ZipData
 
addTo(T3, float) - Method in interface org.jmol.api.JmolModulationSet
 
addTo(T3, float) - Method in class org.jmol.util.ModulationSet
 
addToken(String, T) - Static method in class org.jmol.script.T
 
addToList(int, Lst<Spectrum>) - Method in class jspecview.common.PanelData
 
addTracePt(int, Point3fi) - Method in class org.jmol.util.Vibration
 
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
 
addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
 
addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
 
addTuple(int, P3) - Method in class org.jmol.bspt.Bspf
 
addTuple(T3) - Method in class org.jmol.bspt.Bspt
Iterate through all of your data points, calling addTuple
addUniqueControls() - Method in class jspecview.dialog.IntegrationDialog
 
addUniqueControls() - Method in class jspecview.dialog.JSVDialog
 
addUniqueControls() - Method in class jspecview.dialog.MeasurementsDialog
 
addUniqueControls() - Method in class jspecview.dialog.OverlayLegendDialog
 
addUniqueControls() - Method in class jspecview.dialog.PeakListDialog
 
addUniqueControls() - Method in class jspecview.dialog.ViewsDialog
 
addUniqueControls(DialogManager) - Method in class jspecview.dialog.JSVDialog
 
addUnitCellOffset(P3) - Method in class org.jmol.viewer.Viewer
 
addUTens(String, float) - Method in class org.jmol.util.ModulationSet
 
addV(T3, boolean) - Method in class org.jmol.util.MeshSurface
 
addVC(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addVCVal(T3, float, boolean) - Method in class org.jmol.util.MeshSurface
 
addVectors(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addVertexCopy(T3, float, int, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.data.MeshData
 
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
 
addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addVibrationVectorWithSymmetry(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.HistoryFile
Adds the window informations to the history.
addWindowInfo(String, Component, Point, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
 
addWindowInnerInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
 
addWindowListener() - Method in class org.jmol.console.JmolConsole
 
addX(SV) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAD(double[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAF(float[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAFF(float[][]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAI(int[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAII(int[][]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAS(String[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAV(SV[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXBool(boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
addXBs(BS) - Method in class org.jmol.script.ScriptMathProcessor
 
addXCopy(SV) - Method in class org.jmol.script.ScriptMathProcessor
 
addXFloat(float) - Method in class org.jmol.script.ScriptMathProcessor
 
addXInt(int) - Method in class org.jmol.script.ScriptMathProcessor
 
addXList(Lst<?>) - Method in class org.jmol.script.ScriptMathProcessor
 
addXM3(M3) - Method in class org.jmol.script.ScriptMathProcessor
 
addXM4(M4) - Method in class org.jmol.script.ScriptMathProcessor
 
addXMap(Map<String, ?>) - Method in class org.jmol.script.ScriptMathProcessor
 
addXNum(T) - Method in class org.jmol.script.ScriptMathProcessor
 
addXObj(Object) - Method in class org.jmol.script.ScriptMathProcessor
 
addXPt(P3) - Method in class org.jmol.script.ScriptMathProcessor
 
addXPt4(P4) - Method in class org.jmol.script.ScriptMathProcessor
 
addXStr(String) - Method in class org.jmol.script.ScriptMathProcessor
 
addZipEntry(Object, String) - Method in interface javajs.api.GenericZipTools
 
addZipEntry(Object, String) - Method in class javajs.util.ZipTools
 
AdfReader - Class in org.jmol.adapter.readers.quantum
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
 
AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
 
adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelSet
 
adjustForWindow - Variable in class org.jmol.modelset.Text
 
Adler32 - Class in com.jcraft.jzlib
 
Adler32() - Constructor for class com.jcraft.jzlib.Adler32
 
adpmax - Static variable in class org.jmol.script.T
 
ADPMAX - Enum constant in enum class org.jmol.c.VDW
 
adpmin - Static variable in class org.jmol.script.T
 
ADPMIN - Enum constant in enum class org.jmol.c.VDW
 
adpMode - Variable in class org.jmol.atomdata.AtomData
 
advanceSubSpectrum(int) - Method in class jspecview.common.PanelData
 
advanceSubSpectrum(int) - Method in class jspecview.common.Spectrum
 
AFLOWReader - Class in org.jmol.adapter.readers.more
A reader for various AFLOW file types.
AFLOWReader() - Constructor for class org.jmol.adapter.readers.more.AFLOWReader
 
afterClear - Variable in class jme.JME
 
AimsReader - Class in org.jmol.adapter.readers.xtal
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).
AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
 
AjaxURLConnection - Class in javajs.util
A method to allow a JavaScript Ajax
AjaxURLConnection(URL) - Constructor for class javajs.util.AjaxURLConnection
 
AjaxURLStreamHandler - Class in javajs.util
A method to allow a JavaScript AJAX adapter to deliver web content to JSmol.
AjaxURLStreamHandler(String) - Constructor for class javajs.util.AjaxURLStreamHandler
 
AjaxURLStreamHandlerFactory - Class in javajs.util
For handling URL file IO via AJAX in JavaScript version
AjaxURLStreamHandlerFactory() - Constructor for class javajs.util.AjaxURLStreamHandlerFactory
 
AlchemyReader - Class in org.jmol.adapter.readers.simple
TRIPOS simple Alchemy reader.
AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
 
alert(String) - Method in class org.jmol.viewer.Viewer
 
align - Variable in class org.jmol.modelset.Text
 
align - Static variable in class org.jmol.script.T
 
ALIGN_CENTER - Static variable in class jme.JMEUtil
 
ALIGN_LEFT - Static variable in class jme.JMEUtil
 
ALIGN_RIGHT - Static variable in class jme.JMEUtil
 
alignment - Variable in class jme.AtomDisplayLabel
 
all - Static variable in class org.jmol.script.T
 
ALL - Enum constant in enum class jspecview.common.PanelData.LinkMode
 
ALL - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
 
ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
allconnected - Static variable in class org.jmol.script.T
 
allEmptyString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
ALLENE - Static variable in class org.jmol.smiles.SmilesStereo
 
allfloat - Static variable in class org.jmol.script.T
 
allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
allHs - Variable in class jme.JME
 
allNaN() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
allNull() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
allocateColix(int, boolean) - Static method in class org.jmol.util.C
 
allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
 
allocateExpCouples(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
allocateExpNoes(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
 
allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.java.AwtPlatform
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class jspecview.js2d.JsPlatform
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in interface org.jmol.api.GenericPlatform
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awt.Platform
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs2d.Platform
Create an "image" that is either a canvas with width/height/buf32 (from g3d.Platform32) or just an associative array with those (image writing
allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
a simpler option
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
legacy only
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.api.JmolViewer
This is the older main access point for creating an application or applet vwr.
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.viewer.Viewer
old way...
allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
 
allocMesh(String, Mesh) - Method in class org.jmol.shapecgo.CGO
 
allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
 
allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
 
allocTempEnum(int) - Method in class org.jmol.util.TempArray
 
allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
 
allocTempPoints(int) - Method in class org.jmol.util.TempArray
 
allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
 
allocTempScreens(int) - Method in class org.jmol.util.TempArray
 
allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
 
allow_a_len_1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
allowAromaticBond(Bond) - Method in class org.jmol.modelset.BondCollection
 
allowArrayDotNotation - Variable in class org.jmol.viewer.Viewer
 
allowaudio - Static variable in class org.jmol.script.T
 
allowCapture() - Method in class org.jmol.viewer.Viewer
 
allowDashed - Variable in class org.jmol.render.MeshRenderer
 
allowedQuaternionFrames - Static variable in class org.jmol.viewer.JC
 
allowembeddedscripts - Static variable in class org.jmol.script.T
 
allowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
 
allowgestures - Static variable in class org.jmol.script.T
 
allowJavaConsole - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
allowkeystrokes - Static variable in class org.jmol.script.T
 
allowMenu - Variable in class jspecview.common.JSViewer
 
allowmodelkit - Static variable in class org.jmol.script.T
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
 
allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
allowmoveatoms - Static variable in class org.jmol.script.T
 
allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
allowmultitouch - Static variable in class org.jmol.script.T
 
allowNoOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
allowPDBFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
allowrotateselected - Static variable in class org.jmol.script.T
 
allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
allowSignedFeatures - Variable in class org.jmol.popup.GenericPopup
 
allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
 
allowSubSpec(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
 
allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
 
allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
 
allSame() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
allTrajectories - Variable in class org.jmol.adapter.writers.CMLWriter
 
allZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
alpha - Variable in class org.jmol.util.SimpleUnitCell
 
ALPHA - Static variable in class org.jmol.shapecgo.CGOMesh
 
ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JC
 
ALPHA_SHIFT - Static variable in class org.jmol.util.C
 
ALPHA_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
AlphaMonomer - Class in org.jmol.modelsetbio
 
AlphaMonomer() - Constructor for class org.jmol.modelsetbio.AlphaMonomer
 
AlphaPolymer - Class in org.jmol.modelsetbio
 
ALT - Static variable in class org.jmol.util.ColorEncoder
 
ALT - Static variable in class org.jmol.viewer.binding.Binding
 
ALT_MASK - Static variable in class org.jmol.awtjs.Event
 
altArgbsCpk - Static variable in class org.jmol.viewer.JC
 
altElementCounts - Variable in class org.jmol.util.JmolMolecule
 
altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
 
altElementMax - Static variable in class org.jmol.util.Elements
length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementMax - Variable in class org.jmol.util.JmolMolecule
 
altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
 
altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
 
altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
 
altloc - Variable in class org.jmol.modelset.Atom
 
altloc - Static variable in class org.jmol.script.T
 
altLoc - Variable in class org.jmol.adapter.smarter.Atom
 
ALTLOC - Enum constant in enum class org.jmol.c.PAL
 
altLocCount - Variable in class org.jmol.modelset.Model
 
altType - Variable in class org.jmol.util.Tensor
 
altVertices - Variable in class org.jmol.util.MeshSurface
 
am - Variable in class org.jmol.modelset.ModelSet
 
am - Variable in class org.jmol.viewer.Viewer
 
ambientocclusion - Static variable in class org.jmol.script.T
 
ambientOcclusion - Variable in class org.jmol.util.GData
 
ambientpercent - Static variable in class org.jmol.script.T
 
amino - Static variable in class org.jmol.script.T
 
AMINO - Enum constant in enum class org.jmol.c.PAL
 
AMINO - Static variable in class org.jmol.util.ColorEncoder
 
AminoMonomer - Class in org.jmol.modelsetbio
 
AminoMonomer() - Constructor for class org.jmol.modelsetbio.AminoMonomer
 
AminoPolymer - Class in org.jmol.modelsetbio
 
AML - Enum constant in enum class jspecview.common.ExportType
 
AMLExporter - Class in jspecview.export
class AnIMLExporter contains static methods to export a Graph as as AnIML.
AMLExporter() - Constructor for class jspecview.export.AMLExporter
 
AmpacReader - Class in org.jmol.adapter.readers.simple
A reader for AMPAC output.
AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
 
AmsReader - Class in org.jmol.adapter.readers.quantum
A reader for AMS output subclassing the older AdfReader.
AmsReader() - Constructor for class org.jmol.adapter.readers.quantum.AmsReader
 
anchor - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
and(BS) - Method in class javajs.util.BS
Performs a logical AND of this target bit set with the argument bit set.
andequals - Static variable in class org.jmol.script.T
 
andNot(BS) - Method in class javajs.util.BS
Clears all of the bits in this BitSet whose corresponding bit is set in the specified BitSet.
andNot(BS, BS) - Static method in class org.jmol.util.BSUtil
 
angle - Variable in class javajs.util.A4
The angle.
angle - Static variable in class org.jmol.script.T
 
angle(V3) - Method in class javajs.util.V3
Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
angle(V3d) - Method in class javajs.util.V3d
 
angstroms - Static variable in class org.jmol.script.T
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JC
 
animation - Static variable in class org.jmol.script.T
 
animationfps - Static variable in class org.jmol.script.T
 
animationFps - Variable in class org.jmol.viewer.AnimationManager
 
AnimationManager - Class in org.jmol.viewer
 
animationmode - Static variable in class org.jmol.script.T
 
animationOn - Variable in class org.jmol.viewer.AnimationManager
 
animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
 
animationThread - Variable in class org.jmol.viewer.AnimationManager
 
AnimationThread - Class in org.jmol.thread
 
AnimationThread() - Constructor for class org.jmol.thread.AnimationThread
 
AnimButton(ImageIcon, String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
ANIMFRAME - Enum constant in enum class org.jmol.c.CBK
 
AnIMLReader - Class in jspecview.source
Representation of a XML Source.
AnIMLReader() - Constructor for class jspecview.source.AnIMLReader
 
anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
 
anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
anisotropy - Static variable in class org.jmol.script.T
 
anisotropy() - Method in class org.jmol.util.Tensor
anisotropy = directed distance from (center of two closest) to (the furthest)
Annotation - Class in jspecview.common
The Annotation class stores the spectral x and pixel y values of an annotation text along with its text
Annotation - Class in org.jmol.modelsetbio
 
Annotation() - Constructor for class jspecview.common.Annotation
 
Annotation() - Constructor for class org.jmol.modelsetbio.Annotation
 
ANNOTATION - Enum constant in enum class org.jmol.c.STR
 
Annotation.AType - Enum Class in jspecview.common
 
AnnotationData - Interface in jspecview.api
 
AnnotationParser - Class in org.jmol.dssx
A parser for output from 3DNA web service.
AnnotationParser() - Constructor for class org.jmol.dssx.AnnotationParser
 
antialias - Variable in class org.jmol.render.MeshRenderer
 
antialias - Variable in class org.jmol.viewer.TransformManager
 
antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
antialiasdisplay - Static variable in class org.jmol.script.T
 
antialiasDisplay - Variable in class org.jmol.viewer.GlobalSettings
 
antialiased - Variable in class org.jmol.viewer.Viewer
 
antialiasEnabled - Variable in class org.jmol.util.GData
 
antialiasimages - Static variable in class org.jmol.script.T
 
antialiasThisFrame - Variable in class org.jmol.util.GData
 
antialiastranslucent - Static variable in class org.jmol.script.T
 
aperatureAngle - Variable in class org.jmol.viewer.TransformManager
 
apertureAngle - Variable in class org.jmol.export.___Exporter
 
apiPlatform - Variable in class jspecview.common.JSViewer
 
apiPlatform - Variable in class org.jmol.api.JmolViewer
 
apiPlatform - Variable in class org.jmol.util.GData
 
apivot - Static variable in class org.jmol.script.T
 
apointx - Variable in class jme.JME
 
apointy - Variable in class jme.JME
 
apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
 
app - Variable in class jspecview.appletjs.JSVApplet
 
appCheckItem(String, SC) - Method in class jspecview.popup.JSVGenericPopup
 
appCheckItem(String, SC) - Method in class org.jmol.popup.GenericPopup
Opportunity to do something special with an item.
appCheckItem(String, SC) - Method in class org.jmol.popup.JmolPopup
 
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.GenericPopup
Opportunity to do something special with a given submenu is created
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.JmolPopup
 
AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
 
appConsole - Variable in class org.jmol.viewer.Viewer
 
AppConsole - Class in org.openscience.jmol.app.jmolpanel.console
 
AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
general entry point
append - Static variable in class org.jmol.script.T
 
append(String) - Method in class javajs.util.OC
will go to string buffer if bw == null and os == null
append(String) - Method in class javajs.util.SB
 
append(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
 
append(String) - Method in interface org.jmol.console.GenericTextArea
 
append(String) - Method in class org.jmol.util.JSONWriter
 
appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Appends an AtomSetCollection
appendAttrib(SB, Object, Object) - Static method in class javajs.util.XmlUtil
 
appendB(boolean) - Method in class javajs.util.SB
 
appendC(char) - Method in class javajs.util.SB
 
appendCB(char[], int, int) - Method in class javajs.util.SB
 
appendCdata(SB, String, Object[], String) - Static method in class javajs.util.XmlUtil
" will convert ]]> to ]] >
appendCmd(SB, String) - Static method in class org.jmol.shape.Shape
 
appendContourTriangleIntersection(int, float, float, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.
appendD(double) - Method in class javajs.util.SB
 
appendEmptyTag(SB, String, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
 
appendF(float) - Method in class javajs.util.SB
note that JavaScript could drop off the ".0" in "1.0"
appendFontCmd(SB) - Method in class org.jmol.modelset.Text
 
appendI(int) - Method in class javajs.util.SB
 
appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
appendnew - Static variable in class org.jmol.script.T
 
appendNew - Variable in class org.jmol.viewer.GlobalSettings
 
appendO(Object) - Method in class javajs.util.SB
 
appendSB(SB) - Method in class javajs.util.SB
 
appendTag(SB, String, Object) - Static method in class javajs.util.XmlUtil
standard data" standard "
appendTagAll(SB, String, Object[], Object, boolean, boolean) - Static method in class javajs.util.XmlUtil
 
appendTagObj(SB, String, Object[], Object) - Static method in class javajs.util.XmlUtil
standard data"
appendUunitCellInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
appFixLabel(String) - Method in class jspecview.popup.JSVGenericPopup
 
appFixLabel(String) - Method in class org.jmol.popup.GenericPopup
 
appFixLabel(String) - Method in class org.jmol.popup.JmolGenericPopup
 
appGetBooleanProperty(String) - Method in class jspecview.popup.JSVGenericPopup
 
appGetBooleanProperty(String) - Method in class org.jmol.modelkit.ModelKitPopup
 
appGetBooleanProperty(String) - Method in class org.jmol.popup.GenericPopup
 
appGetBooleanProperty(String) - Method in class org.jmol.popup.JmolGenericPopup
 
appGetMenuAsString(String) - Method in class jspecview.popup.JSVGenericPopup
 
appGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
 
appGetMenuAsString(String) - Method in class org.jmol.popup.JmolPopup
 
appletCodeBase - Static variable in class org.jmol.viewer.Viewer
 
AppletConsole - Class in org.jmol.console
 
AppletConsole - Class in org.jmol.consolejs
An interface to Jmol.Console.
AppletConsole() - Constructor for class org.jmol.console.AppletConsole
 
AppletConsole() - Constructor for class org.jmol.consolejs.AppletConsole
 
appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
appletDocumentBase - Static variable in class jspecview.common.JSVFileManager
 
appletDocumentBase - Static variable in class org.jmol.viewer.Viewer
 
appletFrame - Variable in class jspecview.app.JSVApp
 
AppletFrame - Interface in jspecview.api
 
APPLETID - Enum constant in enum class jspecview.common.ScriptToken
 
appletIdiomaBase - Static variable in class org.jmol.viewer.Viewer
 
appletName - Variable in class jspecview.common.JSViewer
 
appletName - Variable in class org.jmol.viewer.Viewer
 
appletObject - Variable in class org.jmol.util.GenericApplet
 
appletproxy - Static variable in class org.jmol.script.T
 
APPLETREADY - Enum constant in enum class org.jmol.c.CBK
 
appletReadyCallbackFunctionName - Variable in class jspecview.app.JSVApp
 
APPLETREADYCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
 
application - Variable in class jme.JME
 
ApplicationMenu - Class in jspecview.application
The Main Class or Entry point of the JSpecView Application.
ApplicationMenu(MainFrame) - Constructor for class jspecview.application.ApplicationMenu
 
apply(Object[]) - Method in class jspecview.dialog.JSVDialog
 
applyAnaglygh(STER, int[]) - Method in class org.jmol.g3d.Graphics3D
 
applyAnaglygh(STER, int[]) - Method in class org.jmol.util.GData
 
applyFromFields() - Method in class jspecview.dialog.IntegrationDialog
 
applyFromFields() - Method in class jspecview.dialog.JSVDialog
 
applyFromFields() - Method in class jspecview.dialog.ViewsDialog
 
applyFunc(Object, Object) - Method in interface javajs.api.js.J2SObjectInterface
 
applyLeftMouse(int) - Static method in class jspecview.app.GenericMouse
 
applyScale(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
Apply the scale factor to the coordinates
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.CifReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.MMTFReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applySymmetryBio(Map<String, Object>, boolean, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
applysymmetrytobonds - Static variable in class org.jmol.script.T
 
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applySymTrajASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
appRestorePopupMenu() - Method in class jspecview.popup.JSVGenericPopup
 
appRestorePopupMenu() - Method in class org.jmol.popup.GenericPopup
 
appRestorePopupMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
appRestorePopupMenu() - Method in class org.jmol.popup.JmolPopup
 
approx(float, float) - Static method in class javajs.util.PT
 
approx0(float) - Static method in class org.jmol.util.SimpleUnitCell
 
appRunScript(String) - Method in class jspecview.popup.JSVGenericPopup
 
appRunScript(String) - Method in class org.jmol.popup.GenericPopup
 
appRunScript(String) - Method in class org.jmol.popup.JmolGenericPopup
 
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
 
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
 
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
 
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
 
AppToolBar - Class in jspecview.application
 
AppToolBar(MainFrame) - Constructor for class jspecview.application.AppToolBar
 
appUpdateForShow() - Method in class jspecview.popup.JSVGenericPopup
 
appUpdateForShow() - Method in class org.jmol.modelkit.ModelKitPopup
 
appUpdateForShow() - Method in class org.jmol.popup.GenericPopup
 
appUpdateForShow() - Method in class org.jmol.popup.JmolPopup
 
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
 
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
Set the active menu based on updating a value -- usually by the user, but also during setup (ignored).
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
 
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
(1) setOption --> set setOption true or set setOption false
arc - Static variable in class org.jmol.script.T
 
ARC - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
area - Static variable in class org.jmol.script.T
 
areAxesTainted() - Method in class org.jmol.viewer.Viewer
 
areEqual(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
areEqual(String, String) - Method in class org.jmol.smiles.SmilesMatcher
 
areEqual(BS, BS) - Static method in class org.jmol.util.BSUtil
 
areEqual(SV, SV) - Static method in class org.jmol.script.SV
For legacy reasons, "x" == "X" but see isLike()
areEqualTest(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
for JUnit test, mainly
areLinkableX(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
 
areLinkableY(Spectrum, Spectrum) - Static method in class jspecview.common.Spectrum
 
areXScalesCompatible(Spectrum, Spectrum, boolean, boolean) - Static method in class jspecview.common.Spectrum
 
areYScalesSame(int, int) - Method in class jspecview.common.ViewData
 
argb - Variable in class org.jmol.awtjs.swing.Color
 
argbCurrent - Variable in class org.jmol.util.GData
 
argbNoisyDn - Variable in class org.jmol.util.GData
 
argbNoisyUp - Variable in class org.jmol.util.GData
 
argbsChainAtom - Static variable in class org.jmol.util.ColorEncoder
 
argbsChainHetero - Static variable in class org.jmol.util.ColorEncoder
 
argbsCpk - Static variable in enum class org.jmol.c.PAL
Default table of CPK atom colors.
argbsCpkRasmol - Static variable in enum class org.jmol.c.PAL
 
argbsFormalCharge - Static variable in class org.jmol.viewer.JC
 
argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JC
 
argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JC
 
argbsRoygbScale - Static variable in class org.jmol.viewer.JC
 
argbsRwbScale - Static variable in class org.jmol.viewer.JC
 
aromatic - Static variable in class org.jmol.script.T
 
array - Static variable in class org.jmol.script.T
 
arrayAdd(Object) - Method in class org.jmol.util.JSONWriter
 
arrayClose(boolean) - Method in class org.jmol.util.JSONWriter
 
arrayCopyBool(boolean[], int) - Static method in class javajs.util.AU
 
arrayCopyByte(byte[], int) - Static method in class javajs.util.AU
 
arrayCopyF(float[], int) - Static method in class javajs.util.AU
 
arrayCopyI(int[], int) - Static method in class javajs.util.AU
 
arrayCopyII(int[][], int) - Static method in class javajs.util.AU
 
arrayCopyObject(Object, int) - Static method in class javajs.util.AU
note -- cannot copy if array is null! does not copy if length is unchanged
arrayCopyPt(T3[], int) - Static method in class javajs.util.AU
 
arrayCopyRangeI(int[], int, int) - Static method in class javajs.util.AU
a specialized method that allows copying from a starting point either to the end or to the middle (color schemes, especially)
arrayCopyRangeRevI(int[], int, int) - Static method in class javajs.util.AU
 
arrayCopyS(String[], int) - Static method in class javajs.util.AU
 
arrayCopyShort(short[], int) - Static method in class javajs.util.AU
 
ArrayDataReader - Class in javajs.util
ArrayDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with String[] arrays without any further adaptation.
ArrayDataReader() - Constructor for class javajs.util.ArrayDataReader
 
arrayDiv(Quat[], Quat[], int, boolean) - Static method in class javajs.util.Quat
 
arrayOpen(boolean) - Method in class org.jmol.util.JSONWriter
 
arrayToList(SV) - Method in class org.jmol.script.SV
 
arrow - Static variable in class org.jmol.script.T
 
ARROW - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
as - Static variable in class org.jmol.script.T
 
asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
 
asBoolean() - Method in class org.jmol.script.SV
 
asc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ASCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
 
ascent - Variable in class org.jmol.render.LabelsRenderer
 
asFloat() - Method in class org.jmol.script.SV
 
asHTML(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
 
ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
asInt() - Method in class org.jmol.script.SV
 
asLineOnly - Variable in class org.jmol.render.FontLineShapeRenderer
 
asObject - Variable in class javajs.util.CifDataParser
A flag to create and return Java objects, not strings.
asPDF - Variable in class jspecview.common.PrintLayout
 
assign - Static variable in class org.jmol.script.T
 
assignAromaticBondsBs(boolean, BS) - Method in class org.jmol.modelset.BondCollection
algorithm discussed above.
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MepCalculation
 
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MlpCalculation
 
ASSOCIATION - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
asString() - Method in class javajs.util.T3i
 
asString() - Method in class org.jmol.script.SV
 
asString() - Method in class org.jmol.symmetry.SpaceGroup
 
astrType - Static variable in class org.jmol.script.T
 
asymMatrix - Variable in class org.jmol.util.Tensor
 
asymmetry() - Method in class org.jmol.util.Tensor
asymmetry = deviation from a symmetric tensor
async - Static variable in class org.jmol.script.T
 
async - Variable in class org.jmol.viewer.Viewer
 
at - Variable in class org.jmol.modelset.AtomCollection
 
atNos - Variable in class org.jmol.util.JmolMolecule
 
atokenInfix - Variable in class org.jmol.script.ScriptCompiler
 
atom - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
atom - Variable in class org.jmol.minimize.MinAtom
 
Atom - Class in org.jmol.adapter.smarter
 
Atom - Class in org.jmol.modelset
 
Atom() - Constructor for class org.jmol.adapter.smarter.Atom
 
Atom() - Constructor for class org.jmol.modelset.Atom
 
ATOM_INFRAME - Static variable in class org.jmol.modelset.Atom
 
ATOM_INFRAME_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
 
ATOM_NOFLAGS - Static variable in class org.jmol.modelset.Atom
 
ATOM_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
 
ATOM_SHAPE_VIS_MASK - Static variable in class org.jmol.modelset.Atom
 
ATOM_VISIBLE - Static variable in class org.jmol.modelset.Atom
 
ATOM_VISSET - Static variable in class org.jmol.modelset.Atom
 
atom1 - Variable in class org.jmol.modelset.Bond
 
atom2 - Variable in class org.jmol.modelset.Bond
 
atomCenterOrCoordinateParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
 
AtomCollection - Class in org.jmol.modelset
 
AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
 
AtomCollection.AtomSorter - Class in org.jmol.modelset
 
AtomData - Class in org.jmol.atomdata
 
AtomData() - Constructor for class org.jmol.atomdata.AtomData
 
atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
AtomDataServer - Interface in org.jmol.atomdata
 
AtomDisplayLabel - Class in jme
 
AtomDisplayLabel(double, double, String, int, int, int, int, int, int, int, int, FontMetrics, double, boolean) - Constructor for class jme.AtomDisplayLabel
 
atomEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
atomExpression(T[], int, int, boolean, boolean, Object[], boolean) - Method in class org.jmol.script.ScriptEval
 
atomExpressionAt(int) - Method in class org.jmol.script.ScriptEval
 
atomExpressionAt(int) - Method in class org.jmol.scriptext.ScriptExt
 
atomExpressionCommand - Static variable in class org.jmol.script.T
 
atomFormats - Variable in class org.jmol.shape.Hover
 
atomHighlighted - Variable in class org.jmol.viewer.Viewer
 
atomicMass - Static variable in class org.jmol.util.Elements
 
atomicNumber - Variable in class org.jmol.atomdata.AtomData
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
atomicorbital - Static variable in class org.jmol.script.T
 
atomid - Static variable in class org.jmol.script.T
 
atomID - Variable in class org.jmol.modelset.Atom
 
ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JC
 
ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JC
 
ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C2_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C5 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C5M - Static variable in class org.jmol.viewer.JC
 
ATOMID_C6 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C7 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C8 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JC
 
ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JC
 
ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_MAX - Static variable in class org.jmol.modelsetbio.BioResolver
 
ATOMID_N1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N3 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N6 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N7 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N9 - Static variable in class org.jmol.viewer.JC
 
ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_O1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_O1P - Static variable in class org.jmol.viewer.JC
 
ATOMID_O2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O2P - Static variable in class org.jmol.viewer.JC
 
ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_O4_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_O6 - Static variable in class org.jmol.viewer.JC
 
ATOMID_OP1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_OP2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_S4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JC
 
atomindex - Static variable in class org.jmol.script.T
 
atomIndex - Variable in class org.jmol.atomdata.AtomData
 
atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
 
atomIndex - Variable in class org.jmol.shape.Hover
 
atomIndex - Variable in class org.jmol.shape.Mesh
 
atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex1 - Variable in class org.jmol.util.Tensor
 
atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex2 - Variable in class org.jmol.util.Tensor
 
AtomIndexIterator - Interface in org.jmol.api
note: YOU MUST RELEASE THE ITERATOR
AtomIteratorWithinModel - Class in org.jmol.modelset
 
AtomIteratorWithinModelSet - Class in org.jmol.modelset
 
AtomIteratorWithinModelSet(BS) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
 
atomLabelBoundingBox - Variable in class jme.AtomDisplayLabel
 
atomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
atomList - Variable in class org.jmol.util.JmolMolecule
 
atomMapAnyCase - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomMapX - Variable in class jme.AtomDisplayLabel
 
atomMapY - Variable in class jme.AtomDisplayLabel
 
atomMolecule - Variable in class org.jmol.atomdata.AtomData
 
ATOMMOVED - Enum constant in enum class org.jmol.c.CBK
 
atomname - Static variable in class org.jmol.script.T
 
atomName - Variable in class org.jmol.adapter.smarter.Atom
 
atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
atomno - Static variable in class org.jmol.script.T
 
atomNo - Variable in class org.jmol.quantum.SlaterData
 
atomPicked(int) - Method in interface org.jmol.api.JmolJSpecView
 
atomPicked(int) - Method in class org.jmol.jsv.JSpecView
 
atompicking - Static variable in class org.jmol.script.T
 
atomproperty - Static variable in class org.jmol.script.T
 
atomPropertyFloat(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
atomPropertyInt(int) - Method in class org.jmol.modelset.Atom
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
atomPropertyString(Viewer, int) - Method in class org.jmol.modelset.Atom
 
atomPropertyTuple(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
 
atomPt - Variable in class org.jmol.render.LabelsRenderer
 
atomRadius - Variable in class org.jmol.atomdata.AtomData
 
atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
 
atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atoms - Variable in class org.jmol.atomdata.AtomData
 
atoms - Variable in class org.jmol.minimize.Minimizer
 
atoms - Static variable in class org.jmol.script.T
 
atoms - Variable in class org.jmol.shapespecial.Dipole
 
atoms - Variable in class org.jmol.shapesurface.Contact
 
atomSerial - Variable in class org.jmol.adapter.smarter.Atom
 
atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AtomSetChooser - Class in org.openscience.jmol.app.jmolpanel
A JFrame that allows for choosing an Atomset to view.
AtomSetChooser(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
 
AtomSetCollection - Class in org.jmol.adapter.smarter
 
AtomSetCollection(String, AtomSetCollectionReader, AtomSetCollection[], Lst<?>) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetCollectionReader - Class in org.jmol.adapter.smarter
 
AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
 
atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
 
atomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetObject
 
atomSetInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetObject - Class in org.jmol.adapter.smarter
 
AtomSetObject() - Constructor for class org.jmol.adapter.smarter.AtomSetObject
 
AtomShape - Class in org.jmol.shape
 
AtomShape() - Constructor for class org.jmol.shape.AtomShape
 
atomSite - Variable in class org.jmol.adapter.smarter.Atom
 
atomsMax - Variable in class org.jmol.adapter.writers.CMLWriter
 
AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
 
atomStartEnd - Variable in class org.jmol.adapter.smarter.Structure
 
atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSymmetry - Variable in class org.jmol.modelset.Atom
 
atomTensorList - Variable in class org.jmol.modelset.AtomCollection
 
atomTensors - Variable in class org.jmol.modelset.AtomCollection
 
atomtype - Static variable in class org.jmol.script.T
 
AtomType - Class in org.jmol.minimize.forcefield
 
atomtypes - Static variable in class org.jmol.script.T
 
atomx - Static variable in class org.jmol.script.T
 
atomX - Variable in class org.jmol.modelset.Text
 
atomy - Static variable in class org.jmol.script.T
 
atomY - Variable in class org.jmol.modelset.Text
 
atomz - Static variable in class org.jmol.script.T
 
atomZ - Variable in class org.jmol.modelset.Text
 
attEcho - Variable in class org.jmol.console.ScriptEditor
 
attError - Variable in class org.jmol.console.ScriptEditor
 
attHighlight - Variable in class org.jmol.console.ScriptEditor
 
attrList - Variable in class jspecview.source.AnIMLReader
 
atts - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
AU - Class in javajs.util
 
AU() - Constructor for class javajs.util.AU
 
audio - Static variable in class org.jmol.script.T
 
AUDIO - Enum constant in enum class org.jmol.c.CBK
 
auto - Static variable in class org.jmol.script.T
 
AUTO - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
AUTO - Enum constant in enum class org.jmol.c.VDW
 
AUTO_BABEL - Enum constant in enum class org.jmol.c.VDW
 
AUTO_JMOL - Enum constant in enum class org.jmol.c.VDW
 
AUTO_RASMOL - Enum constant in enum class org.jmol.c.VDW
 
autoAddImplicitH - Variable in class org.jmol.smiles.SmilesSearch
 
autoAnimationDelay - Variable in class org.openscience.jmol.app.JmolApp
 
autobond - Static variable in class org.jmol.script.T
 
autoBondBs4(BS, BS, BS, BS, short, boolean, SB) - Method in class org.jmol.modelset.ModelSet
 
autoCalculate(int, String) - Method in class org.jmol.viewer.Viewer
 
autoExit - Variable in class org.jmol.viewer.Viewer
 
autoez - Variable in class jme.JME
 
autofps - Static variable in class org.jmol.script.T
 
autoHbond(BS, BS, boolean) - Method in class org.jmol.modelset.ModelSet
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.
autoHbond(BS, BS, boolean) - Method in class org.jmol.viewer.Viewer
 
autoIntegrate - Variable in class jspecview.common.JSViewer
 
autoIntegrate() - Method in class jspecview.common.IntegralData
 
AUTOINTEGRATE - Enum constant in enum class jspecview.common.ScriptToken
 
autonumber - Variable in class jme.JME
 
autoplaymovie - Static variable in class org.jmol.script.T
 
autoScrolls - Variable in class org.jmol.awtjs.swing.JComponent
 
autoSelectOnLoad() - Method in class jspecview.common.PeakInfo
a spectrum which, when loaded, should fire a message to load first peak -- GC for now
autoShowLegend - Variable in class jspecview.common.JSViewer
 
auxiliaryInfo - Variable in class org.jmol.modelset.Model
 
avail_in - Variable in class com.jcraft.jzlib.ZStream
 
available() - Method in class com.jcraft.jzlib.InflaterInputStream
 
ave(T3, T3) - Method in class javajs.util.T3
average of two tuples
average - Static variable in class org.jmol.script.T
 
AviCreator - Class in org.jmol.image
 
AviCreator() - Constructor for class org.jmol.image.AviCreator
 
awaken(boolean) - Method in class jspecview.application.MainFrame
 
AwtClipboard - Class in jspecview.java
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtClipboard - Class in org.jmol.awt
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtColor - Class in jspecview.java
 
AwtColor - Class in org.jmol.awt
 
AwtColor(int) - Constructor for class jspecview.java.AwtColor
 
AwtColor(int) - Constructor for class org.jmol.awt.AwtColor
 
AwtColor(int, int, int) - Constructor for class jspecview.java.AwtColor
 
AwtColor(int, int, int) - Constructor for class org.jmol.awt.AwtColor
 
AwtColor(int, int, int, int) - Constructor for class jspecview.java.AwtColor
 
AwtColor(int, int, int, int) - Constructor for class org.jmol.awt.AwtColor
 
AwtDialog - Class in jspecview.java
AwtDialog extends JDialog, interpreting DialogManager's requests in terms of Swing and AWT.
AwtDialog(DialogManager, JSVDialog, String) - Constructor for class jspecview.java.AwtDialog
 
AwtDialogFileFilter - Class in jspecview.java
A implementation of the FileFilter that filters out all files except those with extensions that are added.
AwtDialogFileFilter() - Constructor for class jspecview.java.AwtDialogFileFilter
Intialises a JSpecViewFileFilter
AwtDialogFileFilter(String[]) - Constructor for class jspecview.java.AwtDialogFileFilter
Initialises the JSpecViewFileFilter with an list of extensions to filter
AwtDialogFileFilter(String[], String) - Constructor for class jspecview.java.AwtDialogFileFilter
Initialises the JSpecViewFileFilter with an list of extensions to filter and a description of the filter
AwtDialogManager - Class in jspecview.java
just a class I made to separate the construction of the AnnotationDialogs from their use
AwtDialogManager() - Constructor for class jspecview.java.AwtDialogManager
 
AwtFileDropper - Class in jspecview.java
 
AwtFileDropper() - Constructor for class jspecview.java.AwtFileDropper
 
AwtFileHelper - Class in jspecview.java
 
AwtFileHelper() - Constructor for class jspecview.java.AwtFileHelper
 
AwtG2D - Class in jspecview.java
generic 2D drawing methods -- AWT version
AwtG2D - Class in org.jmol.awt
generic 2D drawing methods -- AWT version
AwtG2D() - Constructor for class jspecview.java.AwtG2D
 
AwtG2D() - Constructor for class org.jmol.awt.AwtG2D
 
AwtJmolPopup - Class in org.jmol.awt
 
AwtJmolPopup() - Constructor for class org.jmol.awt.AwtJmolPopup
 
AwtMainPanel - Class in jspecview.java
 
AwtMainPanel(BorderLayout) - Constructor for class jspecview.java.AwtMainPanel
 
AwtModelKitPopup - Class in org.jmol.awt
 
AwtModelKitPopup() - Constructor for class org.jmol.awt.AwtModelKitPopup
 
AwtPanel - Class in jspecview.java
JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
AwtPanel.RequestThread - Class in jspecview.java
 
AwtParameters - Class in jspecview.java
 
AwtParameters() - Constructor for class jspecview.java.AwtParameters
 
AwtPlatform - Class in jspecview.java
 
AwtPlatform() - Constructor for class jspecview.java.AwtPlatform
 
AwtPopup - Class in jspecview.java
 
AwtPopup() - Constructor for class jspecview.java.AwtPopup
 
AwtPopupHelper - Class in org.jmol.awt
all popup-related awt/swing class references are in this file.
AwtPopupHelper(GenericPopup) - Constructor for class org.jmol.awt.AwtPopupHelper
 
AwtPrintDialog - Class in jspecview.java
Dialog to set print preferences for JSpecview.
AwtPrintDialog() - Constructor for class jspecview.java.AwtPrintDialog
 
AwtSwingComponent - Class in org.jmol.awt
A javax.swing implementation of SwingComponent that mirrors org.jmol.awtjs.swing for compatibility with compilation with java2script.
AwtSwingComponent() - Constructor for class org.jmol.awt.AwtSwingComponent
 
AwtTree - Class in jspecview.application
 
AwtTree(JSViewer) - Constructor for class jspecview.application.AwtTree
 
AwtTreeNode - Class in jspecview.application
 
AwtTreeNode(String, PanelNode) - Constructor for class jspecview.application.AwtTreeNode
 
AwtTreePath - Class in jspecview.application
 
AwtTreePath(Object[]) - Constructor for class jspecview.application.AwtTreePath
 
axes - Static variable in class org.jmol.script.T
 
Axes - Class in org.jmol.shape
 
Axes() - Constructor for class org.jmol.shape.Axes
 
AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
axes2 - Variable in class org.jmol.shape.Axes
 
axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
axescolor - Static variable in class org.jmol.script.T
 
axesmode - Static variable in class org.jmol.script.T
 
axesMode - Variable in class org.jmol.viewer.GlobalSettings
 
axesmolecular - Static variable in class org.jmol.script.T
 
axesoffset - Static variable in class org.jmol.script.T
 
axesorientationrasmol - Static variable in class org.jmol.script.T
 
AxesRenderer - Class in org.jmol.render
 
AxesRenderer() - Constructor for class org.jmol.render.AxesRenderer
 
axesscale - Static variable in class org.jmol.script.T
 
axesTypes - Static variable in class org.jmol.viewer.JC
 
axesunitcell - Static variable in class org.jmol.script.T
 
axeswindow - Static variable in class org.jmol.script.T
 
axis - Static variable in class org.jmol.script.T
 
AXIS_A - Static variable in class org.jmol.viewer.JC
 
axis1color - Static variable in class org.jmol.script.T
 
axis2color - Static variable in class org.jmol.script.T
 
axis3color - Static variable in class org.jmol.script.T
 
axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisangle - Static variable in class org.jmol.script.T
 
axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisLabels - Static variable in class org.jmol.viewer.JC
 
axisNX - Static variable in class org.jmol.viewer.JC
 
axisNY - Static variable in class org.jmol.viewer.JC
 
axisNZ - Static variable in class org.jmol.viewer.JC
 
axisPoints - Variable in class org.jmol.shape.Axes
[x, y, z, -x, -y, -z] or [a, b, c, -a, -b, -c]
axisType - Variable in class org.jmol.shape.Axes
 
axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisX - Static variable in class org.jmol.viewer.JC
 
axisXY - Variable in class org.jmol.shape.Axes
 
axisY - Static variable in class javajs.util.Measure
 
axisY - Static variable in class org.jmol.viewer.JC
 
axisZ - Static variable in class org.jmol.viewer.JC
 

B

b - Variable in class org.jmol.g3d.PrecisionRenderer
 
b - Variable in class org.jmol.util.Rgb16
 
b - Variable in class org.jmol.util.SimpleUnitCell
 
b - Variable in class org.jmol.viewer.ActionManager
 
b_ - Variable in class org.jmol.util.SimpleUnitCell
 
babel - Static variable in class org.jmol.script.T
 
BABEL - Enum constant in enum class org.jmol.c.VDW
 
babel21 - Static variable in class org.jmol.script.T
 
BABEL21 - Enum constant in enum class org.jmol.c.VDW
 
back - Static variable in class org.jmol.script.T
 
backbone - Static variable in class org.jmol.script.T
 
Backbone - Class in org.jmol.shapebio
 
Backbone() - Constructor for class org.jmol.shapebio.Backbone
 
backboneBlockVis - Variable in class org.jmol.modelsetbio.Monomer
 
BackboneRenderer - Class in org.jmol.renderbio
 
BackboneRenderer() - Constructor for class org.jmol.renderbio.BackboneRenderer
 
background - Static variable in class org.jmol.script.T
 
backgroundColix - Variable in class org.jmol.export.___Exporter
 
backgroundColix - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
backgroundcolor - Static variable in class org.jmol.script.T
 
BACKGROUNDCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
backgroundImage - Variable in class org.jmol.util.GData
 
backgroundmodel - Static variable in class org.jmol.script.T
 
backlit - Static variable in class org.jmol.script.T
 
backshell - Static variable in class org.jmol.script.T
 
bad() - Method in class org.jmol.script.ScriptError
 
balls - Static variable in class org.jmol.script.T
 
Balls - Class in org.jmol.shape
 
Balls() - Constructor for class org.jmol.shape.Balls
 
BallsRenderer - Class in org.jmol.render
 
BallsRenderer() - Constructor for class org.jmol.render.BallsRenderer
 
bannerFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
BannerFrame - Class in org.openscience.jmol.app.jsonkiosk
A simple class that throws up a white rectangle that has a single centered label.
BannerFrame(int, int) - Constructor for class org.openscience.jmol.app.jsonkiosk.BannerFrame
 
barb - Static variable in class org.jmol.script.T
 
barDistance - Variable in class org.jmol.modelset.Text
 
barPixels - Variable in class org.jmol.modelset.Text
 
barPixelsXYZ - Variable in class org.jmol.modelset.Text
 
barray - Static variable in class org.jmol.script.T
 
BArray - Class in javajs.util
 
BArray(byte[]) - Constructor for class javajs.util.BArray
 
Base64 - Class in javajs.util
 
Base64() - Constructor for class javajs.util.Base64
 
baseAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
first atom index for this collection, current modelset.ac
baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseBlockSize - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
baseBondIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
baseColor - Variable in class org.jmol.jvxl.data.JvxlData
 
baseFont3d - Variable in class org.jmol.shape.Frank
 
baseGroupIndex - Variable in class org.jmol.modelset.ModelLoader
 
basemodel - Static variable in class org.jmol.script.T
 
baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
 
basepair - Static variable in class org.jmol.script.T
 
BasePair - Class in org.jmol.modelsetbio
 
baseStrandOffset - Variable in class org.jmol.renderbio.StrandsRenderer
 
baseSymmetryAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
BasisFunctionReader - Class in org.jmol.adapter.readers.quantum
 
BasisFunctionReader() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
BasisFunctionReader.MOEnergySorter - Class in org.jmol.adapter.readers.quantum
 
Bbcage - Class in org.jmol.shape
 
Bbcage() - Constructor for class org.jmol.shape.Bbcage
 
BbcageRenderer - Class in org.jmol.render
 
BbcageRenderer() - Constructor for class org.jmol.render.BbcageRenderer
 
bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
 
bbCorner0 - Variable in class org.jmol.util.BoxInfo
 
bbCorner1 - Variable in class org.jmol.util.BoxInfo
 
bboxModels - Variable in class org.jmol.modelset.ModelSet
 
BC - Class in javajs.util
byte converter
BC() - Constructor for class javajs.util.BC
 
BCIFReader - Class in org.jmol.adapter.readers.cif
A very simple Binary CIF file reader extention of MMCifReader extends CifReader.
BCIFReader() - Constructor for class org.jmol.adapter.readers.cif.BCIFReader
 
BEGIN - Static variable in class org.jmol.shapecgo.CGOMesh
 
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
 
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.util.GData
 
best - Static variable in class org.jmol.script.T
 
beta - Static variable in class org.jmol.script.T
 
beta - Variable in class org.jmol.util.SimpleUnitCell
 
bfactor - Variable in class org.jmol.adapter.smarter.Atom
 
bgcolix - Variable in class org.jmol.modelset.Text
 
bgcolix - Variable in class org.jmol.render.LabelsRenderer
 
bgcolixes - Variable in class org.jmol.shape.Labels
 
bgcolor - Variable in class jspecview.common.PanelData
 
bgcolor - Variable in class org.jmol.util.GData
 
BGYOR - Static variable in class org.jmol.util.ColorEncoder
 
bigEndian - Variable in class javajs.util.OC
 
BilbaoReader - Class in org.jmol.adapter.readers.xtal
Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.
BilbaoReader() - Constructor for class org.jmol.adapter.readers.xtal.BilbaoReader
 
bin - Static variable in class org.jmol.script.T
 
binary - Static variable in class org.jmol.script.T
 
BinaryDcdReader - Class in org.jmol.adapter.readers.more
DCD binary trajectory file reader.
BinaryDcdReader() - Constructor for class org.jmol.adapter.readers.more.BinaryDcdReader
 
binarydoc - Variable in class org.jmol.jvxl.readers.JvxlReader
 
binarydoc - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
binarydoc - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
binaryDoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
BinaryDocument - Class in javajs.util
 
BinaryDocument() - Constructor for class javajs.util.BinaryDocument
 
binaryOp(T, SV, SV) - Method in class org.jmol.script.ScriptMathProcessor
 
bind - Static variable in class org.jmol.script.T
 
bindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
 
bindAction(String, String) - Method in class org.jmol.viewer.Viewer
 
Binding - Class in org.jmol.viewer.binding
 
Binding() - Constructor for class org.jmol.viewer.binding.Binding
 
bindName(int, String) - Method in class org.jmol.viewer.binding.Binding
 
BioExt - Class in org.jmol.modelsetbio
 
BioExt() - Constructor for class org.jmol.modelsetbio.BioExt
 
BioMeshRenderer - Class in org.jmol.renderbio
 
BioMeshRenderer() - Constructor for class org.jmol.renderbio.BioMeshRenderer
 
BioModel - Class in org.jmol.modelsetbio
 
BioModel() - Constructor for class org.jmol.modelsetbio.BioModel
 
bioModelset - Variable in class org.jmol.modelset.AtomCollection
If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaning
BioModelSet - Class in org.jmol.modelsetbio
 
BioModelSet() - Constructor for class org.jmol.modelsetbio.BioModelSet
 
biomtChainAtomCounts - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
 
bioPolymer - Variable in class org.jmol.shapebio.BioShape
 
BioPolymer - Class in org.jmol.modelsetbio
A "BioPolymer" is a constructed set of contiguous (probably connected) "Monomers", which may be one of Alpha (Calpha atoms), Amino (Calpha + backbone), Phosphorus (P atoms), Nucleic (DNA/RNA), or Carbohydrate.
BioPolymer(Monomer[], boolean) - Constructor for class org.jmol.modelsetbio.BioPolymer
 
bioPolymerIndexInModel - Variable in class org.jmol.modelsetbio.BioPolymer
 
bioPolymers - Variable in class org.jmol.modelsetbio.BioModel
 
BioResolver - Class in org.jmol.modelsetbio
a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.
BioResolver() - Constructor for class org.jmol.modelsetbio.BioResolver
 
BioShape - Class in org.jmol.shapebio
 
BioShapeCollection - Class in org.jmol.shapebio
Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set.
BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
 
bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
 
biosymmetry - Variable in class org.jmol.modelset.Model
 
BIRTH - Static variable in class com.sparshui.common.TouchState
 
BIRTH - Static variable in class org.jmol.multitouch.ActionManagerMT
 
bis - Variable in class javajs.util.BinaryDocument
 
bitset - Static variable in class org.jmol.script.T
 
BLACK - Static variable in class jspecview.common.ColorParameters
 
BLACK - Variable in class jspecview.common.PanelData
 
BLACK - Static variable in class org.jmol.util.C
 
blockdata - Static variable in class org.jmol.script.T
 
blockID - Variable in class jspecview.source.JDXDataObject
 
BLUE - Static variable in class jspecview.common.ColorParameters
 
BLUE - Static variable in class org.jmol.util.C
 
BMPDecoder - Class in javajs.img
src: http://www.javaworld.com/article/2077542/learn-java/java-tip-43--how-to- read-8--and-24-bit-microsoft-windows-bitmaps-in-java-applications.html see also: http://en.wikipedia.org/wiki/BMP_file_format Modified by Bob Hanson hansonr@stolaf.edu
BMPDecoder() - Constructor for class javajs.img.BMPDecoder
 
bo - Variable in class org.jmol.modelset.BondCollection
 
bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
 
bond - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
bond - Variable in class org.jmol.shapespecial.Dipole
 
Bond - Class in org.jmol.adapter.smarter
 
Bond - Class in org.jmol.modelset
 
Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
 
Bond(Atom, Atom, int, short, short) - Constructor for class org.jmol.modelset.Bond
 
BOND_AROMATIC - Static variable in class org.jmol.util.Edge
 
BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.util.Edge
 
BOND_AROMATIC_MASK - Static variable in class org.jmol.util.Edge
 
BOND_AROMATIC_SINGLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_DOUBLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_MASK - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_QUINTUPLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_sextuple - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_SINGLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_TRIPLE - Static variable in class org.jmol.util.Edge
 
BOND_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.BondCollection
 
BOND_H_CALC - Static variable in class org.jmol.util.Edge
 
BOND_H_CALC_MASK - Static variable in class org.jmol.util.Edge
 
BOND_H_MINUS_3 - Static variable in class org.jmol.util.Edge
 
BOND_H_MINUS_4 - Static variable in class org.jmol.util.Edge
 
BOND_H_NUCLEOTIDE - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_2 - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_3 - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_4 - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_5 - Static variable in class org.jmol.util.Edge
 
BOND_H_REGULAR - Static variable in class org.jmol.util.Edge
 
BOND_HBOND_SHIFT - Static variable in class org.jmol.util.Edge
 
BOND_HYDROGEN_MASK - Static variable in class org.jmol.util.Edge
 
BOND_NEW - Static variable in class org.jmol.util.Edge
 
BOND_ORDER_ANY - Static variable in class org.jmol.util.Edge
 
BOND_ORDER_NULL - Static variable in class org.jmol.util.Edge
 
BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL_MASK - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL01 - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL12 - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL23 - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL32 - Static variable in class org.jmol.util.Edge
 
BOND_PYMOL_MULT - Static variable in class org.jmol.util.Edge
 
BOND_PYMOL_NOMULT - Static variable in class org.jmol.util.Edge
 
BOND_RENDER_MASK - Static variable in class org.jmol.util.Edge
Extended Bond Definition Types Originally these were short 16-bit values
BOND_RENDER_SINGLE - Static variable in class org.jmol.util.Edge
 
BOND_STEREO_EITHER - Static variable in class org.jmol.util.Edge
 
BOND_STEREO_FAR - Static variable in class org.jmol.util.Edge
 
BOND_STEREO_MASK - Static variable in class org.jmol.util.Edge
 
BOND_STEREO_NEAR - Static variable in class org.jmol.util.Edge
 
BOND_STRUT - Static variable in class org.jmol.util.Edge
 
BOND_SULFUR_MASK - Static variable in class org.jmol.util.Edge
 
bondAtoms(Atom, Atom, int, short, BS, float, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
 
BondCollection - Class in org.jmol.modelset
 
BondCollection() - Constructor for class org.jmol.modelset.BondCollection
 
bondcount - Static variable in class org.jmol.script.T
 
bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bondCount - Variable in class org.jmol.modelset.BondCollection
 
bondData - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
 
bonded - Static variable in class org.jmol.script.T
 
BONDING - Enum constant in enum class org.jmol.c.VDW
 
bondingradius - Static variable in class org.jmol.script.T
 
bondingRadius - Variable in class org.jmol.adapter.smarter.Atom
 
bondingversion - Static variable in class org.jmol.script.T
 
bondingVersion - Static variable in class org.jmol.util.Elements
 
bondingVersion - Variable in class org.jmol.viewer.GlobalSettings
 
BondIterator - Interface in org.jmol.modelset
 
bondmode - Static variable in class org.jmol.script.T
 
bondmodeor - Static variable in class org.jmol.script.T
 
bondMutually(Atom, Atom, int, short, float) - Method in class org.jmol.modelset.BondCollection
 
bondorder - Static variable in class org.jmol.script.T
 
bondpicking - Static variable in class org.jmol.script.T
 
bondradiusmilliangstroms - Static variable in class org.jmol.script.T
 
bondRotationCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
 
bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bonds - Variable in class org.jmol.minimize.Minimizer
 
bonds - Variable in class org.jmol.modelset.Atom
MAY BE NULL
bonds - Static variable in class org.jmol.script.T
 
bondset - Static variable in class org.jmol.script.T
 
BondSet - Class in org.jmol.modelset
 
BondSet() - Constructor for class org.jmol.modelset.BondSet
 
bondtolerance - Static variable in class org.jmol.script.T
 
booleanparam - Static variable in class org.jmol.script.T
 
BorderLayout - Class in org.jmol.awtjs.swing
 
BorderLayout() - Constructor for class org.jmol.awtjs.swing.BorderLayout
 
bottom - Static variable in class org.jmol.script.T
 
bottomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
bottomMargin - Static variable in class jspecview.common.PanelData
 
boundbox - Static variable in class org.jmol.script.T
 
boundboxAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
boundboxcolor - Static variable in class org.jmol.script.T
 
boundingBox - Variable in class org.jmol.jvxl.data.JvxlData
 
boundingBox - Variable in class org.jmol.jvxl.readers.Parameters
 
boundingBox - Variable in class org.jmol.jvxl.readers.JvxlReader
 
boundingBox - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
boundingBox - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
boxHeight - Variable in class org.jmol.modelset.Text
 
BoxInfo - Class in org.jmol.util
The BoxInfo class holds critical information about boundboxes.
BoxInfo() - Constructor for class org.jmol.util.BoxInfo
 
boxWidth - Variable in class org.jmol.modelset.Text
 
boxX - Variable in class org.jmol.modelset.Text
 
boxXY - Variable in class org.jmol.modelset.Text
 
boxY - Variable in class org.jmol.modelset.Text
 
boxYoff2 - Variable in class org.jmol.modelset.Text
 
bp - Variable in class jspecview.export.AMLExporter
 
bp - Variable in class jspecview.export.CMLExporter
 
bpointx - Variable in class jme.JME
 
bpointy - Variable in class jme.JME
 
br - Variable in class org.jmol.jvxl.readers.JvxlReader
 
br - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
br - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
branch - Static variable in class org.jmol.script.T
 
breakcmd - Static variable in class org.jmol.script.T
 
brillouin - Static variable in class org.jmol.script.T
 
BrukerReader - Class in jspecview.source
A class to read Bruker ZIP files and directories.
BrukerReader() - Constructor for class jspecview.source.BrukerReader
 
BS - Class in javajs.util
a fast 32-bit BitSet optimized for Java2Script -- about 25 times faster than java.util.BitSet
BS() - Constructor for class javajs.util.BS
Creates a new bit set.
bs14 - Variable in class org.jmol.minimize.MinAtom
 
bsA() - Method in class org.jmol.viewer.Viewer
 
bsAll - Variable in class org.jmol.adapter.smarter.Structure
 
bsAll - Variable in class org.jmol.modelset.ModelSet
 
bsAromatic - Variable in class org.jmol.modelset.BondCollection
 
bsAsymmetricUnit - Variable in class org.jmol.modelset.Model
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.
bsAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bsAtoms - Variable in class org.jmol.minimize.Minimizer
 
bsAtoms - Variable in class org.jmol.modelset.Model
Note that this bitset may or may not include bsAtomsDeleted
bsAtomsDeleted - Variable in class org.jmol.modelset.Model
 
bsBgColixSet - Variable in class org.jmol.shape.Labels
 
bsClickable - Variable in class org.jmol.modelset.AtomCollection
 
bsColixSet - Variable in class org.jmol.shape.Shape
 
bsDeleted - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
bsDeleted - Variable in class org.jmol.viewer.SelectionManager
 
bsDisplay - Variable in class org.jmol.shape.MeshCollection
 
bsDisplay - Variable in class org.jmol.util.MeshSurface
 
bsExcluded - Variable in class org.jmol.jvxl.readers.Parameters
 
bsExcluded - Variable in class org.jmol.quantum.QuantumCalculation
 
bsExcludedPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsExcludedTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsExcludedVertices - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
bsFontSet - Variable in class org.jmol.shape.Labels
 
bsFrameOffsets - Variable in class org.jmol.viewer.TransformManager
 
bsHighlight - Variable in class org.jmol.shape.Halos
 
bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
 
bsIgnored - Variable in class org.jmol.atomdata.AtomData
 
bsMeshesVisible - Variable in class org.jmol.shapespecial.DrawMesh
 
bsMinFixed - Variable in class org.jmol.minimize.Minimizer
 
bsModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
bsModulated - Variable in class org.jmol.modelset.AtomCollection
 
bsMolecule - Variable in class org.jmol.shapespecial.Dipole
 
bsMolecules - Variable in class org.jmol.atomdata.AtomData
 
bsOrderSet - Variable in class org.jmol.shape.Sticks
 
bsPartialCharges - Variable in class org.jmol.modelset.AtomCollection
 
bspf - Variable in class org.jmol.modelset.AtomCollection
Binary Space Partitioning Forest
bspf - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
Bspf - Class in org.jmol.bspt
A Binary Space Partitioning Forest
Bspf(int) - Constructor for class org.jmol.bspt.Bspf
 
bsPolygons - Variable in class org.jmol.render.MeshRenderer
 
bsPolygons - Variable in class org.jmol.util.MeshSurface
 
bsPolygonsToExport - Variable in class org.jmol.render.MeshRenderer
 
Bspt - Class in org.jmol.bspt
a Binary Space Partitioning Tree
Bspt(int, int) - Constructor for class org.jmol.bspt.Bspt
Create a bspt with the specified number of dimensions.
bspts - Variable in class org.jmol.bspt.Bspf
 
bsRenderableAtoms - Variable in class org.jmol.viewer.ShapeManager
 
bsSelected - Variable in class org.jmol.atomdata.AtomData
 
bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
 
bsSelected - Variable in class org.jmol.modelset.MeasurementData
 
bsSizeDefault - Variable in class org.jmol.shape.AtomShape
 
bsSizeSet - Variable in class org.jmol.shape.Shape
 
bsSlabbedInternal - Variable in class org.jmol.viewer.ShapeManager
 
bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
 
bsSlabGhost - Variable in class org.jmol.util.MeshSurface
 
bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
 
bsStructuredModels - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bsSubset - Variable in class org.jmol.viewer.SelectionManager
 
bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
 
bsSymmetry - Variable in class org.jmol.modelset.ModelSet
 
bsTemp - Variable in class org.jmol.shape.Mesh
 
bsToArray(BS) - Method in class org.jmol.scriptext.ScriptExt
 
BSUtil - Class in org.jmol.util
 
BSUtil() - Constructor for class org.jmol.util.BSUtil
 
bsValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsVdw - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
bsVdw - Variable in class org.jmol.minimize.MinAtom
 
bsVisible - Variable in class org.jmol.modelset.AtomCollection
 
bsVisible - Variable in class org.jmol.renderbio.BackboneRenderer
 
bsVisible - Variable in class org.jmol.renderbio.CartoonRenderer
 
bsVisible - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
bsVisible - Variable in class org.jmol.renderbio.RibbonsRenderer
 
bsVisible - Variable in class org.jmol.renderbio.RocketsRenderer
 
bsVisible - Variable in class org.jmol.renderbio.StrandsRenderer
 
bsVisible - Variable in class org.jmol.renderbio.TraceRenderer
 
bsVoxelBitSet - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
bsVoxels - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
btnType - Variable in class org.jmol.awtjs.swing.JMenuItem
 
buf - Variable in class com.jcraft.jzlib.InflaterInputStream
 
buffer - Variable in class com.jcraft.jzlib.DeflaterOutputStream
 
bufferSize - Variable in class org.jmol.util.GData
 
buildAtomsPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildBondPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildDispPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildStructure(String) - Method in class jspecview.popup.JSVPopupResourceBundle
 
buildStructure(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
buildStructure(String) - Method in class org.jmol.popup.MainPopupResourceBundle
 
buildStructure(String) - Method in class org.jmol.popup.PopupResource
 
BUTTON_MASK - Static variable in class org.jmol.awtjs.Event
 
BUTTON_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
buttonGroup - Variable in class org.jmol.popup.GenericPopup
 
ButtonGroup - Class in org.jmol.awtjs.swing
 
ButtonGroup() - Constructor for class org.jmol.awtjs.swing.ButtonGroup
 
bValue(T) - Static method in class org.jmol.script.SV
 
BW - Static variable in class org.jmol.util.ColorEncoder
 
bwMode - Variable in class jme.JME
 
BWR - Static variable in class org.jmol.util.ColorEncoder
 
BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
byteArrayToFloat(byte[], int) - Static method in class com.sparshui.common.utils.Converter
 
byteArrayToInt(byte[]) - Static method in class com.sparshui.common.utils.Converter
Converts a byte array to an integer.
byteArrayToInt(byte[], int) - Static method in class com.sparshui.common.utils.Converter
 
byteArrayToJSON(byte[]) - Static method in class javajs.util.PT
 
byteArrayToLong(byte[], int) - Static method in class com.sparshui.common.utils.Converter
 
byteArrayToString(byte[]) - Static method in class com.sparshui.common.utils.Converter
 
bytePos - Variable in class javajs.img.PngEncoder
 
BytePoster - Interface in javajs.api
 
bytesToDoubleToFloat(byte[], int, boolean) - Static method in class javajs.util.BC
see http://en.wikipedia.org/wiki/Binary64 not concerning ourselves with very small or very large numbers and getting this exactly right.
bytesToFloat(byte[], int, boolean) - Static method in class javajs.util.BC
 
bytesToInt(byte[], int, boolean) - Static method in class javajs.util.BC
 
bytesToShort(byte[], int, boolean) - Static method in class javajs.util.BC
 
bz - Variable in class org.jmol.util.BZone
overall object
BZip2Constants - Interface in org.apache.tools.bzip2
Base class for both the compress and decompress classes.
BZone - Class in org.jmol.util
A class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells.
BZone() - Constructor for class org.jmol.util.BZone
 

C

c - Variable in class org.jmol.util.SimpleUnitCell
 
C - Class in org.jmol.util
Note: Color table is now in javajs/util/CU.java
C() - Constructor for class org.jmol.util.C
 
c_ - Variable in class org.jmol.util.SimpleUnitCell
 
cA_ - Variable in class org.jmol.util.SimpleUnitCell
 
cache - Static variable in class org.jmol.script.T
 
cacheClear() - Method in class org.jmol.viewer.Viewer
 
cacheFileByName(String, boolean) - Method in interface javajs.api.JSInterface
 
cacheFileByName(String, boolean) - Method in class jspecview.appletjs.JSVApplet
 
cacheFileByName(String, boolean) - Method in class org.jmol.util.GenericApplet
 
cacheFileByName(String, boolean) - Method in class org.jmol.viewer.Viewer
 
cacheFileByNameAdd(String, boolean) - Method in class org.jmol.viewer.FileManager
 
cacheGet(String) - Static method in class jspecview.common.JSVFileManager
 
cacheGet(String, boolean) - Method in class org.jmol.viewer.FileManager
 
cacheList() - Method in class org.jmol.viewer.FileManager
 
cachePut(String, Object) - Method in interface javajs.api.JSInterface
 
cachePut(String, Object) - Method in class jspecview.appletjs.JSVApplet
 
cachePut(String, Object) - Method in class org.jmol.util.GenericApplet
 
cachePut(String, Object) - Method in class org.jmol.viewer.Viewer
JSInterface -- allows saving files in memory for later retrieval
cachePut(String, String) - Static method in class jspecview.common.JSVFileManager
 
cacheZipContents(BufferedInputStream, String, Map<String, Object>, boolean) - Method in interface javajs.api.GenericZipTools
 
cacheZipContents(BufferedInputStream, String, Map<String, Object>, boolean) - Method in class javajs.util.ZipTools
 
CACTUS_FILE_TYPES - Static variable in class org.jmol.viewer.JC
 
calc(double[][]) - Method in class javajs.util.Eigen
Check for symmetry, then construct the eigenvalue decomposition
CALC_H_ALLOW_H - Static variable in class org.jmol.modelset.AtomCollection
 
CALC_H_DOALL - Static variable in class org.jmol.modelset.AtomCollection
 
CALC_H_HAVEH - Static variable in class org.jmol.modelset.AtomCollection
 
CALC_H_IGNORE_H - Static variable in class org.jmol.modelset.AtomCollection
 
CALC_H_JUSTC - Static variable in class org.jmol.modelset.AtomCollection
 
CALC_H_QUICK - Static variable in class org.jmol.modelset.AtomCollection
 
calc2or3JorNOE(Viewer, Atom[], String, int) - Static method in class org.jmol.quantum.NMRCalculation
Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;
calc3JCH(String, double, boolean) - Static method in class org.jmol.quantum.NMRCalculation
 
calcAllRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
only for base models, not trajectories
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.api.JmolViewer
 
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.modelset.ModelSet
 
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.viewer.Viewer
 
calcAveragePoint(P3, P3, P3) - Static method in class javajs.util.Measure
 
calcAveragePointN(P3[], int, P3) - Static method in class javajs.util.Measure
 
calcAxis() - Method in class org.jmol.modelsetbio.Helix
 
calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
 
calcAxis() - Method in class org.jmol.modelsetbio.Sheet
 
calcBestAxisThroughPoints(P3[], int, P3, V3, V3, int) - Static method in class javajs.util.Measure
 
calcBestPlaneThroughPoints(P3[], int, P4) - Static method in class javajs.util.Measure
Calculate the best ax + by + cz + d = 0 plane through a number of points using a three-step check for the best plane based on normal distance.
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.modelset.ModelSet
 
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.viewer.Viewer
 
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
sets all camera and scale factors needed by the specific perspective model instantiated
calcCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
calcEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
 
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
 
calcJKarplus(double) - Static method in class org.jmol.quantum.NMRCalculation
 
calcJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
calcNavigationPoint() - Method in interface org.jmol.api.JmolNavigatorInterface
 
calcNavigationPoint() - Method in class org.jmol.navigate.Navigator
 
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
All the magic happens here.
calcNOE(Viewer, Atom, Atom) - Static method in class org.jmol.quantum.NMRCalculation
 
calcNOEs() - Method in class org.jmol.quantum.NMRNoeMatrix
calculate the NOESY spectrum at a particular mixing time.
calcNOEs() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
calcNormalizedNormal(T3, T3, T3, T3, T3) - Static method in class javajs.util.Measure
note that if vAB or vAC is dispensible, vNormNorm can be one of them
calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
For reduced density only; coloring is done point by point.
calcPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
Fill this plane with data based on the current set of raw data planes.
calcPlaneForMode(P3[], int, P4, char) - Static method in class javajs.util.Measure
Compact calculation of the best pane using a simple method discussed at https://stackoverflow.com/questions/12299540/plane-fitting-to-4-or-more-xyz-points (A^T A)^-1 A^T B run three times to ensure that at least one is not perpendicular.
calcRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
These are not actual hydrogen bonds.
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
calcRopeMidPoints() - Method in class org.jmol.renderbio.RocketsRenderer
 
calcRotationRadius(int, P3, boolean) - Method in class org.jmol.modelset.ModelSet
 
calcRotationRadiusBs(BS) - Method in class org.jmol.modelset.ModelSet
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.BackboneRenderer
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.CartoonRenderer
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.RibbonsRenderer
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.RocketsRenderer
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.StrandsRenderer
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.TraceRenderer
 
calcScreens(float, short[]) - Method in class org.jmol.renderbio.BackboneRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.CartoonRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.MeshRibbonRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.RibbonsRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.RocketsRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.StrandsRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcScreens(float, short[]) - Method in class org.jmol.renderbio.TraceRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcSelectedGroupsCount() - Method in class org.jmol.modelset.ModelSet
 
calcSelectedMoleculesCount() - Method in class org.jmol.modelset.ModelSet
 
calcSelectedMonomersCount() - Method in class org.jmol.modelset.ModelSet
 
calcSelectedMonomersCount() - Method in class org.jmol.modelsetbio.BioModelSet
 
calcSelectedMonomersCount(BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
 
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager4D
 
calculate - Static variable in class org.jmol.script.T
 
calculate(T3, boolean) - Method in class org.jmol.util.ModulationSet
Calculate r_I internal d-space coordinate of an atom.
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolEnvCalc
 
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calculate(VolumeData, BS, P3[], Atom[], float[], int) - Method in class org.jmol.quantum.MepCalculation
 
calculateAllPolymers(Group[], int, int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
calculateAllStructuresExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
 
calculateAllStuctures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
 
calculateChirality(BS) - Method in class org.jmol.viewer.Viewer
 
calculateChiralityForAtoms(BS, boolean) - Method in class org.jmol.modelset.ModelSet
 
calculateChiralityForSmiles(String) - Method in class org.jmol.viewer.Viewer
 
calculateCIPChiralityForAtoms(Viewer, BS) - Method in interface org.jmol.api.SymmetryInterface
 
calculateCIPChiralityForAtoms(Viewer, BS) - Method in class org.jmol.symmetry.Symmetry
 
calculateCIPChiralityForSmiles(Viewer, String) - Method in interface org.jmol.api.SymmetryInterface
 
calculateCIPChiralityForSmiles(Viewer, String) - Method in class org.jmol.symmetry.Symmetry
 
calculateDssp(Object[], int, Object, boolean, boolean, boolean, int) - Method in class org.jmol.dssx.DSSP
 
calculateDssrProperty(String) - Method in class org.jmol.modelset.ModelSet
 
calculateDSSRStructure(Viewer, BS) - Method in interface org.jmol.api.JmolAnnotationParser
 
calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.AnnotationParser
 
calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.DSSR1
 
calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
 
calculateFormalCharges(BS) - Method in class org.jmol.viewer.Viewer
 
calculateFractionalPoint(float, P3, P3, float, float, P3) - Method in class org.jmol.jvxl.data.VolumeData
 
calculateGeodesicSurface(BS, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
calculateGeodesicSurface(BS, float) - Method in class org.jmol.shapesurface.Isosurface
 
calculateHydrogens(BS, int[], Lst<Atom>, int) - Method in class org.jmol.modelset.AtomCollection
get a list of potential H atom positions based on elemental valence and formal charge
calculateIntegral() - Method in class jspecview.common.IntegralData
 
calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
 
calculateMolecularDipole(int, BS) - Method in class org.jmol.modelset.ModelSet
 
calculateMolecularDipole(BS) - Method in class org.jmol.viewer.Viewer
 
calculatePartialCharges(BS) - Method in class org.jmol.viewer.Viewer
 
calculatePartialCharges(Bond[], int[], Atom[], int[], BS, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
assign partial charges ala MMFF94
calculatePartialCharges(ModelSet, BS, BS) - Method in class org.jmol.minimize.Minimizer
 
calculatePointGroup(BS) - Method in class org.jmol.modelset.ModelSet
 
calculatePolymers(Group[], int, int, BS) - Method in class org.jmol.modelset.ModelSet
 
calculateQuaternionRotation(P3[][], float[]) - Static method in class javajs.util.Measure
Closed-form solution of absolute orientation requiring 1:1 mapping of positions.
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
 
calculateStraightness() - Method in class org.jmol.viewer.Viewer
 
calculateStraightnessAll() - Method in class org.jmol.modelset.ModelSet
 
calculateStraightnessAll() - Method in class org.jmol.modelsetbio.BioModelSet
 
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
Uses Levitt invalid input: '&' Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calculateStructures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
 
calculateStructures(BS, boolean, boolean, int) - Method in class org.jmol.viewer.Viewer
 
calculateStructuresAllExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
allows rebuilding of PDB structures; also accessed by ModelManager from Eval
calculateStruts(BS, BS) - Method in class org.jmol.modelset.ModelSet
see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
calculateStruts(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
calculateStruts(BS, BS) - Method in class org.jmol.viewer.Viewer
 
calculateSurface(BS, float) - Method in class org.jmol.modelset.AtomCollection
 
calculateSurface(BS, float) - Method in class org.jmol.viewer.Viewer
 
calculateVolume(BS, VDW) - Method in class org.jmol.modelset.AtomCollection
 
calculateVolumeOrArea(MeshData, BS, boolean, boolean) - Static method in class org.jmol.jvxl.data.MeshData
 
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
The number of the calculation being interpreted.
calculationType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
calcVertexPoint(int, int, int, int, P3) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
callback(String, String) - Method in class jspecview.dialog.IntegrationDialog
 
callback(String, String) - Method in class jspecview.dialog.JSVDialog
 
callback(String, String) - Method in class jspecview.dialog.MeasurementsDialog
 
callback(String, String) - Method in class jspecview.dialog.OverlayLegendDialog
 
callback(String, String) - Method in class jspecview.dialog.PeakListDialog
 
callback(String, String) - Method in class jspecview.dialog.ViewsDialog
 
callbackAD(String, String) - Method in class jspecview.dialog.JSVDialog
 
callbacks - Variable in class org.jmol.util.GenericApplet
 
callToJavaScript(String, Object[]) - Method in interface jspecview.api.AppletFrame
 
callToJavaScript(String, Object[]) - Method in class jspecview.appletjs.JSVApplet
Calls a javascript function given by the function name passing to it the string parameters as arguments
camera - Variable in class org.jmol.viewer.TransformManager
 
cameradepth - Static variable in class org.jmol.script.T
 
cameraDepth - Variable in class org.jmol.viewer.TransformManager
 
cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
 
cameraDistance - Variable in class org.jmol.export.___Exporter
 
cameraDistance - Variable in class org.jmol.viewer.TransformManager
 
cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
 
cameraPosition - Variable in class org.jmol.export.___Exporter
 
cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
 
cameraSetting - Variable in class org.jmol.viewer.TransformManager
 
canBeNormalized(V3d) - Static method in class org.jmol.minimize.Util
 
canBeSquared(double) - Static method in class org.jmol.minimize.Util
 
canCapCylinders - Variable in class org.jmol.export.__CartesianExporter
 
cancel - Static variable in class org.jmol.script.T
 
cancel() - Method in class javajs.util.OC
 
cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
canConvertTransAbs() - Method in class jspecview.source.JDXDataObject
 
canDo(int) - Method in class org.jmol.viewer.StateManager
 
canDoLineTo() - Method in class javajs.export.PDFCreator
 
canDoLineTo() - Method in class jspecview.common.PDFWriter
 
canDoLineTo() - Method in class jspecview.java.AwtG2D
 
canDoLineTo() - Method in class jspecview.js2d.JsG2D
 
canDoLineTo() - Method in interface org.jmol.api.GenericGraphics
 
canDoLineTo() - Method in class org.jmol.awt.AwtG2D
 
canDoLineTo() - Method in class org.jmol.awtjs2d.JsG2D
 
canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
 
canDownsample - Variable in class org.jmol.jvxl.readers.JvxlReader
 
canDownsample - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
canDownsample - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
canIntegrate() - Method in class jspecview.source.JDXDataObject
 
CANONICAL_DC_LIST - Static variable in class org.jmol.quantum.QS
 
CANONICAL_DS_LIST - Static variable in class org.jmol.quantum.QS
 
CANONICAL_FC_LIST - Static variable in class org.jmol.quantum.QS
 
CANONICAL_FS_LIST - Static variable in class org.jmol.quantum.QS
 
canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
canonize - Variable in class jme.JME
 
canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
 
canSaveAsJDX() - Method in class jspecview.source.JDXDataObject
 
canShowSolutionColor() - Method in class jspecview.source.JDXDataObject
 
canSkipLoad - Variable in class org.jmol.modelset.AtomCollection
 
canvas - Variable in class org.jmol.console.ImageDialog
 
cap - Static variable in class org.jmol.script.T
 
capData(P4, float) - Method in class org.jmol.jvxl.data.VolumeData
 
cappingObject - Variable in class org.jmol.shape.Mesh
 
capture - Static variable in class org.jmol.script.T
 
captureParams - Variable in class org.jmol.viewer.Viewer
 
carbohydrate - Static variable in class org.jmol.script.T
 
CARBOHYDRATE - Enum constant in enum class org.jmol.c.STR
 
CarbohydrateMonomer - Class in org.jmol.modelsetbio
 
CarbohydratePolymer - Class in org.jmol.modelsetbio
 
cardinality() - Method in class javajs.util.BS
Returns the number of bits set to true in this BitSet.
cardinalityN(int) - Method in class javajs.util.BS
 
cardinalityOf(BS) - Static method in class org.jmol.util.BSUtil
cardinality = "total number of set bits"
CARTESIAN_PRECISION - Static variable in class javajs.util.PT
 
cartoon - Static variable in class org.jmol.script.T
 
Cartoon - Class in org.jmol.shapebio
 
Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
 
cartoonbaseedges - Static variable in class org.jmol.script.T
 
cartoonblockheight - Static variable in class org.jmol.script.T
 
cartoonblocks - Static variable in class org.jmol.script.T
 
cartoonladders - Static variable in class org.jmol.script.T
 
CartoonRenderer - Class in org.jmol.renderbio
 
CartoonRenderer() - Constructor for class org.jmol.renderbio.CartoonRenderer
 
cartoonribose - Static variable in class org.jmol.script.T
 
cartoonrockets - Static variable in class org.jmol.script.T
 
cartoonsfancy - Static variable in class org.jmol.script.T
 
cartoonsFancy - Variable in class org.jmol.renderbio.BackboneRenderer
 
cartoonsFancy - Variable in class org.jmol.renderbio.CartoonRenderer
 
cartoonsFancy - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
cartoonsFancy - Variable in class org.jmol.renderbio.RibbonsRenderer
 
cartoonsFancy - Variable in class org.jmol.renderbio.RocketsRenderer
 
cartoonsFancy - Variable in class org.jmol.renderbio.StrandsRenderer
 
cartoonsFancy - Variable in class org.jmol.renderbio.TraceRenderer
 
cartoonsteps - Static variable in class org.jmol.script.T
 
casecmd - Static variable in class org.jmol.script.T
 
casName - Variable in class jspecview.export.AMLExporter
 
casName - Variable in class jspecview.export.CMLExporter
 
casName - Variable in class jspecview.source.AnIMLReader
 
casRN - Variable in class jspecview.export.AMLExporter
 
casRN - Variable in class jspecview.export.CMLExporter
 
casRN - Variable in class jspecview.source.AnIMLReader
 
CastepReader - Class in org.jmol.adapter.readers.xtal
CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.
CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
 
CAT_ASSEM - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_ATOM_SITE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CAT_ATOM_SITES - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CAT_ATOM_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CAT_CELL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CAT_CHEMCOMP - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_COMPBOND - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_NCS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_OPER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_SEQUENCEDIF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_SHEET - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_STRUCSITE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_STRUCTCONF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CAT_STRUCTCONN - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
 
catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
 
catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
 
catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
Returns a Lst of property data in the form name(String), data(float[]), modelIndex (Integer), isGroup (Boolean);
catchcmd - Static variable in class org.jmol.script.T
 
cavity - Static variable in class org.jmol.script.T
 
cB_ - Variable in class org.jmol.util.SimpleUnitCell
 
CBK - Enum Class in org.jmol.c
 
cbl - Variable in class org.jmol.viewer.StatusManager
 
CBZip2InputStream - Class in org.apache.tools.bzip2
An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.
CBZip2InputStream(InputStream) - Constructor for class org.apache.tools.bzip2.CBZip2InputStream
Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
CBZip2InputStream(InputStream, boolean) - Constructor for class org.apache.tools.bzip2.CBZip2InputStream
Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.
CBZip2InputStreamFactory - Class in org.apache.tools.bzip2
 
CBZip2InputStreamFactory() - Constructor for class org.apache.tools.bzip2.CBZip2InputStreamFactory
 
cch - Variable in class javajs.util.CifDataParser
length of str
cd - Static variable in class org.jmol.script.T
 
cd(String) - Method in class org.jmol.viewer.Viewer
 
CDXMLWriter - Class in org.jmol.adapter.writers
Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the basic necessities for XmlCDXReader.
CDXMLWriter() - Constructor for class org.jmol.adapter.writers.CDXMLWriter
 
CDXReader - Class in org.jmol.adapter.readers.more
A reader for ChemDraw binary CDX files.
CDXReader() - Constructor for class org.jmol.adapter.readers.more.CDXReader
 
ce - Variable in class org.jmol.viewer.ColorManager
 
cell - Static variable in class org.jmol.script.T
 
Cell - Class in org.jmol.awtjs.swing
 
Cell(JComponent, GridBagConstraints) - Constructor for class org.jmol.awtjs.swing.Cell
 
CELL_TYPE_CONVENTIONAL - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
CELL_TYPE_MAGNETIC_PARENT - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CELL_TYPE_MAGNETIC_STANDARD - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CELL_TYPE_PRIMITIVE - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
CELL_TYPE_SUPER - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
cellParamNames - Static variable in class org.jmol.api.JmolAdapter
 
cellSlop - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
celshading - Static variable in class org.jmol.script.T
 
celshadingpower - Static variable in class org.jmol.script.T
 
CENATT - Static variable in class javajs.api.GenericZipInputStream
 
CENATX - Static variable in class javajs.api.GenericZipInputStream
 
CENCOM - Static variable in class javajs.api.GenericZipInputStream
 
CENCRC - Static variable in class javajs.api.GenericZipInputStream
 
CENDSK - Static variable in class javajs.api.GenericZipInputStream
 
CENEXT - Static variable in class javajs.api.GenericZipInputStream
 
CENFLG - Static variable in class javajs.api.GenericZipInputStream
 
CENHDR - Static variable in class javajs.api.GenericZipInputStream
 
CENHOW - Static variable in class javajs.api.GenericZipInputStream
 
CENLEN - Static variable in class javajs.api.GenericZipInputStream
 
CENNAM - Static variable in class javajs.api.GenericZipInputStream
 
CENOFF - Static variable in class javajs.api.GenericZipInputStream
 
CENSIG - Static variable in class javajs.api.GenericZipInputStream
 
CENSIZ - Static variable in class javajs.api.GenericZipInputStream
 
center - Variable in class org.jmol.export.___Exporter
 
center - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
center - Static variable in class org.jmol.script.T
 
center - Variable in class org.jmol.shapespecial.Dipole
 
center - Variable in class org.jmol.shapespecial.Ellipsoid
 
center - Variable in class org.jmol.shapespecial.Polyhedron
 
center - Variable in class org.jmol.util.BZone
 
center - Static variable in class org.jmol.viewer.JC
 
center() - Method in class jme.JMEmol
 
CENTER - Static variable in class org.jmol.awtjs.swing.BorderLayout
 
CENTER - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
 
CENTER - Static variable in class org.jmol.awtjs.swing.SwingConstants
 
centerat - Static variable in class org.jmol.script.T
 
centerAt(int, int, P3) - Method in class org.jmol.viewer.TransformManager
 
centerDialog() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
centerDialog() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Centers the dialog on the screen.
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
centerings - Variable in class org.jmol.symmetry.WyckoffFinder
 
centeringStr - Variable in class org.jmol.symmetry.WyckoffFinder
 
centerParameter(int) - Method in class org.jmol.scriptext.ScriptExt
 
centerParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
 
centerParameterForModel(int, int, Object[]) - Method in class org.jmol.script.ScriptParam
 
CENTIM - Static variable in class javajs.api.GenericZipInputStream
 
centralAtom - Variable in class org.jmol.shapespecial.Polyhedron
 
centralize() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
centroid - Static variable in class org.jmol.script.T
 
centroidPacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
CENVEM - Static variable in class javajs.api.GenericZipInputStream
 
CENVER - Static variable in class javajs.api.GenericZipInputStream
 
CgdReader - Class in org.jmol.adapter.readers.xtal
A reader for TOPOS systre file Crystal Graph Data format.
CgdReader() - Constructor for class org.jmol.adapter.readers.xtal.CgdReader
 
cgo - Static variable in class org.jmol.script.T
 
CGO - Class in org.jmol.shapecgo
 
CGO() - Constructor for class org.jmol.shapecgo.CGO
 
CGOMesh - Class in org.jmol.shapecgo
 
CGORenderer - Class in org.jmol.rendercgo
Something like a PyMOL Compiled Graphical Object, but more interesting!
CGORenderer() - Constructor for class org.jmol.rendercgo.CGORenderer
 
chain - Variable in class org.jmol.modelset.Group
required
chain - Static variable in class org.jmol.script.T
 
Chain - Class in org.jmol.modelset
A Model is a collection of Chains of Groups of Atoms.
CHAIN - Enum constant in enum class org.jmol.c.PAL
 
chaincasesensitive - Static variable in class org.jmol.script.T
 
chainCount - Variable in class org.jmol.modelset.Model
 
chainID - Variable in class org.jmol.adapter.smarter.Atom
 
chainID - Variable in class org.jmol.modelset.Chain
chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string
chainMap - Variable in class org.jmol.viewer.Viewer
 
chainno - Static variable in class org.jmol.script.T
 
chainNo - Variable in class org.jmol.modelset.Chain
chainNo is for information purposes only; retrieved by {atoms}.chainNo
chains - Variable in class org.jmol.modelset.Model
 
chainToUpper(int) - Method in class org.jmol.modelset.AtomCollection
 
CHANGEABLE_MASK - Static variable in class org.jmol.util.C
 
changeableColixMap - Variable in class org.jmol.util.GData
 
changeColixArgb(int, int) - Method in class org.jmol.util.GData
 
CHAR - Static variable in class org.jmol.shapecgo.CGOMesh
 
characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
CHARACTERS - Static variable in class jspecview.source.XMLParser
 
charAt(int) - Method in class javajs.util.SB
 
charCodeAt(int) - Method in class javajs.util.SB
 
chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
check - Static variable in class org.jmol.script.T
 
check(boolean, boolean) - Method in class org.jmol.renderbio.BioMeshRenderer
 
check(int, int, int, int, long, long) - Method in class org.jmol.viewer.MouseState
 
check(String) - Method in class jspecview.dialog.ViewsDialog
 
CHECK_DIMS - Static variable in interface org.jmol.api.JmolScriptManager
 
CHECK1 - Static variable in class org.jmol.thread.JmolThread
 
CHECK2 - Static variable in class org.jmol.thread.JmolThread
 
CHECK3 - Static variable in class org.jmol.thread.JmolThread
 
checkAllFieldsPresent(String[], int, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
 
checkAndRemoveFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkAromaticDefined() - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
 
checkAtomicSymbol(String) - Static method in class jme.JMEUtil
Return the JME atoming number associated to the given symbol
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.JvxlReader
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAutoIntegrate() - Method in class jspecview.common.JSViewer
 
checkBoundsMinMax(P3, P3) - Method in class org.jmol.shape.Shape
 
CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
checkByteCount - Variable in class org.jmol.shape.Mesh
 
checkcir - Static variable in class org.jmol.script.T
 
checkColixLength(short, int) - Method in class org.jmol.shape.AtomShape
 
checkCommandLineForTip(char, String, boolean) - Method in class jspecview.common.JSViewer
 
checkConsoleScript(String) - Method in class org.jmol.viewer.Viewer
 
checkCoordinatesChanged(BS) - Method in class org.jmol.viewer.Viewer
 
checkCurrentLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
 
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.UnitCell
 
checkEnables() - Method in class jspecview.dialog.JSVDialog
 
checkEnables() - Method in class jspecview.dialog.ViewsDialog
 
checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
 
checkExtension(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
 
checkFileExists(String, boolean, String, int, boolean) - Method in class org.jmol.script.ScriptEval
 
checkFileIndex(String, String, String) - Method in class jspecview.common.PeakInfo
 
checkFileTypeModel(String, String, String) - Method in class jspecview.common.PeakInfo
type checks true for MS in GC/MS; reverse of checkType
checkFilterAssembly(String, Map<String, Object>) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
checkFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkFront(short, short, short) - Method in class org.jmol.render.MeshRenderer
 
checkHalt(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
 
checkHalt(String, boolean) - Method in class org.jmol.script.ScriptManager
 
checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
 
checkHKL(T3) - Method in class org.jmol.script.ScriptParam
Note - this check does not allow a 0 for h, k, or l.
checkHover() - Method in class org.jmol.viewer.ActionManager
 
checkInheritedShapes() - Method in class org.jmol.viewer.ShapeManager
starting with Jmol 13.1.13, isosurfaces can use "property color" to inherit the color of the underlying atoms.
checkInMotion(int) - Method in class org.jmol.viewer.Viewer
 
checkIntegral(Parameters, String) - Method in class jspecview.common.PanelData
 
checkInterrupted(JmolThread) - Method in class org.jmol.thread.JmolThread
 
checkJDXRequiredTokens() - Method in class jspecview.source.JDXDataObject
for JDXReader only
checkKeyControl(int, boolean) - Method in class jspecview.common.PanelData
 
checkLast(int) - Method in class org.jmol.script.ScriptParam
 
checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
sets continuing and doProcessLines
checkLength(int) - Method in class org.jmol.script.ScriptParam
 
checkLength(int) - Method in class org.jmol.scriptext.ScriptExt
 
checkLength23() - Method in class org.jmol.script.ScriptParam
 
checkLength34() - Method in class org.jmol.script.ScriptParam
 
checkLengthErrorPt(int, int) - Method in class org.jmol.script.ScriptParam
 
checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.AFLOWReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
checkLine() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Reads a Collection of AtomSets from a BufferedReader.
checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.FAHReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.InputReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.OrcaReader
 
checkLine() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
Valid blocks include [calculation] [atoms] [magres]; all magres entries must be prefaced with a corresponding unit; Use of < > instead of [ ] is allowed.
checkLine() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkMemory() - Static method in class org.jmol.util.Logger
 
checkMenuFocus(String, String, boolean) - Method in class jspecview.java.AwtPopup
 
checkMenuUpdate() - Method in class org.jmol.viewer.Viewer
 
checkMod(int, int) - Method in class jspecview.common.PanelData
 
checkMotionRendering(int) - Method in class org.jmol.viewer.Viewer
check motion for rendering during mouse movement, spin, vibration, and animation
checkMovedAtoms(BS, BS, P3[]) - Method in class org.jmol.modelkit.ModelKit
Something has changed atom positions.
checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
checkNearAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkNewModel() - Method in class org.jmol.modelkit.ModelKit
 
checkNoEmptyModel() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
checkObjectClicked(boolean, int, int, BS) - Method in class org.jmol.modelset.Text
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Labels
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Shape
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Sticks
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.TextShape
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Draw
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Ellipsoids
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapesurface.Isosurface
 
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Labels
 
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Shape
 
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shapespecial.Draw
 
checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Frank
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Shape
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Sticks
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.TextShape
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Draw
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapesurface.Isosurface
 
checkOption(char, String) - Method in class org.jmol.modelkit.ModelKit
MODELKIT SET options for syntax checking.
checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
 
checkOvelayInterface(String) - Method in class jspecview.common.JSViewer
 
checkOverlay() - Method in class jspecview.common.JSViewer
 
checkPaused(Viewer) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
 
checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
checkPeriodic(P3) - Method in interface org.jmol.api.SymmetryInterface
 
checkPeriodic(P3) - Method in class org.jmol.symmetry.Symmetry
 
checkPointCount() - Method in class jspecview.source.AnIMLReader
 
checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet.
checkPropertyParameter(String) - Method in interface org.jmol.api.JmolPropertyManager
 
checkPropertyParameter(String) - Method in class org.jmol.viewer.PropertyManager
 
checkPropertyParameter(String) - Method in class org.jmol.viewer.Viewer
 
checkRange(int, double) - Method in class jspecview.common.PeakInfo
 
checkRemark() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
 
checkRemark() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
checkScript(int) - Method in class org.jmol.console.ScriptEditor
 
checkScript(String) - Method in interface jspecview.api.JSVAppletInterface
 
checkScript(String) - Method in class jspecview.app.JSVApp
 
checkScript(String) - Method in class jspecview.appletjs.JSVApplet
 
checkScript(String) - Method in class jspecview.application.MainFrame
 
checkScript(String) - Method in class jspecview.common.JSViewer
 
checkScriptSilent(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
checkScriptSilent(String) - Method in class org.jmol.script.ScriptEval
a method for just checking a script
checkSelect(Map<String, SV>, T[]) - Method in interface org.jmol.api.JmolScriptEvaluator
 
checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptEval
Check a map for a WHERE phrase
checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.viewer.Viewer
 
checkStart() - Method in class jspecview.source.AnIMLReader
 
checkStereoForAtom(SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesStereo
 
checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
 
checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
Checksum - Interface in com.jcraft.jzlib
 
checkSupercell(Viewer, Symmetry, BS, int, P3) - Method in class org.jmol.symmetry.SpaceGroupFinder
Look for a supercell and adjust lattice down if necessary.
checkTickTemps() - Method in class org.jmol.render.FontLineShapeRenderer
 
checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
 
checkToken(int) - Method in class org.jmol.script.ScriptParam
 
checkTrailingText(String, int, int) - Static method in class javajs.util.PT
 
checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
 
checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
checkTypeMatch(PeakInfo) - Method in class jspecview.common.PeakInfo
 
checkTypeModel(String, String) - Method in class jspecview.common.PeakInfo
 
checkUndoEnabled() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
checkVisible() - Method in class org.jmol.modelset.Atom
 
checkWithin(T3, Lst<P3>, float, boolean) - Static method in class org.jmol.shape.Mesh
 
chemFileProperty - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
chemical - Static variable in class org.jmol.script.T
 
chemicalshift - Static variable in class org.jmol.script.T
 
CHequation - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
 
children() - Method in interface jspecview.api.JSVTreeNode
 
children() - Method in class jspecview.tree.SimpleTreeNode
 
ChimeMessenger - Class in org.jmol.viewer
A legacy Chime-compatible messenger.
ChimeMessenger() - Constructor for class org.jmol.viewer.ChimeMessenger
 
chirality - Static variable in class org.jmol.script.T
 
chk - Variable in class org.jmol.script.ScriptError
 
chk - Variable in class org.jmol.scriptext.ScriptExt
 
chord - Variable in class org.jmol.util.ContactPair
 
Cif2DataParser - Class in org.jmol.adapter.readers.cif
Fully implemented 2016.12.1 see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html Will deliver JSON versions of the data while file reading and Java List/Map structures when called by x = getProperty("cifInfo", filename) Validated using the test-data suite by John Bollinger (John.Bollinger@stjude.org) found at https://github.com/COMCIFS/cif_api
Cif2DataParser() - Constructor for class org.jmol.adapter.readers.cif.Cif2DataParser
 
Cif2Reader - Class in org.jmol.adapter.readers.cif
Preliminary Cif2 reader.
Cif2Reader() - Constructor for class org.jmol.adapter.readers.cif.Cif2Reader
 
CifDataParser - Class in javajs.util
A CIF 1.0 tokenizer class for dealing with quoted strings in CIF files.
CifDataParser() - Constructor for class javajs.util.CifDataParser
 
CifReader - Class in org.jmol.adapter.readers.cif
A true line-free CIF file reader for CIF files.
CifReader() - Constructor for class org.jmol.adapter.readers.cif.CifReader
 
CIFWriter - Class in org.jmol.adapter.writers
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
CIFWriter() - Constructor for class org.jmol.adapter.writers.CIFWriter
 
CIP_CHIRALITY_AXIAL_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_CANTDETERMINE - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_EZ_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_m_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_M_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_NAME_MASK - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_NAME_OFFSET - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_NONE - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_p_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_P_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_PSEUDO_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_r_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_R_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_s_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_S_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_seqcis_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_seqCis_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_seqtrans_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_seqTrans_FLAG - Static variable in class org.jmol.viewer.JC
 
CIP_CHIRALITY_UNKNOWN - Static variable in class org.jmol.viewer.JC
 
CIPChirality - Class in org.jmol.symmetry
A fully validated relatively efficient implementation of Cahn-Ingold-Prelog rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
CIPChirality() - Constructor for class org.jmol.symmetry.CIPChirality
 
CIPData - Class in org.jmol.symmetry
A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles.
CIPData() - Constructor for class org.jmol.symmetry.CIPData
 
CIPDataSmiles - Class in org.jmol.symmetry
A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")
CIPDataSmiles() - Constructor for class org.jmol.symmetry.CIPDataSmiles
 
CIPDataTracker - Class in org.jmol.symmetry
An optional class to track digraph paths to decisions.
CIPDataTracker() - Constructor for class org.jmol.symmetry.CIPDataTracker
 
ciprule - Static variable in class org.jmol.script.T
 
ciprule6full - Static variable in class org.jmol.script.T
 
circle - Static variable in class org.jmol.script.T
 
CIRCLE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
CircleRenderer - Class in org.jmol.g3d
Implements flat circle drawing/filling routines.
CircleRenderer() - Constructor for class org.jmol.g3d.CircleRenderer
 
CIRCULARPLANE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
clash - Static variable in class org.jmol.script.T
 
clean() - Method in class org.jmol.shape.MeshCollection
 
clean() - Method in class org.jmol.shapecgo.CGO
 
clean() - Method in class org.jmol.shapespecial.Draw
 
clean(float) - Method in class org.jmol.adapter.writers.XtlWriter
 
clean(String) - Static method in class javajs.util.PT
 
cleanLabel(String) - Static method in class jspecview.source.JDXSourceStreamTokenizer
Extracts spaces, underscores etc.
cleanSmiles(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
cleanSmiles(String) - Method in class org.jmol.smiles.SmilesMatcher
 
cleanT(float) - Method in class org.jmol.adapter.writers.XtlWriter
right-zero-trimmed
cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
clear - Static variable in class org.jmol.script.T
 
clear() - Method in class jme.JME
 
clear() - Method in class jspecview.app.GenericMouse
 
clear() - Method in class jspecview.common.IntegralData
 
clear() - Method in interface org.jmol.api.GenericMouseInterface
 
clear() - Method in interface org.jmol.api.JmolDataManager
 
clear() - Method in class org.jmol.awtjs2d.Mouse
 
clear() - Method in class org.jmol.g3d.Graphics3D
 
clear() - Method in class org.jmol.jvxl.data.JvxlData
 
clear() - Method in class org.jmol.minimize.forcefield.ForceField
 
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
clear() - Method in class org.jmol.multitouch.ActionManagerMT
 
clear() - Method in class org.jmol.shape.Measures
 
clear() - Static method in exception class org.jmol.smiles.InvalidSmilesException
 
clear() - Method in class org.jmol.util.CommandHistory
clears the history.
clear() - Method in class org.jmol.util.GData
 
clear() - Method in class org.jmol.util.TempArray
 
clear() - Method in class org.jmol.viewer.ActionManager
 
clear() - Method in class org.jmol.viewer.DataManager
 
clear() - Method in class org.openscience.jmol.app.HistoryFile
 
clear(boolean) - Method in interface org.jmol.api.JmolScriptManager
 
clear(boolean) - Method in class org.jmol.script.ScriptManager
 
clear(double, double) - Method in class jspecview.common.MeasurementData
 
clear(int) - Method in class javajs.util.BS
Sets the bit specified by the index to false.
clear(int) - Method in interface org.jmol.api.JmolRepaintManager
 
clear(int) - Method in class org.jmol.render.RepaintManager
 
clear(String) - Method in class org.jmol.shape.Mesh
 
clear(String) - Method in class org.jmol.shapecgo.CGOMesh
 
clear(String) - Method in class org.jmol.shapespecial.DrawMesh
 
clear(Map<String, Object>) - Static method in class org.jmol.thread.TimeoutThread
 
CLEAR - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
clear33() - Method in class javajs.util.M34
 
clearAll() - Method in class javajs.util.BS
Sets all of the bits in this BitSet to false.
clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearAllView() - Method in class jspecview.common.PanelData
Clears all views in the zoom list
clearAtomConstraints() - Method in class org.jmol.modelkit.ModelKit
 
clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
 
clearBindings() - Method in class org.jmol.viewer.ActionManager
 
clearBits(int, int) - Method in class javajs.util.BS
Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to false.
clearCache() - Method in class org.jmol.modelset.ModelSet
 
clearCache() - Method in class org.jmol.util.ColorEncoder
 
clearCommandWatcherThread() - Method in class org.jmol.script.ScriptManager
 
clearConsole() - Method in class org.jmol.viewer.StatusManager
 
clearConsole(JSAppletObject) - Method in interface javajs.api.js.J2SObjectInterface
 
clearContent(String) - Method in class org.jmol.console.GenericConsole
 
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelSet
 
clearDB(int) - Method in class org.jmol.modelset.ModelSet
 
clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEval
 
clearFontCache() - Method in class org.jmol.g3d.Graphics3D
 
clearFontCache() - Method in class org.jmol.util.GData
 
clearFunctions() - Method in class org.jmol.viewer.Viewer
 
clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
clearInButton - Variable in class org.jmol.console.GenericConsole
 
clearLastModelSet() - Method in class org.jmol.modelkit.ModelKitPopup
 
clearLinkViews(GraphSet) - Method in class jspecview.common.PanelData
 
clearMeasurements() - Method in class org.jmol.api.JmolViewer
 
clearMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearMesh(String) - Method in class org.jmol.shape.Mesh
 
clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
 
clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
 
clearOrbitals() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
clearOutButton - Variable in class org.jmol.console.GenericConsole
 
clearQueue() - Method in interface org.jmol.api.JmolScriptManager
 
clearQueue() - Method in class org.jmol.script.ScriptManager
 
clearScriptQueue() - Method in class org.jmol.viewer.Viewer
 
clearSelection() - Method in class org.jmol.api.JmolViewer
 
clearSelection() - Method in class org.jmol.awtjs.swing.JTable
 
clearSelection() - Method in class org.jmol.viewer.Viewer
 
clearSg() - Method in class org.jmol.shapesurface.Isosurface
 
clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
 
clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
 
clearSourceMenu(JDXSource) - Method in class jspecview.application.ApplicationMenu
 
clearStructures() - Method in class org.jmol.modelsetbio.AlphaPolymer
 
clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
 
clearThreads() - Method in class org.jmol.viewer.Viewer
 
clearTimeout(String) - Method in class org.jmol.viewer.Viewer
 
clearTimeouts() - Method in class org.jmol.viewer.Viewer
 
clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
clearUnitCell(int) - Method in class org.jmol.modelset.ModelSet
 
clearVisibleSets() - Method in class org.jmol.modelset.AtomCollection
 
click(HTMLElement, HTMLWindowEvent) - Method in interface org.jmol.awtjs.swing.SwingController
Fired from clicking an element such as a button or check box or table entry, or from entering text in a text box.
CLICK - Enum constant in enum class org.jmol.c.CBK
 
CLICK - Static variable in class com.sparshui.common.TouchState
 
CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
 
CLICK - Static variable in class org.jmol.viewer.binding.Binding
 
CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
clickabilityFlags - Variable in class org.jmol.modelset.Atom
 
clickable - Static variable in class org.jmol.script.T
 
clickAssignAtom(int, String, P3) - Method in class org.jmol.modelkit.ModelKit
From Mouse or handleAtomOrBondBicked
clicked(long, int, int, int, int) - Method in class jspecview.app.GenericMouse
 
CLICKED - Static variable in class org.jmol.awtjs.Event
 
clickedCount - Variable in class org.jmol.viewer.ActionManager
 
clickProcessXtal(String, String) - Method in class org.jmol.modelkit.ModelKit
 
client - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
CLIENT - Static variable in class com.sparshui.common.ConnectionType
 
CLIENT_PORT - Static variable in class com.sparshui.common.NetworkConfiguration
 
ClientProtocol - Class in com.sparshui.common
The abstract class for the client protocol that defines members common to both the server-side and client-side protocols.
ClientProtocol(Socket) - Constructor for class com.sparshui.common.ClientProtocol
Create a new ClientProtocol object.
ClientProtocol.MessageType - Class in com.sparshui.common
 
ClientServerConnection - Class in com.sparshui.client
Represents the connection to the GestureServer.
ClientServerConnection(String, SparshClient) - Constructor for class com.sparshui.client.ClientServerConnection
Instantiate a Server Connection object.
clientService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ClientToServerProtocol - Class in com.sparshui.client
ClientToServerProtocol implements the Client side protocol.
ClientToServerProtocol(Socket) - Constructor for class com.sparshui.client.ClientToServerProtocol
Constructor calls ClientProtocol's constructor and sets up data input and output streams for the specified socket.
clipboard - Static variable in class org.jmol.script.T
 
clipCode(int) - Method in class org.jmol.util.GData
 
clipCode(int, int, int) - Method in class org.jmol.export.Export3D
 
clipCode3(int, int, int) - Method in class org.jmol.util.GData
 
clipImageOrPasteText(String) - Method in class org.jmol.api.JmolViewer
 
clipImageOrPasteText(String) - Method in class org.jmol.viewer.Viewer
 
cList - Variable in class org.jmol.shapecgo.CGOMesh
 
clone() - Method in class com.jcraft.jzlib.GZIPHeader
 
clone() - Method in class com.sparshui.server.TouchPoint
 
clone() - Method in class javajs.util.BS
Cloning this BitSet produces a new BitSet that is equal to it.
clone() - Method in class javajs.util.Matrix
Clone the Matrix object.
clone() - Method in class org.jmol.adapter.smarter.Structure
 
clone() - Method in class org.jmol.util.Vibration
 
cloneAtomSetWithBonds(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneFirstAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
cloneLastAtomSetFromPoints(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
close() - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
close() - Method in class com.jcraft.jzlib.InflaterInputStream
 
close() - Method in class com.sparshui.client.ClientServerConnection
 
close() - Method in interface javajs.api.GenericBinaryDocument
 
close() - Method in class javajs.img.GifEncoder
 
close() - Method in class javajs.img.ImageEncoder
 
close() - Method in class javajs.util.BinaryDocument
 
close() - Method in class javajs.util.OC
Deprecated.
close() - Method in class jspecview.common.JSVZipFileSequentialReader
 
close() - Method in class org.apache.tools.bzip2.CBZip2InputStream
 
close() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
close() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
close() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
close() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
close(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
close(String) - Method in class jspecview.common.JSViewer
 
CLOSE - Enum constant in enum class jspecview.common.ScriptToken
 
closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CloseAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
 
closeAllDialogsExcept(Annotation.AType) - Method in class jspecview.common.PanelData
 
closeChannel() - Method in interface javajs.api.GenericOutputChannel
 
closeChannel() - Method in class javajs.util.OC
 
closeDocument() - Method in class javajs.export.PDFCreator
 
closeMe() - Method in interface org.jmol.api.GenericImageDialog
 
closeMe() - Method in class org.jmol.console.ImageDialog
 
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
closeReader() - Method in class org.jmol.jvxl.readers.JvxlReader
 
closeReader() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
closeReader() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
closeReaderSFR() - Method in class org.jmol.jvxl.readers.JvxlReader
 
closeReaderSFR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
closeReaderSFR() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
closeSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
closeSelected() - Method in class jspecview.dialog.ViewsDialog
 
closeSource(JDXSource) - Method in class jspecview.common.JSViewer
 
closeSpectrum() - Method in class jspecview.common.PanelData
 
closest - Variable in class org.jmol.modelset.ModelSet
 
closeStream() - Method in class org.jmol.util.JSONWriter
 
closeTag(SB, String) - Static method in class javajs.util.XmlUtil
 
closeTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
 
closeZipEntry(Object) - Method in interface javajs.api.GenericZipTools
 
closeZipEntry(Object) - Method in class javajs.util.ZipTools
 
cm - Variable in class org.jmol.viewer.Viewer
 
cmdAssignAddAtoms(String, P3[], BS, String, String) - Method in class org.jmol.modelkit.ModelKit
MODELKIT ADD @3 ...
cmdAssignAtom(BS, P3, String, String) - Method in class org.jmol.modelkit.ModelKit
A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom via MODELKIT ASSIGN ATOM
cmdAssignBond(int, char, String) - Method in class org.jmol.modelkit.ModelKit
 
cmdAssignConnect(int, int, char, String) - Method in class org.jmol.modelkit.ModelKit
 
cmdAssignDeleteAtoms(BS) - Method in class org.jmol.modelkit.ModelKit
Delete all atoms that are equivalent to this atom.
cmdAssignMoveAtoms(BS, int, P3, P3[], boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
 
cmdAssignSpaceGroup(BS, String, Object, boolean, boolean, String) - Method in class org.jmol.modelkit.ModelKit
MODELKIT SPACEGROUP Assign a given space group, currently only "P1" Do all the necessary changes in unit cells and atom site assignments.
cmdAssignSpaceGroupPacked(BS, String, String) - Method in class org.jmol.modelkit.ModelKit
MODELKIT SPACEGROUP ....
CmdExt - Class in org.jmol.scriptext
 
CmdExt() - Constructor for class org.jmol.scriptext.CmdExt
 
CmdfReader - Class in org.jmol.adapter.readers.xtal
A reader for CrystalMaker CMDF binary/text files.
CmdfReader() - Constructor for class org.jmol.adapter.readers.xtal.CmdfReader
 
cmdLoad() - Method in class org.jmol.script.ScriptEval
 
cmdMinimize(JmolScriptEvaluator, BS, int, float, float, int) - Method in class org.jmol.modelkit.ModelKit
Minimize a unit cell with full symmetry constraints.
cmdRotate(boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
cmdRotateAtoms(BS, P3[], float) - Method in class org.jmol.modelkit.ModelKit
 
cmds - Variable in class org.jmol.shapecgo.CGOMesh
 
cmdScript(int, String, String, Lst<SV>) - Method in class org.jmol.script.ScriptEval
 
cmdUndoRedo(int) - Method in class org.jmol.script.ScriptEval
 
cmi - Variable in class org.jmol.viewer.AnimationManager
current model index
CML - Enum constant in enum class jspecview.common.ExportType
 
CML - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CMLExporter - Class in jspecview.export
class CMLExporter contains static methods to export a Graph as as CIML.
CMLExporter() - Constructor for class jspecview.export.CMLExporter
 
CMLWriter - Class in org.jmol.adapter.writers
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
CMLWriter() - Constructor for class org.jmol.adapter.writers.CMLWriter
 
code - Variable in class org.jmol.i18n.Language
 
codeBase - Variable in class org.jmol.util.GenericApplet
 
codePath - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
coef - Variable in class org.jmol.quantum.SlaterData
 
coeffs - Variable in class org.jmol.quantum.MOCalculation
 
col - Static variable in class org.jmol.script.T
 
colix - Variable in class org.jmol.adapter.smarter.Bond
 
colix - Variable in class org.jmol.modelset.Bond
 
colix - Variable in class org.jmol.modelset.Measurement
 
colix - Variable in class org.jmol.modelset.MeasurementData
 
colix - Variable in class org.jmol.modelset.Text
 
colix - Variable in class org.jmol.render.ShapeRenderer
 
colix - Variable in class org.jmol.shape.Measures
 
colix - Variable in class org.jmol.shape.MeshCollection
 
colix - Variable in class org.jmol.shapespecial.Dipole
 
colix - Variable in class org.jmol.shapespecial.Ellipsoid
 
colix - Variable in class org.jmol.shapespecial.Polyhedron
 
colix - Variable in class org.jmol.util.MeshSurface
 
COLIX_CONTRAST - Static variable in class org.jmol.util.C
 
colixA - Variable in class org.jmol.render.FontLineShapeRenderer
 
colixAtom - Variable in class org.jmol.modelset.Atom
 
colixB - Variable in class org.jmol.render.FontLineShapeRenderer
 
colixBack - Variable in class org.jmol.util.MeshSurface
 
colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
 
colixCurrent - Variable in class org.jmol.util.GData
 
colixEdge - Variable in class org.jmol.shapespecial.Polyhedron
 
colixes - Variable in class org.jmol.renderbio.BackboneRenderer
 
colixes - Variable in class org.jmol.renderbio.CartoonRenderer
 
colixes - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
colixes - Variable in class org.jmol.renderbio.RibbonsRenderer
 
colixes - Variable in class org.jmol.renderbio.RocketsRenderer
 
colixes - Variable in class org.jmol.renderbio.StrandsRenderer
 
colixes - Variable in class org.jmol.renderbio.TraceRenderer
 
colixes - Variable in class org.jmol.shape.AtomShape
 
colixesBack - Variable in class org.jmol.renderbio.BackboneRenderer
 
colixesBack - Variable in class org.jmol.renderbio.CartoonRenderer
 
colixesBack - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
colixesBack - Variable in class org.jmol.renderbio.RibbonsRenderer
 
colixesBack - Variable in class org.jmol.renderbio.RocketsRenderer
 
colixesBack - Variable in class org.jmol.renderbio.StrandsRenderer
 
colixesBack - Variable in class org.jmol.renderbio.TraceRenderer
 
colixesBack - Variable in class org.jmol.shapebio.BioShape
 
colixHighlight - Variable in class org.jmol.shape.Halos
 
colixRubberband - Variable in class org.jmol.viewer.ColorManager
 
colixSelection - Variable in class org.jmol.shape.Halos
 
collapsed - Static variable in class org.jmol.script.T
 
collapsed - Variable in class org.jmol.shapespecial.Polyhedron
 
colon - Static variable in class org.jmol.script.T
 
color - Variable in class org.jmol.jvxl.data.JvxlData
 
color - Static variable in class org.jmol.script.T
 
color - Variable in class org.jmol.shape.Mesh
 
color - Variable in class org.jmol.shape.MeshCollection
 
color - Variable in class org.jmol.util.BZone
 
Color - Class in org.jmol.awtjs.swing
 
Color() - Constructor for class org.jmol.awtjs.swing.Color
 
COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
 
COLOR_CONTRAST - Static variable in class org.jmol.viewer.JC
 
colorCommand - Variable in class org.jmol.shape.Mesh
 
colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
 
colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
 
colorDensity - Variable in class org.jmol.shape.Mesh
 
ColoredAnnotation - Class in jspecview.common
ColoredAnnotation is a label on the spectrum; not an integralRegion
ColoredAnnotation() - Constructor for class jspecview.common.ColoredAnnotation
 
colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
 
colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
ColorEncoder - Class in org.jmol.util
 
ColorEncoder(ColorEncoder, Viewer) - Constructor for class org.jmol.util.ColorEncoder
 
colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
ColorManager - Class in org.jmol.viewer
 
colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
 
ColorParameters - Class in jspecview.common
This a representation of the Display Scheme for the spectral display.
ColorParameters() - Constructor for class jspecview.common.ColorParameters
 
colorPhased - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
colorPos - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPtFromInt(int, P3) - Static method in class javajs.util.CU
 
colorPtFromString(String) - Static method in class javajs.util.CU
 
colorPtToFFRGB(T3) - Static method in class javajs.util.CU
 
colorrasmol - Static variable in class org.jmol.script.T
 
colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
 
colorscheme - Static variable in class org.jmol.script.T
 
colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
 
colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
 
colorsExplicit - Variable in class org.jmol.util.MeshSurface
 
colorTriadToFFRGB(float, float, float) - Static method in class javajs.util.CU
 
colorType - Variable in class org.jmol.shape.Mesh
 
columnCount - Variable in class javajs.util.CifDataParser
 
columnNames - Variable in class javajs.util.CifDataParser
 
ColumnSelectionModel - Interface in org.jmol.awtjs.swing
 
com.jcraft.jzlib - package com.jcraft.jzlib
 
com.sparshui - package com.sparshui
 
com.sparshui.client - package com.sparshui.client
 
com.sparshui.common - package com.sparshui.common
 
com.sparshui.common.messages.events - package com.sparshui.common.messages.events
 
com.sparshui.common.utils - package com.sparshui.common.utils
 
com.sparshui.gestures - package com.sparshui.gestures
 
com.sparshui.inputdevice - package com.sparshui.inputdevice
 
com.sparshui.server - package com.sparshui.server
 
combineSelected() - Method in class jspecview.dialog.ViewsDialog
 
combineSpectra(String) - Method in class jspecview.common.JSViewer
 
combo1 - Variable in class jspecview.dialog.JSVDialog
 
comma - Static variable in class org.jmol.script.T
 
command - Static variable in class org.jmol.script.T
 
commandExpected() - Method in class org.jmol.script.ScriptCompiler
 
CommandHistory - Class in jspecview.application
CommandHistory keeps a command history and responds to key events
CommandHistory - Class in org.jmol.util
Implements a queue for a bash-like command history.
CommandHistory() - Constructor for class org.jmol.util.CommandHistory
Creates a new instance using the default size (100)
CommandHistory(JSViewer, JTextField) - Constructor for class jspecview.application.CommandHistory
 
commandHistoryLevelMax - Static variable in class org.jmol.script.ScriptEval
 
commandLineOptions - Variable in class org.jmol.export.___Exporter
 
commands - Static variable in class org.jmol.script.T
 
commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CommandWatcherThread - Class in org.jmol.script
 
CommandWatcherThread() - Constructor for class org.jmol.script.CommandWatcherThread
 
commensurateSection1 - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
COMMENT - Static variable in class jspecview.source.XMLParser
 
commentChar - Variable in class org.jmol.export.___Exporter
 
COMPARABLE_COMAPRATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
 
comparator - Static variable in class org.jmol.script.T
 
compare - Static variable in class org.jmol.script.T
 
compare(JmolTouchSimulator.TouchData, JmolTouchSimulator.TouchData) - Method in class com.sparshui.inputdevice.JmolTouchSimulator.TouchDataComparator
 
compare(Object[], Object[]) - Method in class org.jmol.shapespecial.Polyhedra
 
compare(Object, Object) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
 
compare(String[], String[]) - Method in class org.jmol.modelsetbio.BioResolver
 
compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
 
compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
 
compare(SV, SV) - Method in class org.jmol.script.SV.Sort
 
compare(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.MeshCapperSorter
 
compareAngles(double, double, double, double) - Static method in class jme.JMEUtil
 
compareAtoms(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
compareAtoms(int, int) - Method in interface org.jmol.api.PymolAtomReader
 
compareFloat(int, float, float) - Method in class org.jmol.script.ScriptEval
 
compareFloatData(int, float[], int, float) - Method in class org.jmol.script.ScriptEval
 
compareTo(Measure) - Method in class org.openscience.jmol.app.janocchio.Measure
 
Comparision to Daylight SMARTS - Search tag in package org.jmol.smiles
Section
Comparision to Daylight SMILES - Search tag in package org.jmol.smiles
Section
compile(String, boolean) - Method in class org.jmol.util.PatternMatcher
 
compile(Viewer, String, char, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
Compiles a set of tokens for each primitive element of a label.
compileExpr(String) - Method in class org.jmol.viewer.Viewer
 
compileExpression() - Method in class org.jmol.script.ScriptCompiler
 
compileExpressions() - Method in class org.jmol.script.ScriptCompiler
 
compiler - Variable in class org.jmol.script.ScriptEval
 
compiler - Variable in class org.jmol.viewer.Viewer
 
compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEval
 
compileScriptFile(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
compileScriptFile(String, boolean) - Method in class org.jmol.script.ScriptEval
 
compileScriptString(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEval
 
compileSearchTarget(Node[], int, BS) - Method in interface org.jmol.api.SmilesMatcherInterface
 
compileSearchTarget(Node[], int, BS) - Method in class org.jmol.smiles.SmilesMatcher
 
compileSmartsPattern(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
compileSmartsPattern(String) - Method in class org.jmol.smiles.SmilesMatcher
 
completeCommand(String) - Method in class org.jmol.console.GenericConsole
 
completeCommand(Map<String, ?>, boolean, boolean, String, int) - Static method in class org.jmol.script.T
 
completeMolecule() - Method in class jme.JMEmol
 
Component - Class in org.jmol.awtjs.swing
 
Component(String) - Constructor for class org.jmol.awtjs.swing.Component
 
componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
CompoundDocument - Class in javajs.util
 
CompoundDocument() - Constructor for class javajs.util.CompoundDocument
 
COMPOUNDMENUON - Enum constant in enum class jspecview.common.ScriptToken
 
computeAngle(T3, T3, T3, V3, V3, boolean) - Static method in class javajs.util.Measure
 
computeAngleABC(T3, T3, T3, boolean) - Static method in class javajs.util.Measure
 
computeHelicalAxis(P3, P3, Quat) - Static method in class javajs.util.Measure
This method calculates measures relating to two points in space with related quaternion frame difference.
computeTorsion(T3, T3, T3, T3, boolean) - Static method in class javajs.util.Measure
 
concatList(SV, SV, boolean) - Static method in class org.jmol.script.SV
 
CONE - Static variable in class org.jmol.shapecgo.CGOMesh
 
configuration - Static variable in class org.jmol.script.T
 
confirm(String, String) - Method in class jspecview.java.AwtPlatform
 
confirm(String, String) - Method in class jspecview.js2d.JsPlatform
 
confirm(String, String) - Method in interface org.jmol.api.GenericPlatform
 
confirm(String, String) - Method in class org.jmol.awt.Platform
 
confirm(String, String) - Method in class org.jmol.awtjs2d.Platform
 
confirm(String, String) - Method in class org.jmol.viewer.Viewer
 
connect - Static variable in class org.jmol.script.T
 
connect() - Method in class javajs.util.AjaxURLConnection
 
connect(float[][]) - Method in class org.jmol.modelset.ModelSet
 
connected - Static variable in class org.jmol.script.T
 
connectedAtoms - Variable in class org.jmol.shape.Mesh
 
connections - Variable in class org.jmol.shape.MeshCollection
 
ConnectionType - Class in com.sparshui.common
 
ConnectionType() - Constructor for class com.sparshui.common.ConnectionType
 
connectNBO(int, String) - Method in class org.jmol.adapter.readers.quantum.NBOParser
 
connectNBO(String) - Method in class org.jmol.viewer.Viewer
 
console - Static variable in class org.jmol.script.T
 
console - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ConsoleAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
 
consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
consoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
consoleGetImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
 
ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel.console
 
ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
 
ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
 
constraint - Static variable in class org.jmol.script.T
 
constraints - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
 
constraints - Variable in class org.jmol.minimize.Minimizer
 
contact - Static variable in class org.jmol.script.T
 
Contact - Class in org.jmol.shapesurface
 
Contact() - Constructor for class org.jmol.shapesurface.Contact
 
contactPair - Variable in class org.jmol.jvxl.readers.Parameters
 
ContactPair - Class in org.jmol.util
 
ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
 
ContactRenderer - Class in org.jmol.rendersurface
 
ContactRenderer() - Constructor for class org.jmol.rendersurface.ContactRenderer
 
contactType - Variable in class org.jmol.util.ContactPair
 
Container - Class in org.jmol.awtjs.swing
 
Container(String) - Constructor for class org.jmol.awtjs.swing.Container
 
contains(int[], int) - Static method in class jme.JMEUtil
 
contains(int, int) - Method in class org.jmol.util.Rectangle
 
contentDisabled - Variable in class org.molecularplayground.MPJmolApp
 
context - Static variable in class org.jmol.script.T
 
CONTEXT_DELAY - Static variable in class org.jmol.script.ScriptEval
 
CONTEXT_HOLD_QUEUE - Static variable in class org.jmol.script.ScriptEval
 
contextdepthmax - Static variable in class org.jmol.script.T
 
contextFunctions - Variable in class org.jmol.script.ScriptParam
 
contextPath - Variable in class org.jmol.script.ScriptContext
 
contextVariables - Variable in class org.jmol.script.ScriptParam
 
continuecmd - Static variable in class org.jmol.script.T
 
continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
continuous - Variable in class jspecview.export.AMLExporter
 
continuous - Variable in class jspecview.export.CMLExporter
 
continuous - Variable in class jspecview.source.AnIMLReader
 
contour - Static variable in class org.jmol.script.T
 
CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
 
contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
 
contourColors - Variable in class org.jmol.jvxl.data.JvxlData
 
contourlines - Static variable in class org.jmol.script.T
 
contours - Static variable in class org.jmol.script.T
 
contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourType - Variable in class org.jmol.jvxl.readers.Parameters
 
contourValues - Variable in class org.jmol.jvxl.data.JvxlData
 
contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
 
contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
contrastColix - Variable in class org.jmol.util.GData
WHITE or BLACK
controlPoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
controlPoints - Variable in class org.jmol.renderbio.BackboneRenderer
 
controlPoints - Variable in class org.jmol.renderbio.CartoonRenderer
 
controlPoints - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
controlPoints - Variable in class org.jmol.renderbio.RibbonsRenderer
 
controlPoints - Variable in class org.jmol.renderbio.RocketsRenderer
 
controlPoints - Variable in class org.jmol.renderbio.StrandsRenderer
 
controlPoints - Variable in class org.jmol.renderbio.TraceRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.BackboneRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.CartoonRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.RocketsRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.StrandsRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.TraceRenderer
 
Converter - Class in com.sparshui.common.utils
Contains conversion methods that are needed by several elements of the Gesture Server.
Converter() - Constructor for class com.sparshui.common.utils.Converter
 
convertPointFromScreen(Object, P3) - Method in class jspecview.java.AwtPlatform
 
convertPointFromScreen(Object, P3) - Method in class jspecview.js2d.JsPlatform
 
convertPointFromScreen(Object, P3) - Method in interface org.jmol.api.GenericPlatform
 
convertPointFromScreen(Object, P3) - Method in class org.jmol.awt.Platform
 
convertPointFromScreen(Object, P3) - Method in class org.jmol.awtjs2d.Platform
 
convertToMegabytes(long) - Static method in class org.jmol.popup.GenericPopup
 
convertTransform(String, M4) - Method in interface org.jmol.api.SymmetryInterface
 
convertTransform(String, M4) - Method in class org.jmol.symmetry.Symmetry
Convert to/from string/matrix representation
convertValue(Map<String, Object>, String) - Static method in class org.qcschema.QCSchemaUnits
Read a {value:xxxx, units:["name",toAU]} map, converting it to the desired units.
coord - Variable in class org.jmol.minimize.MinAtom
 
coord - Static variable in class org.jmol.script.T
 
COORDCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
 
coordClicked - Variable in class jspecview.common.PanelData
 
Coordinate - Class in jspecview.common
The Coordinate class stores the x and y values of a coordinate.
Coordinate() - Constructor for class jspecview.common.Coordinate
Constructor
coordinateInRange(int, int, T3, int, P3i) - Method in class org.jmol.shape.Shape
 
coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
coordinatesAreFractional - Variable in class org.jmol.script.ScriptParam
set in getPointOrPlane
coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
Get the boolean whether coordinates are fractional.
coordinatesColor - Variable in class jspecview.common.PanelData
 
COORDINATESCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
COORDINATESON - Enum constant in enum class jspecview.common.ScriptToken
 
coordsClicked - Variable in class jspecview.common.PanelData
 
coordStr - Variable in class jspecview.common.PanelData
 
copy() - Method in class javajs.util.Matrix
Make a deep copy of a matrix
copy() - Method in class jspecview.common.ColorParameters
Returns a copy of this DisplayScheme
copy() - Method in class jspecview.common.Coordinate
Returns a new coordinate that has the same x and y values of this coordinate
copy() - Method in class jspecview.common.Spectrum
specifically for Abs/Trans conversion.
copy() - Method in class org.jmol.util.Point3fi
 
copy(String) - Method in class jspecview.common.ColorParameters
Returns a copy of this DisplayScheme with a new name
copy(String) - Method in class jspecview.java.AwtParameters
 
copy(String) - Method in class jspecview.js2d.JsParameters
 
copy(BS) - Static method in class javajs.util.BS
fast copy
copy(BS) - Static method in class org.jmol.util.BSUtil
 
copy2(BS, BS) - Static method in class org.jmol.util.BSUtil
 
copyArray(double[]) - Static method in class jme.JMEUtil
 
copyArray(int[]) - Static method in class jme.JMEUtil
 
copyArray(int[], int) - Static method in class jme.JMEUtil
 
copyArray(String[]) - Static method in class jme.JMEUtil
 
copyColixTranslucency(short, short) - Static method in class org.jmol.util.C
 
copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CopyImageAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
 
copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
copyInvert(BS, int) - Static method in class org.jmol.util.BSUtil
 
copyM() - Method in class jspecview.common.Measurement
 
copyOf(T[], int) - Static method in class jme.JMEUtil
Copies the specified array, truncating or padding with nulls (if necessary) so the copy has the specified length.
copyOf(U[], int, Class<? extends T[]>) - Static method in class jme.JMEUtil
Copies the specified array, truncating or padding with nulls (if necessary) so the copy has the specified length.
copyright - Static variable in class org.jmol.viewer.JC
 
copySafely(SV) - Static method in class org.jmol.script.SV
Make a copy if this is a variable -- if it has myName != null.
copyScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CopyScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
 
copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
copyTensor() - Method in class org.jmol.util.Tensor
 
copyTo(P3, AtomSetCollection) - Method in class org.jmol.adapter.smarter.Atom
 
copyTo(JDXDataObject) - Method in class jspecview.source.JDXDataObject
 
cordMidPoints - Variable in class org.jmol.renderbio.RocketsRenderer
 
corners - Static variable in class org.jmol.script.T
 
cos - Static variable in class org.jmol.script.T
 
cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
 
cosBeta - Variable in class org.jmol.util.SimpleUnitCell
 
cosGamma - Variable in class org.jmol.util.SimpleUnitCell
 
count - Variable in class org.jmol.modelset.Measurement
 
count - Static variable in class org.jmol.script.T
 
COUNT_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
countChar(String, char) - Static method in class javajs.util.PT
 
counter - Variable in class org.jmol.script.ScriptParallelProcessor
 
countPlusIndices - Variable in class org.jmol.modelset.Measurement
 
countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
 
countTokens(String, int) - Static method in class javajs.util.PT
 
coupleColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
 
CoupleColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
 
CoupleColourSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
 
CoupleParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
 
CoupleParameterSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
Creates new form noeParameterSelectionPanel
couples - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
 
couplesWhole - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
 
coupleTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
CoupleTable - Class in org.openscience.jmol.app.janocchio
 
CoupleTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.CoupleTable
Constructor
covalentradius - Static variable in class org.jmol.script.T
 
covalentVersion - Static variable in class org.jmol.util.Elements
 
CPK - Enum constant in enum class org.jmol.c.PAL
 
cr - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
CRC32 - Class in com.jcraft.jzlib
 
CRC32() - Constructor for class com.jcraft.jzlib.CRC32
 
create - Static variable in class org.jmol.script.T
 
create(BZone) - Method in class org.jmol.util.BZone
 
createAndShowGUI(Viewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
createArray(int) - Static method in class jme.JMEUtil
 
createArray(int, int) - Static method in class jme.JMEUtil
 
createArrayOfArrayList(int) - Static method in class javajs.util.AU
Helper method for creating a List[] without warnings.
createArrayOfHashtable(int) - Static method in class javajs.util.AU
Helper method for creating a Mapinvalid input: '<'K, V>[] without warnings.
createAtomDataSet(Viewer, ModelSet, int, Object, BS) - Static method in class org.jmol.modelset.ModelLoader
 
createBArray(int) - Static method in class jme.JMEUtil
 
createBZ(Viewer, int, Object[], boolean, String, float, float, P3) - Method in class org.jmol.util.BZone
Create a Brillouin zone.
createColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
 
createCompatibleUnitCell(SpaceGroup, float[], float[], boolean) - Static method in class org.jmol.symmetry.UnitCell
Create a unit cell compatible with
createCube() - Method in class org.jmol.quantum.MepCalculation
 
createCube() - Method in class org.jmol.quantum.MOCalculation
 
createCube() - Method in class org.jmol.quantum.NciCalculation
 
createCube() - Method in class org.jmol.quantum.QuantumCalculation
 
CREATED - Enum constant in enum class org.jmol.c.FIL
 
createDArray(int) - Static method in class jme.JMEUtil
 
createDFMap(int[], String, String, int) - Static method in class org.jmol.quantum.QS
 
createDialog(Component) - Method in class org.jmol.dialog.FileChooser
 
createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
createEllipsoidShades() - Method in class org.jmol.util.Shader
 
createFileData(String) - Method in interface org.jmol.api.JmolDataManager
 
createFileData(String) - Method in class org.jmol.viewer.DataManager
 
createFont3D(int, int, float, float, FontManager, Object) - Static method in class org.jmol.util.Font
 
createGeodesic(int) - Static method in class org.jmol.util.Geodesic
 
createGuiMap() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
createGuiMap() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
createImage(Object) - Method in class jspecview.java.AwtPlatform
could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in class jspecview.js2d.JsPlatform
could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in interface org.jmol.api.GenericPlatform
can be ignored (return null) if platform cannot save images
createImage(Object) - Method in class org.jmol.awt.Platform
could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in class org.jmol.awtjs2d.Platform
 
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
Starting with Jmol 11.8.RC5, for a context where the Jmol application is embedded in another application simply to send the returned message to the application.
createImage(String, String, Object, int) - Method in class org.jmol.util.GenericApplet
 
createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
createImage(String, OC, Map<String, Object>) - Method in interface javajs.api.GenericImageEncoder
 
createImage(String, OC, Map<String, Object>) - Method in class javajs.img.ImageEncoder
 
createItemKeys(JmolPanel) - Method in class org.jmol.console.KeyJMenu
 
createJDXSource(GenericFileInterface, Object, String, boolean, boolean, int, int, float) - Static method in class jspecview.source.JDXReader
general entrance method
createJDXSourceFromStream(InputStream, boolean, boolean, float) - Static method in class jspecview.source.JDXReader
used only for preferences display and Android
createLArray(int) - Static method in class jme.JMEUtil
 
createMainPanel(JSViewer) - Method in interface jspecview.api.AppletFrame
 
createMainPanel(JSViewer) - Method in class jspecview.appletjs.JSVApplet
 
createMatrix(Viewer, BS, String[], NMRNoeMatrix.NOEParams) - Static method in class org.jmol.quantum.NMRNoeMatrix
 
createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create a menu for the app.
createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create the menubar for the app.
createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
This is the hook through which all menu items are created.
createModels(int) - Method in class org.jmol.modelset.ModelSet
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
 
createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
create a movie from a set of image files
createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.image.AviCreator
 
createPdfDocument(OC, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
 
createPdfDocument(JSVPanel, PrintLayout, OutputStream) - Method in interface jspecview.api.JSVPdfWriter
 
createPdfDocument(JSVPanel, PrintLayout, OutputStream) - Method in class jspecview.common.PDFWriter
 
createSArray(int) - Static method in class jme.JMEUtil
 
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerAwt
 
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerJS
 
createSpaceGroup(int, String, Object, int) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
createSpaceGroup(int, String, Object, int) - Static method in class org.jmol.symmetry.SpaceGroup
 
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.CsfReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createStatusBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
createStatusBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
createTable(Object[][], String[], int[]) - Method in interface jspecview.api.PlatformDialog
 
createTable(Object[][], String[], int[]) - Method in class jspecview.dialog.JSVDialog
 
createTable(Object[][], String[], int[]) - Method in class jspecview.java.AwtDialog
 
createTable(Object[][], String[], int[]) - Method in class jspecview.js2d.JsDialog
 
createToolBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
createToolBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create the toolbar.
createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create a button to go inside of the toolbar.
createTree(int, JDXSource, JSVPanel[]) - Method in interface jspecview.api.JSVTree
 
createTree(int, JDXSource, JSVPanel[]) - Method in class jspecview.application.AwtTree
 
createTree(int, JDXSource, JSVPanel[]) - Method in class jspecview.tree.SimpleTree
 
createURLStreamHandler(String) - Method in class javajs.util.AjaxURLStreamHandlerFactory
 
createView(Lst<Spectrum>) - Static method in class jspecview.source.JDXSource
 
createZip(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
CREATING_MODELSET - Enum constant in enum class org.jmol.c.FIL
 
creatingImage - Variable in class org.jmol.viewer.Viewer
 
CREDITS - Static variable in class jspecview.app.JSVApp
 
creditsAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CreditsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
 
CreditsDialog - Class in org.openscience.jmol.app.jmolpanel
 
CreditsDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.CreditsDialog
 
criterion - Static variable in class org.jmol.script.T
 
cross - Static variable in class org.jmol.script.T
 
cross(T3, T3) - Method in class javajs.util.T3
Sets this tuple to be the vector cross product of vectors v1 and v2.
cross(V3d, V3d) - Method in class javajs.util.V3d
Sets this vector to be the vector cross product of vectors v1 and v2.
crossed - Static variable in class org.jmol.script.T
 
CRYSTAL - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY_TRANSFORM3 - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CrystalReader - Class in org.jmol.adapter.readers.xtal
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
 
crystalReaderLatticeOpsOnly - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
CsfReader - Class in org.jmol.adapter.readers.quantum
CSF file reader based on CIF idea -- fluid property fields.
CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
 
cterm - Variable in class javajs.util.CifDataParser
optional token terminator; in CIF 2.0 could be } or ]
CTRL - Static variable in class org.jmol.viewer.binding.Binding
 
CTRL_ALT - Static variable in class org.jmol.awtjs.Event
 
CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
 
CTRL_MASK - Static variable in class org.jmol.awtjs.Event
 
CTRL_SHIFT - Static variable in class org.jmol.awtjs.Event
 
CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
 
ctrlPressed - Variable in class jspecview.common.PanelData
 
CU - Class in javajs.util
ColorUtility
CU() - Constructor for class javajs.util.CU
 
cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
CubeIterator - Class in org.jmol.bspt
Iterator used for finding all points within a box or a hemi-box
CubeReader - Class in org.jmol.adapter.readers.simple
Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
 
cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
 
cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
current - Variable in class org.jmol.viewer.ActionManager
 
currentCursor - Variable in class org.jmol.viewer.Viewer
 
currentDir - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
currentFont - Variable in class org.jmol.util.GData
 
currentFrameIs(int) - Method in class org.jmol.viewer.AnimationManager
 
currentIsLast() - Method in class org.jmol.viewer.AnimationManager
 
currentlocalpath - Static variable in class org.jmol.script.T
 
currentlyRendering - Variable in class org.jmol.util.GData
 
currentMenuItemId - Variable in class org.jmol.popup.GenericPopup
 
currentMesh - Variable in class org.jmol.shape.MeshCollection
 
currentPalette - Variable in class org.jmol.util.ColorEncoder
 
currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
 
currentSource - Variable in class jspecview.common.JSViewer
 
currentSplitPoint - Variable in class jspecview.common.PanelData
 
currentTime - Variable in class org.jmol.thread.JmolThread
 
CURSOR_CROSSHAIR - Static variable in interface org.jmol.api.GenericPlatform
 
CURSOR_DEFAULT - Static variable in interface org.jmol.api.GenericPlatform
 
CURSOR_HAND - Static variable in interface org.jmol.api.GenericPlatform
 
CURSOR_MOVE - Static variable in interface org.jmol.api.GenericPlatform
 
CURSOR_WAIT - Static variable in interface org.jmol.api.GenericPlatform
 
CURSOR_ZOOM - Static variable in interface org.jmol.api.GenericPlatform
 
curve - Static variable in class org.jmol.script.T
 
CURVE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
CUSTOM - Enum constant in enum class org.jmol.c.STER
 
CUSTOM - Static variable in class org.jmol.util.ColorEncoder
 
CUSTOM_CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
 
cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cutoff - Variable in class org.jmol.jvxl.data.JvxlData
 
cutoff - Variable in class org.jmol.jvxl.readers.Parameters
 
cutoff - Static variable in class org.jmol.script.T
 
cutoffRange - Variable in class org.jmol.jvxl.data.JvxlData
 
cutoffRange - Variable in class org.jmol.jvxl.readers.Parameters
 
CYAN - Static variable in class org.jmol.util.C
 
cyclicFlag - Variable in class org.jmol.modelsetbio.BioPolymer
 
cylinder - Static variable in class org.jmol.script.T
 
CYLINDER - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
 

D

d - Variable in class org.jmol.util.ContactPair
 
DARK_GRAY - Static variable in class jspecview.common.ColorParameters
 
dashDots - Variable in class org.jmol.render.FontLineShapeRenderer
 
dashes - Static variable in class org.jmol.render.FontLineShapeRenderer
 
data - Variable in class javajs.util.BArray
 
data - Variable in class org.jmol.minimize.MinObject
 
data - Static variable in class org.jmol.script.T
 
DATA_ATOM_PROP_ENTRY - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_LABEL - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_SAVE_IN_STATE - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_SELECTION - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_AF - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_AFF - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_AFFF - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_LAST - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_STRING - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_UNKNOWN - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_VALUE - Static variable in interface org.jmol.api.JmolDataManager
 
DataAdder - Interface in org.jmol.quantum.mo
 
DataAdder11H - Class in org.jmol.quantum.mo
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical H orbital contributions
DataAdder11H() - Constructor for class org.jmol.quantum.mo.DataAdder11H
 
DataAdder13I - Class in org.jmol.quantum.mo
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical I orbital contributions
DataAdder13I() - Constructor for class org.jmol.quantum.mo.DataAdder13I
 
DataAdder7F - Class in org.jmol.quantum.mo
adds 7 spherical F orbital contributions
DataAdder7F() - Constructor for class org.jmol.quantum.mo.DataAdder7F
 
DataAdder9G - Class in org.jmol.quantum.mo
change QS.MAX_TYPE_SUPPORTED if you implement this adds 9 spherical G orbital contributions
DataAdder9G() - Constructor for class org.jmol.quantum.mo.DataAdder9G
 
DataAdderF - Class in org.jmol.quantum.mo
adds 10 cartesian F orbital contributions
DataAdderF() - Constructor for class org.jmol.quantum.mo.DataAdderF
 
DataAdderG - Class in org.jmol.quantum.mo
change QS.MAX_TYPE_SUPPORTED if you implement this adds 15 cartesian G orbital contributions
DataAdderG() - Constructor for class org.jmol.quantum.mo.DataAdderG
 
DataAdderH - Class in org.jmol.quantum.mo
change QS.MAX_TYPE_SUPPORTED if you implement this adds 21 cartesian H orbital contributions
DataAdderH() - Constructor for class org.jmol.quantum.mo.DataAdderH
 
DataAdderI - Class in org.jmol.quantum.mo
change QS.MAX_TYPE_SUPPORTED if you implement this adds 28 cartesian I orbital contributions
DataAdderI() - Constructor for class org.jmol.quantum.mo.DataAdderI
 
dataClass - Variable in class jspecview.source.JDXHeader
 
dataLen - Variable in class javajs.img.PngEncoder
 
DataManager - Class in org.jmol.viewer
 
DataManager() - Constructor for class org.jmol.viewer.DataManager
 
dataMax - Variable in class org.jmol.jvxl.data.JvxlData
 
dataMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataMean - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataMin - Variable in class org.jmol.jvxl.data.JvxlData
 
dataMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataOnly - Variable in class org.jmol.util.MeshSurface
 
DataReader - Class in javajs.util
Just a simple abstract class to join a String reader and a String[] reader under the same BufferedReader umbrella.
DataReader() - Constructor for class javajs.util.DataReader
 
DataReader(Reader) - Constructor for class javajs.util.DataReader
 
dataseparator - Static variable in class org.jmol.script.T
 
datatype - Variable in class jspecview.export.AMLExporter
 
datatype - Variable in class jspecview.export.CMLExporter
 
dataType - Variable in class jspecview.source.JDXHeader
 
dataType - Variable in class org.jmol.jvxl.readers.Parameters
 
dataType - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
date - Variable in class javajs.img.ImageEncoder
 
date - Static variable in class jspecview.common.JSVersion
 
date - Variable in class jspecview.common.PrintLayout
 
date - Variable in class jspecview.export.AMLExporter
 
date - Variable in class jspecview.export.CMLExporter
 
date - Variable in class jspecview.source.JDXHeader
 
date - Static variable in class org.jmol.viewer.JC
 
dBb(BS, boolean) - Method in class org.jmol.modelset.BondCollection
 
DBLCLK_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
DBLCLK_EVENT - Static variable in class com.sparshui.GestureType
 
DBLCLK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DBLCLK_GESTURE - Static variable in class com.sparshui.GestureType
 
DBLCLK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DC - Static variable in class org.jmol.quantum.QS
 
dclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
 
ddata - Variable in class org.jmol.minimize.MinObject
 
DEATH - Static variable in class com.sparshui.common.TouchState
 
DEATH - Static variable in class org.jmol.multitouch.ActionManagerMT
 
debug - Static variable in class org.jmol.script.T
 
debug(String) - Method in class org.jmol.util.DefaultLogger
 
debug(String) - Static method in class org.jmol.util.Logger
Writes a log at DEBUG level.
debug(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at DEBUG level.
DEBUG - Enum constant in enum class jspecview.common.ScriptToken
 
debugging - Variable in class javajs.util.CifDataParser
debugging flag passed from reader; unused
debugging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
debugging - Static variable in class org.jmol.util.Logger
 
debuggingHigh - Static variable in class org.jmol.util.Logger
 
debughigh - Static variable in class org.jmol.script.T
 
debugHigh - Variable in class org.jmol.script.ScriptEval
 
DebugJS - Class in javajs.util
A class to insert a JavaScript debug statement for Firefox or Chrome debugger
DebugJS() - Constructor for class javajs.util.DebugJS
 
debugPrint(String) - Method in class org.jmol.export._ObjExporter
Debug print utility.
debugscript - Static variable in class org.jmol.script.T
 
decimal - Static variable in class org.jmol.script.T
 
decimalScale - Static variable in class javajs.util.PT
 
decode(byte[]) - Static method in class javajs.util.MessagePackReader
This single method takes care of all MMTF needs.
decodeBase64(String) - Static method in class javajs.util.Base64
 
decodeInchiStereo(SimpleNode[]) - Method in class org.jmol.inchi.InChIJNI
 
decodeKey(Integer) - Static method in class org.jmol.minimize.MinObject
 
decodeWindowsBMP(byte[]) - Method in class javajs.img.BMPDecoder
original comment: loadbitmap() method converted from Windows C code.
decompressData(SB) - Method in class jspecview.source.JDXDecompressor
Determines the type of compression, decompresses the data and stores coordinates in an array to be returned
deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
deducePdbElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.ForceFieldReader
 
deepCopy(Object, boolean, boolean) - Static method in class org.jmol.script.SV
Copies a hash or array deeply; invoked by Jmol script x = @a where a.type == "hash" or a.type == "varray"
DEF_WBITS - Static variable in class com.jcraft.jzlib.JZlib
 
DEFAULT - Static variable in class org.jmol.smiles.SmilesStereo
 
DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JC
 
DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JC
 
DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_BUFSIZE - Static variable in class com.jcraft.jzlib.InflaterInputStream
 
DEFAULT_DRAG_DROP_SCRIPT - Static variable in class org.jmol.viewer.JC
 
DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_GESTURE_SWIPE_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MINY - Static variable in class jspecview.common.IntegralData
 
DEFAULT_MOUSE_DRAG_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_MOUSE_WHEEL_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_OFFSET - Static variable in class jspecview.common.IntegralData
 
DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JC
 
DEFAULT_RANGE - Static variable in class jspecview.common.IntegralData
 
DEFAULT_STEREO_DEGREES - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JC
 
DEFAULT_VISUAL_RANGE - Static variable in class org.jmol.viewer.TransformManager
 
defaultAlignment - Variable in class org.jmol.shape.Labels
 
defaultanglelabel - Static variable in class org.jmol.script.T
 
defaultBgcolix - Variable in class org.jmol.shape.Labels
 
defaultBondingMars - Static variable in class org.jmol.util.Elements
Default table of bonding radii stored as a short mar ...
defaultcmd - Static variable in class org.jmol.script.T
 
defaultColix - Variable in class org.jmol.shape.Labels
 
defaultColorFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultColorFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultcolorscheme - Static variable in class org.jmol.script.T
 
defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
 
defaultdirectory - Static variable in class org.jmol.script.T
 
defaultDisplaySchemeName - Variable in class jspecview.application.JSpecView
 
defaultdistancelabel - Static variable in class org.jmol.script.T
 
defaultdrawarrowscale - Static variable in class org.jmol.script.T
 
defaultdropscript - Static variable in class org.jmol.script.T
 
defaultDropScript - Variable in class org.jmol.viewer.GlobalSettings
 
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultFontId - Variable in class org.jmol.shape.Labels
 
defaultFontId - Variable in class org.jmol.shapespecial.Draw
 
defaultFontId0 - Variable in class org.jmol.shapespecial.Draw
 
defaultHeight - Variable in class org.jmol.awtjs.swing.JDialog
 
defaultlabelpdb - Static variable in class org.jmol.script.T
 
defaultLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
defaultlabelxyz - Static variable in class org.jmol.script.T
 
defaultlattice - Static variable in class org.jmol.script.T
 
defaultloadfilter - Static variable in class org.jmol.script.T
 
defaultLoadFilter - Variable in class org.jmol.viewer.GlobalSettings
 
defaultloadscript - Static variable in class org.jmol.script.T
 
defaultLoadScript - Variable in class org.jmol.viewer.GlobalSettings
 
DEFAULTLOADSCRIPT - Enum constant in enum class jspecview.common.ScriptToken
 
DefaultLogger - Class in org.jmol.util
Default implementation of the logger.
DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
 
defaultMacroDirectory - Static variable in class org.jmol.viewer.JC
 
defaultMessage - Variable in class org.jmol.console.GenericConsole
 
defaultMode - Variable in class org.jmol.viewer.TransformManager
 
DEFAULTNMRNORMALIZATION - Enum constant in enum class jspecview.common.ScriptToken
 
defaultOffset - Variable in class org.jmol.shape.Labels
 
defaultON - Static variable in class org.jmol.script.T
 
defaultPaletteID - Variable in class org.jmol.shape.Labels
 
defaultPlotColorNames - Static variable in class jspecview.common.ColorParameters
 
defaultPlotColors - Static variable in class jspecview.common.ColorParameters
 
defaultPointer - Variable in class org.jmol.shape.Labels
 
defaultPrintHeight - Static variable in class jspecview.common.PanelData
 
defaultPrintWidth - Static variable in class jspecview.common.PanelData
 
defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultQuality - Variable in class javajs.img.JpgEncoder
 
defaults - Static variable in class org.jmol.script.T
 
defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
 
defaultstructuredssp - Static variable in class org.jmol.script.T
 
defaultTickInfo - Variable in class org.jmol.shape.Measures
 
defaulttorsionlabel - Static variable in class org.jmol.script.T
 
defaulttranslucent - Static variable in class org.jmol.script.T
 
defaultvdw - Static variable in class org.jmol.script.T
 
defaultZPos - Variable in class org.jmol.shape.Labels
 
deferred - Variable in class org.jmol.awt.AwtSwingComponent
 
define - Static variable in class org.jmol.script.T
 
define(JmolMeasurementClient, ModelSet) - Method in class org.jmol.modelset.MeasurementData
called by the client to generate a set of measurements
defineAtomSets(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
defineCenterAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
definedAtomSets - Variable in class org.jmol.viewer.Viewer
 
definesStereo() - Method in class org.jmol.smiles.SmilesAtom
for InChI or any other system that self-defines stereochemistry.
deflate(int) - Method in class com.jcraft.jzlib.Deflater
 
deflate(int) - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
Deflate - Class in com.jcraft.jzlib
 
deflater - Variable in class com.jcraft.jzlib.DeflaterOutputStream
 
Deflater - Class in com.jcraft.jzlib
 
Deflater() - Constructor for class com.jcraft.jzlib.Deflater
 
DeflaterOutputStream - Class in com.jcraft.jzlib
 
DeflaterOutputStream() - Constructor for class com.jcraft.jzlib.DeflaterOutputStream
 
DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
 
degreesPerRadian - Static variable in class org.jmol.export.___Exporter
 
degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
 
delay - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
 
delay - Static variable in class org.jmol.script.T
 
delaymaximumms - Static variable in class org.jmol.script.T
 
delayScript(int) - Method in class org.jmol.script.ScriptEval
 
delete - Static variable in class org.jmol.script.T
 
delete(BS) - Method in class org.jmol.modelset.Atom
 
deleteAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
 
deleteAllBonds2() - Method in class org.jmol.modelset.BondCollection
 
deleteAtom(Atom) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
 
deleteAtoms(int, int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
deleteAtoms(int, BS, BS) - Method in class org.jmol.modelset.StateScript
 
deleteAtoms(BS) - Method in class org.jmol.modelset.ModelSet
 
deleteAtoms(BS, boolean) - Method in class org.jmol.viewer.Viewer
 
deleteAtomsInVariables(BS) - Method in interface org.jmol.api.JmolScriptEvaluator
 
deleteAtomsInVariables(BS) - Method in class org.jmol.script.ScriptEval
 
deleteBits(BS, BS) - Static method in class org.jmol.util.BSUtil
this one slides deleted bits out of a pattern.
deleteBonds(BS) - Method in class org.jmol.viewer.Viewer
 
deleteBonds(BS, boolean) - Method in class org.jmol.modelset.ModelSet
 
deleteConnections(float, float, int, BS, BS, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
 
DELETED - Enum constant in enum class org.jmol.c.FIL
 
deleteElements(Object, int, int) - Static method in class javajs.util.AU
 
deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
 
deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
 
deleteMeshI(int) - Method in class org.jmol.shape.MeshCollection
 
deleteMeshKey(String) - Method in class org.jmol.shape.MeshCollection
 
deleteModelAtoms(int, int, int, BS) - Method in class org.jmol.viewer.Viewer
 
deleteModelAtoms(int, int, BS) - Method in interface org.jmol.api.JmolDataManager
 
deleteModelAtoms(int, int, BS) - Method in class org.jmol.modelset.AtomCollection
 
deleteModelAtoms(int, int, BS) - Method in class org.jmol.viewer.DataManager
 
deleteModelBonds(int) - Method in class org.jmol.modelset.ModelSet
 
deleteModels(int) - Method in class org.jmol.shapecgo.CGO
 
deleteModels(int, BS) - Method in class org.jmol.viewer.Viewer
called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1
deleteModels(BS) - Method in class org.jmol.modelset.ModelSet
 
deleteNodes(Lst<JSVTreeNode>) - Method in interface jspecview.api.JSVTree
 
deleteNodes(Lst<JSVTreeNode>) - Method in class jspecview.application.AwtTree
 
deleteNodes(Lst<JSVTreeNode>) - Method in class jspecview.tree.SimpleTree
 
deleteSaved(String) - Method in class org.jmol.viewer.StateManager
 
deleteShapeAtoms(Object[], BS) - Method in class org.jmol.viewer.ShapeManager
 
deltaX - Variable in class jspecview.export.AMLExporter
 
deltaX - Variable in class jspecview.export.CMLExporter
 
deltaX - Variable in class jspecview.source.AnIMLReader
 
deltaX(double, double, int) - Static method in class jspecview.common.Coordinate
Returns the Delta X value
density - Static variable in class org.jmol.script.T
 
depict - Variable in class jme.JME
 
depictBorder - Variable in class jme.JME
 
deprecatedparam - Static variable in class org.jmol.script.T
 
depth - Static variable in class org.jmol.script.T
 
depth - Variable in class org.jmol.util.GData
 
depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
depthValue - Variable in class org.jmol.viewer.TransformManager
 
depthZ - Variable in class org.jmol.export.___Exporter
 
DESCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
 
descent - Variable in class org.jmol.modelset.Text
 
descent - Variable in class org.jmol.render.LabelsRenderer
 
desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
desiredVibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
destroy() - Method in interface javajs.api.JSInterface
 
destroy() - Method in class jspecview.appletjs.JSVApplet
 
destroy() - Method in interface org.jmol.api.JmolAppletInterface
 
destroy() - Method in class org.jmol.g3d.Graphics3D
 
destroy() - Method in class org.jmol.util.GData
 
destroy() - Method in class org.jmol.util.GenericApplet
 
destroy() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
destroy() - Method in interface org.openscience.jmol.app.JmolPlugin
 
destroyConsole() - Method in class org.jmol.console.GenericConsole
 
DetachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
 
Detailed Jmol SMARTS/Jmol bioSMARTS Specification - Search tag in package org.jmol.smiles
Section
Detailed Jmol SMILES/bioSMILES Specification - Search tag in package org.jmol.smiles
Section
detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
 
determinant3() - Method in class javajs.util.M34
 
determinant4() - Method in class javajs.util.M4
Computes the determinant of this matrix.
determineAtomSetCollectionReader(Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
the main resolver method.
determineSurfaceFileType(BufferedReader) - Static method in class org.jmol.viewer.FileManager
Try to determine a surface file type based on its header.
DEVICE_PORT - Static variable in class com.sparshui.common.NetworkConfiguration
 
DF - Class in javajs.util
created to remove ambiguities and make a simpler DecimalFormat
DF() - Constructor for class javajs.util.DF
 
dfCoefMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
DgridReader - Class in org.jmol.adapter.readers.quantum
A reader for Dgrid BASISFILE data.
DgridReader() - Constructor for class org.jmol.adapter.readers.quantum.DgridReader
 
dialog - Variable in class jspecview.dialog.JSVDialog
 
Dialog - Class in org.jmol.dialog
 
Dialog() - Constructor for class org.jmol.dialog.Dialog
 
Dialog.ExportChoiceListener - Class in org.jmol.dialog
 
Dialog.QualityListener - Class in org.jmol.dialog
 
Dialog.TypeFilter - Class in org.jmol.dialog
 
dialogAsk(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
Ask for new file name when saving or opening a file in Java and saving a file in JavaScript.
DialogManager - Class in jspecview.dialog
Dialogs include Integration, PeakListing, Views, OverlayLegend, and Measurements These dialogs have been generalized for platform independence.' This manager is subclassed as AwtDialogManager and JsDialogManager, which apply their own interpretation of how to create the dialog and get its event callbacks.
DialogManager() - Constructor for class jspecview.dialog.DialogManager
 
DialogParams - Class in jspecview.dialog
DialogParams handles all the platform-independent needs of AwtAnnotationDialog and subclasses of it.
DialogParams() - Constructor for class jspecview.dialog.DialogParams
 
dialogsToFront(Spectrum) - Method in class jspecview.common.PanelData
 
dialogType - Variable in class org.jmol.dialog.Dialog
 
diameter - Variable in class org.jmol.jvxl.data.JvxlData
 
diameter - Variable in class org.jmol.render.MeshRenderer
 
diameter - Static variable in class org.jmol.script.T
 
diameter - Variable in class org.jmol.shape.Mesh
 
DIF - Enum constant in enum class jspecview.common.ExportType
 
DIFDUP - Enum constant in enum class jspecview.common.ExportType
 
diff - Variable in class org.openscience.jmol.app.janocchio.Measure
 
diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
 
diffusepercent - Static variable in class org.jmol.script.T
 
dimension - Variable in class org.jmol.util.SimpleUnitCell
 
Dimension - Class in org.jmol.awtjs.swing
 
Dimension(int, int) - Constructor for class org.jmol.awtjs.swing.Dimension
 
dimSize - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
dipole - Static variable in class org.jmol.script.T
 
Dipole - Class in org.jmol.shapespecial
 
Dipole() - Constructor for class org.jmol.shapespecial.Dipole
 
dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
 
dipoles - Variable in class org.jmol.shapespecial.Dipoles
 
Dipoles - Class in org.jmol.shapespecial
 
Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
 
dipolescale - Static variable in class org.jmol.script.T
 
DipolesRenderer - Class in org.jmol.renderspecial
 
DipolesRenderer() - Constructor for class org.jmol.renderspecial.DipolesRenderer
 
dipoleValue - Variable in class org.jmol.shapespecial.Dipole
 
directedDistanceToPlane(P3, P4, P3) - Static method in class javajs.util.Measure
 
direction - Static variable in class org.jmol.script.T
 
dirLastExported - Variable in class jspecview.java.AwtFileHelper
 
dirLastOpened - Variable in class jspecview.java.AwtFileHelper
 
DISABLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
disablepopupmenu - Static variable in class org.jmol.script.T
 
discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains(String) - Method in class jspecview.source.JDXReader
 
discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains(String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
discardLinesUntilContains2(String, String) - Method in class jspecview.source.JDXReader
 
discardLinesUntilContains2(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains2(String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
discardLinesUntilNonBlank() - Method in class jspecview.source.JDXReader
 
discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilNonBlank() - Method in interface org.jmol.api.JmolJDXMOLReader
 
discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardPreviousAtoms() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
 
discardTempDataSR(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
discrete - Static variable in class org.jmol.script.T
 
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.CmdExt
The command dispatcher for the set of commands extended by this class.
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.IsoExt
 
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.ScriptExt
 
dispatchCommands(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
dispatchTouchEvent(JmolTouchSimulator.TouchData) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
protocol modified by Bob Hanson for Jmol to demonstrate extended SparshUI protocol to include a return from the server indicating whether or not to consume this event.
displacement - Static variable in class org.jmol.script.T
 
display - Variable in class jspecview.common.JSViewer
 
display - Variable in class org.jmol.i18n.Language
 
display - Static variable in class org.jmol.script.T
 
display - Variable in class org.jmol.viewer.Viewer
 
display - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
display1D - Variable in class jspecview.common.PanelData
 
DISPLAY1D - Enum constant in enum class jspecview.common.ScriptToken
 
DISPLAY2D - Enum constant in enum class jspecview.common.ScriptToken
 
displayAtoms(BS, boolean, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
 
displayBonds(BondSet, boolean) - Method in class org.jmol.modelset.BondCollection
 
displaycellparameters - Static variable in class org.jmol.script.T
 
displayConsole() - Method in class org.jmol.console.GenericConsole
 
displayed - Static variable in class org.jmol.script.T
 
displayFontName - Variable in class jspecview.common.ColorParameters
 
DISPLAYFONTNAME - Enum constant in enum class jspecview.common.ScriptToken
 
displayLoadErrors - Variable in class org.jmol.viewer.Viewer
 
displayMaxX - Variable in class org.jmol.util.GData
 
displayMaxX2 - Variable in class org.jmol.util.GData
 
displayMaxY - Variable in class org.jmol.util.GData
 
displayMaxY2 - Variable in class org.jmol.util.GData
 
displayMinX - Variable in class org.jmol.util.GData
 
displayMinX2 - Variable in class org.jmol.util.GData
 
displayMinY - Variable in class org.jmol.util.GData
 
displayMinY2 - Variable in class org.jmol.util.GData
 
displayName - Variable in class org.jmol.symmetry.SpaceGroup
 
DisplayPanel - Class in org.openscience.jmol.app.jmolpanel
 
DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app.jmolpanel
Action calling evalStringQuiet(<action> + CheckBoxState)
DisplayPanel.MoveToAction - Class in org.openscience.jmol.app.jmolpanel
Action calling moveTo()
DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app.jmolpanel
Action calling setStatus()
DisplaySchemesProcessor - Class in jspecview.application
DisplaySchemesProcessor loads and saves the display schemes of Jspecview.
DisplaySchemesProcessor() - Constructor for class jspecview.application.DisplaySchemesProcessor
Initialises the DisplaySchemesProcessor
displaySpeed - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
displayType - Variable in class org.jmol.shapesurface.Contact
 
displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
displayWithinDistance2 - Variable in class org.jmol.shape.MeshCollection
 
displayWithinPoints - Variable in class org.jmol.shape.MeshCollection
 
dispose() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
dispose() - Method in class com.sparshui.server.GestureServer
 
dispose() - Method in interface jspecview.api.JSVViewPanel
 
dispose() - Method in interface jspecview.api.PlatformDialog
 
dispose() - Method in class jspecview.app.GenericMouse
 
dispose() - Method in class jspecview.app.JSVApp
 
dispose() - Method in class jspecview.common.IntegralData
 
dispose() - Method in class jspecview.common.JSViewer
 
dispose() - Method in class jspecview.common.PanelData
 
dispose() - Method in class jspecview.common.PanelNode
 
dispose() - Method in class jspecview.common.Spectrum
 
dispose() - Method in class jspecview.dialog.JSVDialog
 
dispose() - Method in class jspecview.java.AwtDialog
 
dispose() - Method in class jspecview.java.AwtMainPanel
 
dispose() - Method in class jspecview.java.AwtPanel
 
dispose() - Method in class jspecview.java.FileDropperJmol
 
dispose() - Method in class jspecview.js2d.JsDialog
 
dispose() - Method in class jspecview.js2d.JsMainPanel
 
dispose() - Method in class jspecview.js2d.JsPanel
 
dispose() - Method in class jspecview.source.JDXSource
 
dispose() - Method in interface org.jmol.api.GenericMouseInterface
 
dispose() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
dispose() - Method in interface org.jmol.api.JmolGestureServerInterface
 
dispose() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
dispose() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
dispose() - Method in class org.jmol.api.JmolViewer
 
dispose() - Method in class org.jmol.awt.FileDropper
 
dispose() - Method in class org.jmol.awtjs.swing.JDialog
 
dispose() - Method in class org.jmol.awtjs2d.Mouse
 
dispose() - Method in class org.jmol.console.GenericConsole
 
dispose() - Method in class org.jmol.console.JmolConsole
 
dispose() - Method in class org.jmol.console.ScriptEditor
 
dispose() - Method in class org.jmol.consolejs.AppletConsole
 
dispose() - Method in class org.jmol.modelkit.ModelKit
 
dispose() - Method in class org.jmol.multitouch.ActionManagerMT
 
dispose() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
dispose() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
dispose() - Method in class org.jmol.multitouch.jni.JmolJniClientAdapter
 
dispose() - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
dispose() - Method in class org.jmol.viewer.ActionManager
 
dispose() - Method in class org.jmol.viewer.Viewer
end of life for this viewer
dispose() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dispose() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
dispose(SC) - Method in class org.jmol.awt.AwtPopupHelper
 
dispose(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
dispose(SC) - Method in interface org.jmol.popup.PopupHelper
 
dispose(Component) - Method in interface org.jmol.awtjs.swing.SwingController
Remove this component's HTML5 equivalent and clear references to it.
disposeGraphics(Object) - Method in class jspecview.java.AwtPlatform
 
disposeGraphics(Object) - Method in class jspecview.js2d.JsPlatform
 
disposeGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
 
disposeGraphics(Object) - Method in class org.jmol.awt.Platform
 
disposeGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
 
disposeMenu() - Method in class org.jmol.awtjs.swing.JPopupMenu
 
distance - Variable in class org.jmol.adapter.smarter.Bond
 
distance - Static variable in class org.jmol.script.T
 
distance(T3) - Method in class javajs.util.T3
Returns the distance between this point and point p1.
distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
 
distance2V(V3d, V3d) - Static method in class org.jmol.minimize.Util
 
distance4(P4) - Method in class javajs.util.P4
Returns the distance between this point and point p1.
distancefactor - Static variable in class org.jmol.script.T
 
distanceMode - Variable in class org.jmol.quantum.MepCalculation
 
distancePointToPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
 
distances - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
 
distanceSquared(T3) - Method in class javajs.util.T3
Computes the square of the distance between this point and point p1.
distanceToMappingPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
 
distanceToPlane(P4, T3) - Static method in class javajs.util.Measure
 
distanceToPlaneD(P4, float, P3) - Static method in class javajs.util.Measure
 
distanceToPlaneV(V3, float, P3) - Static method in class javajs.util.Measure
 
distinguishAndPropagateGroup(Chain, String, int, int, int, int[], Atom[]) - Method in class org.jmol.modelsetbio.BioResolver
 
div - Static variable in class org.jmol.script.T
 
div(Quat) - Method in class javajs.util.Quat
 
divide - Static variable in class org.jmol.script.T
 
divLeft(Quat) - Method in class javajs.util.Quat
 
dmesh - Variable in class org.jmol.renderspecial.DrawRenderer
 
DmolReader - Class in org.jmol.adapter.readers.xtal
 
DmolReader() - Constructor for class org.jmol.adapter.readers.xtal.DmolReader
 
dna - Static variable in class org.jmol.script.T
 
DNA - Enum constant in enum class org.jmol.c.STR
 
DNA_MASK - Static variable in class org.jmol.viewer.JC
 
doAction() - Method in class jme.JME
 
doAction(Object) - Method in class org.jmol.console.GenericConsole
 
doAdvanced(String) - Method in class jspecview.app.JSVApp
called by Pro's popup window Advanced...
doAjax(Object, String, Object, boolean) - Method in interface javajs.api.js.J2SObjectInterface
 
doAjax(String, String, Object, Object) - Method in interface javajs.api.js.J2SObjectInterface
 
doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doCentralize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doCheckUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doCircle(int, int, int, boolean) - Method in class javajs.export.PDFCreator
 
doClose - Variable in class javajs.img.ImageEncoder
 
doClose(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
doClose(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
Document - Interface in org.jmol.awtjs.swing
 
documentBase - Variable in class org.jmol.util.GenericApplet
 
doDebug - Variable in class org.jmol.quantum.QuantumCalculation
 
doDrop(PropertyChangeEvent) - Method in class jspecview.java.FileDropperJmol
 
doDrop(PropertyChangeEvent) - Method in class org.jmol.awt.FileDropper
 
doEval(String) - Method in class org.jmol.util.GenericApplet
return RAW JAVASCRIPT OBJECT, NOT A STRING
doExitJmol() - Method in interface jspecview.api.AppletFrame
 
doExitJmol() - Method in class jspecview.appletjs.JSVApplet
 
doExitJmol() - Method in class jspecview.appletjs.JSVAppletPro
 
doFixPeriodic - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
doFormatText - Variable in class org.jmol.modelset.Text
 
doFullMolecular - Variable in class org.jmol.jvxl.readers.Parameters
 
doGetModel(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doGetVibration(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doIterate - Variable in class org.jmol.jvxl.data.VolumeData
 
dollarsign - Static variable in class org.jmol.script.T
 
doLogLevel(boolean) - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
domains - Static variable in class org.jmol.script.T
 
doMenu - Variable in class jme.JME
 
doMenuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
 
doMenuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
 
doMenuSelected() - Method in class jspecview.application.ApplicationMenu
 
doMouseAtomAction() - Method in class jme.JME
 
doMouseBondAction() - Method in class jme.JME
 
doMouseClicked(int, int, boolean) - Method in class jspecview.common.PanelData
 
doMouseDragged(int, int) - Method in class jspecview.common.PanelData
 
doMouseMoved(int, int) - Method in class jspecview.common.PanelData
 
doMousePressed(int, int) - Method in class jspecview.common.PanelData
 
doMouseReleased(int, int, boolean) - Method in class jspecview.common.PanelData
 
DOMReader - Class in org.jmol.io
 
DOMReader() - Constructor for class org.jmol.io.DOMReader
 
DOMResolve(Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.
done - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
done() - Method in class jspecview.dialog.JSVDialog
 
doNewMoleculeAction(int, int) - Method in class jme.JME
 
DONOR - Enum constant in enum class org.jmol.c.HB
 
doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doPolygon(int[], int[], int, boolean) - Method in class javajs.export.PDFCreator
 
doPreSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
 
doPreSymmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
doPreSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doPreviewAction(boolean) - Method in class org.jmol.dialog.FilePreview
 
doProcessLines - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doReadMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doRect(int, int, int, int, boolean) - Method in class javajs.export.PDFCreator
 
doRepaint(boolean) - Method in interface jspecview.api.JSVPanel
 
doRepaint(boolean) - Method in class jspecview.java.AwtPanel
 
doRepaint(boolean) - Method in class jspecview.js2d.JsPanel
 
doReport() - Method in class org.jmol.script.ScriptEval
 
doResume() - Method in class org.jmol.console.ScriptEditor
 
doSendCallback(CBK, Object, Object[], String) - Method in class org.jmol.util.GenericApplet
 
doShowDocument(URL) - Method in class org.jmol.util.GenericApplet
 
doShowStatus(String) - Method in class org.jmol.util.GenericApplet
 
doSort - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
doStep() - Method in class org.jmol.console.ScriptEditor
 
doStroke(Object, boolean) - Method in class jspecview.common.PDFWriter
 
doStroke(Object, boolean) - Method in class jspecview.java.AwtG2D
 
doStroke(Object, boolean) - Method in class jspecview.js2d.JsG2D
 
doStroke(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
 
doStroke(Object, boolean) - Method in class org.jmol.awt.AwtG2D
 
doStroke(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
 
dot - Static variable in class org.jmol.script.T
 
dot(Quat) - Method in class javajs.util.Quat
 
dot(T3) - Method in class javajs.util.T3
Vector dot product.
dot(V3d) - Method in class javajs.util.V3d
Computes the dot product of the this vector and vector v.
doTags - Variable in class jme.JME
 
dotdensity - Static variable in class org.jmol.script.T
 
dotProduct(double, double, double, double) - Static method in class jme.JMEUtil
 
doTransform - Variable in class org.jmol.adapter.writers.CMLWriter
 
doTransform4D - Variable in class org.jmol.viewer.TransformManager
 
doTranslate - Variable in class org.jmol.util.GenericApplet
 
dots - Static variable in class org.jmol.script.T
 
Dots - Class in org.jmol.shapespecial
 
Dots() - Constructor for class org.jmol.shapespecial.Dots
 
dotscale - Static variable in class org.jmol.script.T
 
dotsOrDashes - Variable in class org.jmol.render.FontLineShapeRenderer
 
DotsRenderer - Class in org.jmol.renderspecial
 
DotsRenderer() - Constructor for class org.jmol.renderspecial.DotsRenderer
 
dotsselectedonly - Static variable in class org.jmol.script.T
 
dotsurface - Static variable in class org.jmol.script.T
 
dotted - Static variable in class org.jmol.script.T
 
DOTWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
 
DOUBLE - Enum constant in enum class org.jmol.c.STER
 
DOUBLE - Static variable in class org.jmol.viewer.binding.Binding
 
doubleLength(Object) - Static method in class javajs.util.AU
Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
doubleLengthBool(boolean[]) - Static method in class javajs.util.AU
 
doubleLengthByte(byte[]) - Static method in class javajs.util.AU
 
doubleLengthF(float[]) - Static method in class javajs.util.AU
 
doubleLengthI(int[]) - Static method in class javajs.util.AU
 
doubleLengthS(String[]) - Static method in class javajs.util.AU
 
doubleLengthShort(short[]) - Static method in class javajs.util.AU
 
doubleprecision - Static variable in class org.jmol.script.T
 
DOWN - Static variable in class org.jmol.viewer.binding.Binding
 
downsample - Static variable in class org.jmol.script.T
 
downsample2d(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.JvxlReader
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
downsampleRemainders - Variable in class org.jmol.jvxl.readers.JvxlReader
 
downsampleRemainders - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
downsampleRemainders - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
doZoomLinked(GraphSet, double, double, boolean, boolean, boolean) - Method in class jspecview.common.PanelData
 
DRAG - Static variable in class org.jmol.viewer.binding.Binding
 
DRAG_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
DRAG_EVENT - Static variable in class com.sparshui.GestureType
 
DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DRAG_GESTURE - Static variable in class com.sparshui.GestureType
 
DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DragBinding - Class in org.jmol.viewer.binding
 
DragBinding() - Constructor for class org.jmol.viewer.binding.DragBinding
 
DRAGDROP - Enum constant in enum class org.jmol.c.CBK
 
dragEnter(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
 
dragEnter(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
 
dragEnter(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
 
DragEvent - Class in com.sparshui.common.messages.events
 
DragEvent() - Constructor for class com.sparshui.common.messages.events.DragEvent
 
DragEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.DragEvent
Constructs a dragEvent from a complete serialized version of the drag event.
DragEvent(float, float, int, long) - Constructor for class com.sparshui.common.messages.events.DragEvent
 
dragExit(DropTargetEvent) - Method in class jspecview.java.AwtFileDropper
 
dragExit(DropTargetEvent) - Method in class jspecview.java.FileDropperJmol
 
dragExit(DropTargetEvent) - Method in class org.jmol.awt.FileDropper
 
dragged(long, int, int, int) - Method in class jspecview.app.GenericMouse
 
DRAGGED - Static variable in class org.jmol.awtjs.Event
 
dragOver(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
 
dragOver(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
 
dragOver(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
 
dragselected - Static variable in class org.jmol.script.T
 
draw - Static variable in class org.jmol.script.T
 
draw(Graphics) - Method in class jme.AtomDisplayLabel
 
draw(Graphics) - Method in class jme.JMEmol
 
Draw - Class in org.jmol.shapespecial
 
Draw() - Constructor for class org.jmol.shapespecial.Draw
 
DRAW_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
Draw.EnumDrawType - Enum Class in org.jmol.shapespecial
 
draw000 - Variable in class org.jmol.render.FontLineShapeRenderer
 
drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
 
drawAtom(Atom, float) - Method in interface org.jmol.api.JmolRendererInterface
 
drawAtom(Atom, float) - Method in class org.jmol.export.Export3D
 
drawAtom(Atom, float) - Method in class org.jmol.g3d.Graphics3D
 
drawAxes(String, String) - Method in class org.jmol.modelkit.ModelKit
 
drawBond(P3, P3, short, short, byte, short, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.export.Export3D
 
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
 
drawCircle(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
draws a simple circle (draw circle)
drawCircle(Object, int, int, int) - Method in class jspecview.common.PDFWriter
 
drawCircle(Object, int, int, int) - Method in class jspecview.java.AwtG2D
 
drawCircle(Object, int, int, int) - Method in class jspecview.js2d.JsG2D
 
drawCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawCoordinates(Object, int, int, int) - Method in class jspecview.common.PanelData
 
drawDashedCylinder(JmolRendererInterface, int, int, int, int, int, int, int[], int, short, short, int, boolean, P3i) - Static method in class org.jmol.render.FontLineShapeRenderer
 
drawDashedLineBits(int, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.export.Export3D
 
drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
drawEdge(int, int, boolean, T3, T3, P3i, P3i) - Method in class org.jmol.render.MeshRenderer
 
drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
 
drawEllipse(P3, P3, P3, boolean, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.export.Export3D
 
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
 
drawFilledCircle(short, short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a ring and filled circle (halos, draw CIRCLE, draw handles)
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a screened circle ...
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawfontsize - Static variable in class org.jmol.script.T
 
drawGraph(Object, Object, Object, int, int, boolean) - Method in class jspecview.common.PanelData
Draws the Spectrum to the panel
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.common.PDFWriter
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.java.AwtG2D
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class jspecview.js2d.JsG2D
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawHermite4(int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
 
drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.export.Export3D
 
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.g3d.Graphics3D
 
drawHKL(Viewer, String, P4, P3[]) - Method in class org.jmol.util.BZone
 
drawhover - Static variable in class org.jmol.script.T
 
drawImage(Object, int, int, int, int, int, int, int, int) - Method in class javajs.export.PDFCreator
 
drawImage(Object, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
 
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawImage(Object, Object, int, int, int, int, boolean) - Method in class jspecview.java.AwtPlatform
 
drawImage(Object, Object, int, int, int, int, boolean) - Method in class jspecview.js2d.JsPlatform
 
drawImage(Object, Object, int, int, int, int, boolean) - Method in interface org.jmol.api.GenericPlatform
 
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awt.Platform
 
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs.Platform
 
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Platform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class jspecview.java.AwtPlatform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class jspecview.js2d.JsPlatform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
 
drawing - Static variable in class org.jmol.script.T
 
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.MeasuresRenderer
 
drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawLine(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
 
drawLine(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
 
drawLine(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
 
drawLine(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawLine(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawLine(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawLine2(JmolRendererInterface, int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawLineAB(P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLineAB(P3, P3) - Method in class org.jmol.export.Export3D
 
drawLineAB(P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
drawLineABBits(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
 
drawLineBits(short, short, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLineBits(short, short, P3, P3) - Method in class org.jmol.export.Export3D
 
drawLineBits(short, short, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
drawLineBits(P3, P3, short, short) - Method in class org.jmol.export.Export3D
 
drawLinePixels(P3i, P3i, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.export.Export3D
 
drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.util.GData
 
drawLineXYZ(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
DrawMesh - Class in org.jmol.shapespecial
 
DrawMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapespecial.DrawMesh
 
drawpicking - Static variable in class org.jmol.script.T
 
drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
 
drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawPoints(int, int[], int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPoints(int, int[], int) - Method in class org.jmol.export.Export3D
 
drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
 
drawPolygon(Object, int[], int[], int) - Method in class jspecview.common.PDFWriter
 
drawPolygon(Object, int[], int[], int) - Method in class jspecview.java.AwtG2D
 
drawPolygon(Object, int[], int[], int) - Method in class jspecview.js2d.JsG2D
 
drawPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
 
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
 
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawQuadrilateralBits(JmolRendererInterface, short, P3, P3, P3, P3) - Method in class org.jmol.util.GData
 
drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.util.Escape
 
drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws a rectangle
drawRect(Graphics) - Method in class jme.AtomDisplayLabel
 
drawRect(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
 
drawRect(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
 
drawRect(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
 
drawRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
DrawRenderer - Class in org.jmol.renderspecial
 
DrawRenderer() - Constructor for class org.jmol.renderspecial.DrawRenderer
 
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.BackboneRenderer
 
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.CartoonRenderer
 
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.RibbonsRenderer
 
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.RocketsRenderer
 
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.StrandsRenderer
 
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.TraceRenderer
 
drawString(int, int, int, int, boolean, boolean, boolean, int, String) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawString(Object, String, int, int) - Method in class jspecview.common.PDFWriter
 
drawString(Object, String, int, int) - Method in class jspecview.java.AwtG2D
 
drawString(Object, String, int, int) - Method in class jspecview.js2d.JsG2D
 
drawString(Object, String, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawString(Object, String, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawString(Object, String, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawString(String, Font, int, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawStringRotated(Object, String, int, int, double) - Method in class jspecview.common.PDFWriter
 
drawStringRotated(Object, String, int, int, double) - Method in class jspecview.java.AwtG2D
 
drawStringRotated(Object, String, int, int, double) - Method in class jspecview.js2d.JsG2D
 
drawStringRotated(Object, String, int, int, double) - Method in interface org.jmol.api.GenericGraphics
 
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awt.AwtG2D
 
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awtjs2d.JsG2D
 
drawStringRotated(String, int, int, int) - Method in class javajs.export.PDFCreator
 
drawSurface(MeshSurface, short) - Method in interface org.jmol.api.JmolRendererInterface
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export._ObjExporter
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export.Export3D
 
drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
 
drawSymmetry(String, boolean, int, String, int, P3, P3, P3, int, int, int, int[], boolean) - Method in class org.jmol.modelkit.ModelKit
 
drawSymop(int, int) - Method in class org.jmol.modelkit.ModelKit
from set picking symop
drawTicks(int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawTitle(Object, int, int, String) - Method in class jspecview.common.PanelData
Draws Title
drawTriangle(P3i, short, P3i, short, P3i, short, int, int) - Method in class org.jmol.render.MeshRenderer
 
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.export.Export3D
 
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.g3d.Graphics3D
 
drawTriangleBits(JmolRendererInterface, P3, short, P3, short, P3, short, int) - Method in class org.jmol.util.GData
 
drawTriangles - Variable in class org.jmol.shape.Mesh
 
drawType - Variable in class org.jmol.shapespecial.DrawMesh
 
drawUnitCell(String, T3, String) - Method in class org.jmol.modelkit.ModelKit
 
drawXAxisLeftToRight - Variable in class jspecview.common.PanelData
 
DRIVER_NONE - Static variable in class com.sparshui.common.messages.events.EventType
 
DRIVER_NONE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
drop(DropTargetDropEvent) - Method in class jspecview.java.AwtFileDropper
 
drop(DropTargetDropEvent) - Method in class jspecview.java.FileDropperJmol
 
drop(DropTargetDropEvent) - Method in class org.jmol.awt.FileDropper
 
dropActionChanged(DropTargetDragEvent) - Method in class jspecview.java.AwtFileDropper
 
dropActionChanged(DropTargetDragEvent) - Method in class jspecview.java.FileDropperJmol
 
dropActionChanged(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
 
DS - Static variable in class org.jmol.quantum.QS
 
dslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
 
dssp - Static variable in class org.jmol.script.T
 
DSSP - Class in org.jmol.dssx
 
DSSP() - Constructor for class org.jmol.dssx.DSSP
 
dsspcalchydrogen - Static variable in class org.jmol.script.T
 
dssr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
dssr - Static variable in class org.jmol.script.T
 
DSSR0 - Class in org.jmol.dssx
The original non-JSON parser for output from 3DNA web service.
DSSR0() - Constructor for class org.jmol.dssx.DSSR0
 
DSSR1 - Class in org.jmol.dssx
A parser for output from 3DNA web service.
DSSR1() - Constructor for class org.jmol.dssx.DSSR1
 
dssrBox - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
dssrBoxHeight - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
dssrCache - Variable in class org.jmol.modelset.Model
 
dssrFrame - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
dssrNT - Variable in class org.jmol.modelset.Group
 
DTI - Enum constant in enum class org.jmol.c.STER
 
dumpArray(String, float[][], int, int, int, int) - Static method in class javajs.util.AU
 
dumpContainer(Container, String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
dumpInfo() - Method in class org.jmol.symmetry.SpaceGroup
 
dumpIntArray(int[], int) - Static method in class javajs.util.AU
 
dumpList - Static variable in class jspecview.popup.JSVGenericPopup
 
dVal(String) - Static method in class javajs.util.PT
 
dyMode - Variable in class jme.JME
 
dynamicmeasurements - Static variable in class org.jmol.script.T
 

E

e - Variable in class org.jmol.scriptext.ScriptExt
 
e(Object) - Static method in class org.jmol.util.Escape
 
E_MINUS_D - Static variable in class org.jmol.quantum.MepCalculation
 
E_MINUS_D_OVER_2 - Static variable in class org.jmol.quantum.MepCalculation
 
eAD(double[]) - Static method in class org.jmol.util.Escape
 
eAF(float[]) - Static method in class org.jmol.util.Escape
 
eAI(int[]) - Static method in class org.jmol.util.Escape
 
eAP(T3[]) - Static method in class org.jmol.util.Escape
 
eAS(String[], boolean) - Static method in class org.jmol.util.Escape
 
EAST - Static variable in class org.jmol.awtjs.swing.BorderLayout
 
EAST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
 
eBond(BS) - Static method in class org.jmol.util.Escape
 
eBS(BS) - Static method in class org.jmol.util.Escape
 
ec - Variable in class org.jmol.shapespecial.Dots
 
eccentricity - Static variable in class org.jmol.script.T
 
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityRatio - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityScale - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
echo - Static variable in class org.jmol.script.T
 
Echo - Class in org.jmol.shape
 
Echo() - Constructor for class org.jmol.shape.Echo
 
ECHO - Enum constant in enum class org.jmol.c.CBK
 
ECHO_BOTTOM - Static variable in class org.jmol.viewer.JC
 
ECHO_MIDDLE - Static variable in class org.jmol.viewer.JC
 
ECHO_TOP - Static variable in class org.jmol.viewer.JC
 
ECHO_XY - Static variable in class org.jmol.viewer.JC
 
ECHO_XYZ - Static variable in class org.jmol.viewer.JC
 
EchoRenderer - Class in org.jmol.render
 
EchoRenderer() - Constructor for class org.jmol.render.EchoRenderer
 
ed - Static variable in class org.jmol.script.T
 
Edge - Class in org.jmol.util
 
Edge() - Constructor for class org.jmol.util.Edge
 
EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgePointIndexes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edges - Static variable in class org.jmol.script.T
 
edges - Static variable in class org.jmol.util.BoxInfo
 
EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_ONLY - Static variable in class org.jmol.shapespecial.Polyhedra
 
edgesonly - Static variable in class org.jmol.script.T
 
edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexes - Static variable in class org.jmol.util.TriangleData
 
edgeVertexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPlanesHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPlanesLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointers - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointersHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointersLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
editArea - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
editButton - Variable in class org.jmol.console.GenericConsole
 
editor - Variable in class org.jmol.console.ScriptEditor
 
EDITOR_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
editorAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
editPane - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
eds - Static variable in class org.jmol.script.T
 
edsdiff - Static variable in class org.jmol.script.T
 
Eigen - Class in javajs.util
Eigenvalues and eigenvectors of a real matrix.
Eigen() - Constructor for class javajs.util.Eigen
 
EigenInterface - Interface in javajs.api
 
eigenSignMask - Variable in class org.jmol.util.Tensor
 
eigenValues - Variable in class org.jmol.util.Tensor
 
eigenVectors - Variable in class org.jmol.util.Tensor
 
element - Static variable in class org.jmol.script.T
 
ELEMENT_NUMBER_MASK - Static variable in class org.jmol.util.Elements
 
elementColors - Variable in class jspecview.common.ColorParameters
 
elementCounts - Variable in class org.jmol.util.JmolMolecule
 
elementkey - Static variable in class org.jmol.script.T
 
elementLabel - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
 
elementNames - Static variable in class org.jmol.util.Elements
 
elementNumber - Variable in class org.jmol.adapter.smarter.Atom
 
elementNumberFromName(String) - Static method in class org.jmol.util.Elements
 
elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
 
elementNumberMax - Static variable in class org.jmol.util.Elements
one larger than the last elementNumber, same as elementSymbols.length
elementNumberMax - Variable in class org.jmol.util.JmolMolecule
 
Elements - Class in org.jmol.util
 
Elements() - Constructor for class org.jmol.util.Elements
 
elementsPresent - Variable in class org.jmol.modelset.ModelSet
 
elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
 
elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
 
elementSymbols - Static variable in class org.jmol.util.Elements
The default elementSymbols.
elemisono - Static variable in class org.jmol.script.T
 
elemno - Static variable in class org.jmol.script.T
 
elemNo - Variable in class org.jmol.quantum.SlaterData
 
ellipsoid - Static variable in class org.jmol.script.T
 
Ellipsoid - Class in org.jmol.shapespecial
 
ELLIPSOID - Static variable in class org.jmol.shapecgo.CGOMesh
 
ellipsoidarcs - Static variable in class org.jmol.script.T
 
ellipsoidarrows - Static variable in class org.jmol.script.T
 
ellipsoidaxes - Static variable in class org.jmol.script.T
 
ellipsoidaxisdiameter - Static variable in class org.jmol.script.T
 
ellipsoidball - Static variable in class org.jmol.script.T
 
ellipsoiddotcount - Static variable in class org.jmol.script.T
 
ellipsoiddots - Static variable in class org.jmol.script.T
 
ellipsoidfill - Static variable in class org.jmol.script.T
 
Ellipsoids - Class in org.jmol.shapespecial
 
Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
 
ellipsoidShades - Variable in class org.jmol.util.Shader
 
EllipsoidsRenderer - Class in org.jmol.renderspecial
 
EllipsoidsRenderer() - Constructor for class org.jmol.renderspecial.EllipsoidsRenderer
 
elsecmd - Static variable in class org.jmol.script.T
 
elseif - Static variable in class org.jmol.script.T
 
embedded - Variable in class jme.JME
 
EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JC
 
embedScript(String) - Static method in class org.jmol.viewer.JC
 
EMPTY - Static variable in interface javajs.api.GenericCifDataParser
 
EMPTY - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
emptySet - Static variable in class org.jmol.util.BSUtil
 
ENABLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
enabled - Variable in class org.jmol.awtjs.swing.Component
 
enableShell(int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...
enableStatus(boolean) - Method in class jspecview.application.MainFrame
 
enableToolbar(boolean) - Method in class jspecview.application.MainFrame
 
ENABLEZOOM - Enum constant in enum class jspecview.common.ScriptToken
 
ENC_CALC_MAX_DIST - Static variable in class org.jmol.viewer.JC
 
encapsulateData(String, Object, int) - Static method in class org.jmol.util.Escape
 
encodeColor(short) - Static method in class org.jmol.shape.Shape
 
encodeRadiusParameter(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
Encoding - Enum Class in javajs.util
 
end - Static variable in class org.jmol.script.T
 
end() - Method in class com.jcraft.jzlib.Deflater
 
end() - Method in class com.jcraft.jzlib.Inflater
 
end() - Method in class org.jmol.util.PatternMatcher.JSPattern
 
END - Static variable in class org.jmol.shapecgo.CGOMesh
 
END_ELEMENT - Static variable in class jspecview.source.XMLParser
 
endAssignment() - Method in class org.jmol.script.ScriptMathProcessor
 
endcap - Variable in class org.jmol.render.FontLineShapeRenderer
 
ENDCAPS_FLAT - Static variable in class org.jmol.util.GData
 
ENDCAPS_FLAT_TO_SPHERICAL - Static variable in class org.jmol.util.GData
 
ENDCAPS_HIDDEN - Static variable in class org.jmol.util.GData
 
ENDCAPS_NONE - Static variable in class org.jmol.util.GData
 
ENDCAPS_OPEN_TO_SPHERICAL - Static variable in class org.jmol.util.GData
 
ENDCAPS_SPHERICAL - Static variable in class org.jmol.util.GData
 
endChainID - Variable in class org.jmol.adapter.smarter.Structure
 
ENDCOM - Static variable in class javajs.api.GenericZipInputStream
 
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
ENDHDR - Static variable in class javajs.api.GenericZipInputStream
 
endifcmd - Static variable in class org.jmol.script.T
 
endIndex - Variable in class jspecview.export.AMLExporter
 
endIndex - Variable in class jspecview.export.CMLExporter
 
ENDINDEX - Enum constant in enum class jspecview.common.ScriptToken
 
endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
endLayout() - Method in interface jspecview.api.PlatformDialog
 
endLayout() - Method in class jspecview.java.AwtDialog
 
endLayout() - Method in class jspecview.js2d.JsDialog
 
endMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
 
endOfData - Variable in class org.jmol.jvxl.readers.JvxlReader
 
endOfData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
endOfData - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
ENDOFF - Static variable in class javajs.api.GenericZipInputStream
 
endRecording() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
endRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
endRendering() - Method in class org.jmol.g3d.Graphics3D
 
endRendering() - Method in class org.jmol.util.GData
 
endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
ENDSIG - Static variable in class javajs.api.GenericZipInputStream
 
ENDSIZ - Static variable in class javajs.api.GenericZipInputStream
 
ENDSUB - Static variable in class javajs.api.GenericZipInputStream
 
ENDTOT - Static variable in class javajs.api.GenericZipInputStream
 
energy - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
energy - Static variable in class org.jmol.script.T
 
ENERGY - Enum constant in enum class org.jmol.c.PAL
 
energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyunits - Static variable in class org.jmol.script.T
 
energyUnits - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
energyUnits - Variable in class org.jmol.viewer.GlobalSettings
 
ensureLength(Object, int) - Static method in class javajs.util.AU
Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
ensureLengthA(float[], int) - Static method in class javajs.util.AU
 
ensureLengthByte(byte[], int) - Static method in class javajs.util.AU
 
ensureLengthI(int[], int) - Static method in class javajs.util.AU
 
ensureLengthS(String[], int) - Static method in class javajs.util.AU
 
ensureLengthShort(short[], int) - Static method in class javajs.util.AU
 
ensureSignedBytes(byte[]) - Static method in class javajs.util.AU
Ensure that we have signed and not unsigned bytes coming out of any process, but particularly out of file reading.
entered(long, int, int) - Method in class jspecview.app.GenericMouse
 
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
ENV_CALC_MAX_LEVEL - Static variable in class org.jmol.viewer.JC
 
EnvelopeCalculation - Class in org.jmol.geodesic
 
EnvelopeCalculation() - Constructor for class org.jmol.geodesic.EnvelopeCalculation
 
eof - Variable in class com.jcraft.jzlib.InflaterInputStream
 
EOF - Static variable in class jspecview.source.XMLParser
 
eP(T3) - Static method in class org.jmol.util.Escape
must be its own, because of the possibility of being null
eP4(P4) - Static method in class org.jmol.util.Escape
 
equals(int[], int[]) - Static method in class jme.JMEUtil
 
equals(Object) - Method in class javajs.util.A4
Returns true if the Object o is of type AxisAngle4f and all of the data members of o1 are equal to the corresponding data members in this AxisAngle4f.
equals(Object) - Method in class javajs.util.BArray
 
equals(Object) - Method in class javajs.util.BS
Compares this object against the specified object.
equals(Object) - Method in class javajs.util.M3
Returns true if the Object o is of type Matrix3f and all of the data members of t1 are equal to the corresponding data members in this Matrix3f.
equals(Object) - Method in class javajs.util.M4
Returns true if the Object o is of type Matrix4f and all of the data members of t1 are equal to the corresponding data members in this Matrix4f.
equals(Object) - Method in class javajs.util.T3
Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this
equals(Object) - Method in class javajs.util.T3d
Returns true if all of the data members of Tuple3d t1 are equal to the corresponding data members in this
equals(Object) - Method in class javajs.util.T3i
Returns true if the Object o is of type Tuple3i and all of the data members of t are equal to the corresponding data members in this Tuple3i.
equals(Object) - Method in class javajs.util.T4
Returns true if all of the data members of Object are equal to the corresponding data members in this
equals(Object) - Method in class org.jmol.modelset.Atom
 
equals(Object) - Method in class org.jmol.script.T
 
equals(Coordinate) - Method in class jspecview.common.Coordinate
Indicates whether some other Coordinate is equal to this one
err() - Method in class javajs.util.M34
 
error - Variable in class org.jmol.script.ScriptError
 
error - Variable in class org.jmol.script.ScriptParallelProcessor
 
error - Static variable in class org.jmol.script.T
 
error(int) - Method in class org.jmol.script.ScriptError
 
error(int) - Method in class org.jmol.script.ScriptCompiler
 
error(int) - Method in class org.jmol.scriptext.ScriptExt
 
error(String) - Method in class org.jmol.util.DefaultLogger
 
error(String) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level.
error(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level.
error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
ERROR - Enum constant in enum class org.jmol.c.CBK
 
ERROR - Static variable in class jspecview.source.JDXDataObject
Error number that is returned when a min value is undefined
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptError
 
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_badContext - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_badRGBColor - Static variable in class org.jmol.script.ScriptError
 
ERROR_cannotSet - Static variable in class org.jmol.script.ScriptError
 
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_endOfCommandUnexpected - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_endOfStatementUnexpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_expressionExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_fileNotFoundException - Static variable in class org.jmol.script.ScriptError
 
ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
 
ERROR_incompatibleArguments - Static variable in class org.jmol.script.ScriptError
 
ERROR_insufficientArguments - Static variable in class org.jmol.script.ScriptError
 
ERROR_invalidArgument - Static variable in class org.jmol.script.ScriptError
 
ERROR_invalidExpressionToken - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_invalidParameterOrder - Static variable in class org.jmol.script.ScriptError
 
ERROR_keywordExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_MESSAGE - Static variable in class jspecview.dialog.DialogManager
 
ERROR_missingEnd - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_moCoefficients - Static variable in class org.jmol.script.ScriptError
 
ERROR_moIndex - Static variable in class org.jmol.script.ScriptError
 
ERROR_moModelError - Static variable in class org.jmol.script.ScriptError
 
ERROR_moOccupancy - Static variable in class org.jmol.script.ScriptError
 
ERROR_moOnlyOne - Static variable in class org.jmol.script.ScriptError
 
ERROR_multipleModelsDisplayedNotOK - Static variable in class org.jmol.script.ScriptError
 
ERROR_noData - Static variable in class org.jmol.script.ScriptError
 
ERROR_noPartialCharges - Static variable in class org.jmol.script.ScriptError
 
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_operationCanceled - Static variable in class org.jmol.script.ScriptError
 
ERROR_tokenExpected - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_tokenUnexpected - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_unrecognizedToken - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR_what - Static variable in class org.jmol.script.ScriptError
 
ERROR_writeWhat - Static variable in class org.jmol.script.ScriptError
 
errorEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
errorEx(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level with detail on exception.
errorEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
errorIntStr2(int, String, String) - Method in class org.jmol.script.ScriptCompiler
 
errorLine - Variable in class org.jmol.script.ScriptCompiler
 
errorLog - Variable in class jspecview.source.AnIMLReader
 
errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
errorMessage - Variable in class org.jmol.script.ScriptContext
 
errorMessage - Variable in class org.jmol.script.ScriptError
 
errorMessage - Variable in class org.jmol.script.ScriptCompiler
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptError
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptCompiler
 
errorStr(int, String) - Method in class org.jmol.script.ScriptError
 
errorStr(int, String) - Method in class org.jmol.script.ScriptCompiler
 
errorStr2(int, String, String) - Method in class org.jmol.script.ScriptError
 
errorStr2(String, String) - Method in class org.jmol.script.ScriptCompiler
 
errorType - Variable in class org.jmol.script.ScriptContext
 
errorType - Variable in class org.jmol.script.ScriptError
 
errorType - Variable in class org.jmol.script.ScriptCompiler
 
esc(String) - Static method in class javajs.util.PT
 
escape() - Method in class org.jmol.script.SV
 
escape(BS, char, char) - Static method in class javajs.util.BS
 
Escape - Class in org.jmol.util
 
Escape() - Constructor for class org.jmol.util.Escape
 
escapeColor(int) - Static method in class org.jmol.util.Escape
 
escapeFloatA(float[], boolean) - Static method in class org.jmol.util.Escape
 
escapeFloatAA(float[][], boolean) - Static method in class org.jmol.util.Escape
 
escapeFloatAAA(float[][][], boolean) - Static method in class org.jmol.util.Escape
 
escapeHelical(String, int, P3, P3, T3[]) - Static method in class org.jmol.util.Escape
Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxis
escapeHTML(String) - Static method in class org.jmol.i18n.GT
 
escapeKeyPressed(boolean) - Method in class jspecview.common.PanelData
 
escapeMap(Map<String, Object>) - Static method in class org.jmol.util.Escape
 
escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
 
escapeMultiplier(T3) - Static method in class org.jmol.util.SimpleUnitCell
Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}
escapeUrl(String) - Static method in class javajs.util.PT
 
escF(float) - Static method in class javajs.util.PT
ensures that a float turned to string has a decimal point
escUnicode(String) - Static method in class javajs.util.PT
 
EspressoReader - Class in org.jmol.adapter.readers.xtal
 
EspressoReader() - Constructor for class org.jmol.adapter.readers.xtal.EspressoReader
 
eta - Static variable in class org.jmol.script.T
 
eV(Lst<SV>) - Static method in class org.jmol.util.Escape
 
eval - Static variable in class org.jmol.script.T
 
eval - Variable in class org.jmol.thread.JmolThread
 
eval - Variable in class org.jmol.viewer.Viewer
 
eval(String) - Method in interface org.jmol.api.JmolStatusListener
 
eval(String) - Method in class org.jmol.util.GenericApplet
 
eval(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
EVAL - Enum constant in enum class org.jmol.c.CBK
 
evalCallback(String, Object[], boolean) - Method in interface org.jmol.api.JmolScriptManager
 
evalCallback(String, Object[], boolean) - Method in class org.jmol.script.ScriptManager
 
evalCallback(String, Object[], boolean) - Method in class org.jmol.viewer.Viewer
 
evalError(String, String) - Method in class org.jmol.script.ScriptError
 
evalFile(String) - Method in interface org.jmol.api.JmolScriptManager
 
evalFile(String) - Method in class org.jmol.api.JmolViewer
 
evalFile(String) - Method in class org.jmol.script.ScriptManager
 
evalFile(String) - Method in class org.jmol.viewer.Viewer
 
evalFileArgs(String, String) - Method in interface org.jmol.api.JmolScriptManager
 
evalFileArgs(String, String) - Method in class org.jmol.api.JmolViewer
 
evalFileArgs(String, String) - Method in class org.jmol.script.ScriptManager
 
evalFileArgs(String, String) - Method in class org.jmol.viewer.Viewer
 
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.atomdata.AtomDataServer
 
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.script.ScriptEval
 
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.viewer.Viewer
 
evalParallel(ScriptContext, ShapeManager) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptEval
 
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.scriptext.CmdExt
used for TRY command
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.viewer.Viewer
 
evalString(String) - Method in class org.jmol.api.JmolViewer
 
evalString(String) - Method in class org.jmol.viewer.Viewer
 
evalStringGUI(String) - Method in class org.jmol.viewer.Viewer
Run a script asynchronously, adding the GUI flag to indicate that we should fire the SELECT callback at the end if there is one.
evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
 
evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
 
evalStringQuietSync(String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
 
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
 
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evaluate(ScriptMathProcessor, T, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateCompiledScript(Object[], boolean, boolean, boolean, boolean, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evaluateCompiledScript(Object[], boolean, boolean, boolean, boolean, SB, boolean) - Method in class org.jmol.script.ScriptEval
 
evaluateExpression(Object) - Method in class org.jmol.api.JmolViewer
 
evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable
evaluateExpression(Object, boolean, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evaluateExpression(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
a general-use method to evaluate a "SET" type expression.
evaluateExpressionAsVariable(Object) - Method in class org.jmol.api.JmolViewer
 
evaluateExpressionAsVariable(Object) - Method in class org.jmol.viewer.Viewer
 
Event - Class in org.jmol.awtjs
 
Event - Interface in com.sparshui.common
This interface must be implemented by all user-defined events.
Event() - Constructor for class org.jmol.awtjs.Event
 
EVENT - Static variable in class com.sparshui.common.ClientProtocol.MessageType
 
eventApply() - Method in class jspecview.dialog.JSVDialog
 
eventFocus() - Method in class jspecview.dialog.JSVDialog
 
EventManager - Interface in org.jmol.api
 
EventType - Class in com.sparshui.common.messages.events
This is an enumeration of all event types currently available.
EventType() - Constructor for class com.sparshui.common.messages.events.EventType
 
evspoints - Variable in class jspecview.source.AnIMLReader
 
EX - Variable in class org.jmol.quantum.MOCalculation
 
excludeAtoms(BS, boolean) - Method in class org.jmol.viewer.SelectionManager
 
excludedTriangleCount - Variable in class org.jmol.jvxl.data.JvxlData
 
excludedVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
execHidden(boolean) - Method in class jspecview.application.MainFrame
 
execLoad(String, String) - Method in class jspecview.common.JSViewer
 
execute(String) - Method in class org.jmol.console.AppletConsole
 
execute(String) - Method in class org.jmol.console.GenericConsole
 
execute(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
executeScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
 
executionPaused - Variable in class org.jmol.script.ScriptContext
 
executionStepping - Variable in class org.jmol.script.ScriptContext
 
executor - Variable in class org.jmol.viewer.Viewer
 
execView(String, boolean) - Method in class jspecview.common.JSViewer
 
exit - Static variable in class org.jmol.script.T
 
exitAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExitAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
 
exitBondRotation() - Method in class org.jmol.awt.AwtModelKitPopup
 
exitBondRotation() - Method in class org.jmol.modelkit.ModelKitPopup
 
exitBondRotation(String) - Method in class org.jmol.modelkit.ModelKit
 
exited(long, int, int) - Method in class jspecview.app.GenericMouse
 
exitjmol - Static variable in class org.jmol.script.T
 
exitJmol() - Method in class org.jmol.viewer.Viewer
 
exitJSpecView(boolean, Object) - Method in class jspecview.app.JSVAppPro
 
exitJSpecView(boolean, Object) - Method in class jspecview.application.JSpecView
 
exitJSpecView(boolean, Object) - Method in interface org.jmol.api.JSVInterface
 
exitJSpecView(boolean, Object) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
exitMeasurementMode(String) - Method in class org.jmol.viewer.ActionManager
 
expandFloatArray(float[], int, boolean) - Method in class org.jmol.script.ScriptEval
Accepts a float array and expands [1 -3] to [1 2 3], for example.
explicitID - Variable in class org.jmol.shape.MeshCollection
 
export(String, int) - Method in class jspecview.appletjs.JSVApplet
Deprecated.
export(String, int) - Method in class jspecview.common.JSViewer
 
EXPORT_CARTESIAN - Static variable in class org.jmol.util.GData
 
EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JC
 
EXPORT_NOT - Static variable in class org.jmol.util.GData
 
EXPORT_RAYTRACER - Static variable in class org.jmol.util.GData
 
export3D - Variable in class org.jmol.export.___Exporter
 
Export3D - Class in org.jmol.export
 
Export3D() - Constructor for class org.jmol.export.Export3D
 
exportAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExportAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
 
exportActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExportChoiceListener() - Constructor for class org.jmol.dialog.Dialog.ExportChoiceListener
 
exportCmd(JSVPanel, Lst<String>, boolean) - Method in interface jspecview.export.ExportInterface
from EXPORT command
exporter - Variable in class org.jmol.export.Export3D
 
Exporter - Class in jspecview.export
 
Exporter() - Constructor for class jspecview.export.Exporter
 
ExportInterface - Interface in jspecview.api
 
ExportInterface - Interface in jspecview.export
 
exportPass - Variable in class org.jmol.render.MeshRenderer
 
exportPrecision - Variable in class jspecview.common.ScaleData
 
exportscale - Static variable in class org.jmol.script.T
 
exportScale - Variable in class org.jmol.export.___Exporter
 
exportSpectrum(String, int) - Method in interface jspecview.api.JSVAppletInterface
Delivers spectrum coded as desired: XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML, PDF(base64-encoded)
exportSpectrum(String, int) - Method in class jspecview.app.JSVApp
Delivers spectrum coded as desired: XY, SQZ, PAC, DIF, DIFDUP, FIX, AML, CML
exportSpectrum(String, int) - Method in class jspecview.appletjs.JSVApplet
 
exportSpectrum(String, int) - Method in class jspecview.application.MainFrame
 
exportSpectrum(JSViewer, String) - Method in interface jspecview.export.ExportInterface
 
exportSurface(short) - Method in class org.jmol.render.MeshRenderer
 
exportTheSpectrum(String, String, Spectrum, int, int) - Method in interface jspecview.export.ExportInterface
returns message if path is not null, otherwise full string of text (unsigned applet)
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in interface jspecview.api.JSVExporter
 
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.AMLExporter
Exports the Spectrum that is displayed by JSVPanel to a file given by fileName If display is zoomed then export the current view
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.CMLExporter
Exports the Spectrum that is displayed by JSVPanel to a file given by fileName If display is zoomed then export the current view
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.Exporter
 
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.JDXExporter
Exports spectrum in one of several formats
exportTheSpectrum(JSViewer, ExportType, OC, Spectrum, int, int, PanelData, boolean) - Method in class jspecview.export.SVGExporter
Export a Graph as SVG to a file given by fileName
exportType - Variable in class org.jmol.render.ShapeRenderer
 
ExportType - Enum Class in jspecview.common
 
expressionBegin - Static variable in class org.jmol.script.T
 
expressionEnd - Static variable in class org.jmol.script.T
 
EXTCRC - Static variable in class javajs.api.GenericZipInputStream
 
extendGrid - Variable in class org.jmol.jvxl.readers.Parameters
 
externalContainer - Variable in class org.jmol.console.JmolConsole
 
EXTHDR - Static variable in class javajs.api.GenericZipInputStream
 
EXTLEN - Static variable in class javajs.api.GenericZipInputStream
 
extractMolData(String) - Method in class org.jmol.api.JmolViewer
 
extractMolData(String) - Method in class org.jmol.viewer.Viewer
 
extractProperty(Object, Object, int) - Method in class org.jmol.viewer.Viewer
 
extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in class org.jmol.viewer.PropertyManager
 
extractTagOnly(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
 
EXTSIG - Static variable in class javajs.api.GenericZipInputStream
 
EXTSIZ - Static variable in class javajs.api.GenericZipInputStream
 
EY - Variable in class org.jmol.quantum.MOCalculation
 
EZ - Variable in class org.jmol.quantum.MOCalculation
 

F

facecenteroffset - Static variable in class org.jmol.script.T
 
faceMap - Variable in class org.jmol.renderspecial.DotsRenderer
 
faceOrder - Static variable in class org.jmol.util.BoxInfo
 
facePoints - Static variable in class org.jmol.util.BoxInfo
 
faces - Variable in class org.jmol.shapespecial.Polyhedron
 
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.AdfReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.AmsReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.DgridReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.AdfReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.AmsReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.DgridReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
 
fact_2n - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
FACTOR - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
 
factorType - Variable in class org.jmol.atomdata.RadiusData
 
FAHReader - Class in org.jmol.adapter.readers.simple
FoldingAtHome json reader.
FAHReader() - Constructor for class org.jmol.adapter.readers.simple.FAHReader
 
falsifyMesh() - Method in class org.jmol.shapebio.BioShape
 
fatal(String) - Method in class org.jmol.util.DefaultLogger
 
fatal(String) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level.
fatal(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at FATAL level.
fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
fatalEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
fatalEx(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level with detail on exception.
fatalEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
FC - Static variable in class org.jmol.quantum.QS
 
fclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
 
fcoord(T3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
fcoord(T3, String) - Static method in class org.jmol.symmetry.SymmetryOperation
Get string version of fraction
FD_PROPERTY_INLINE - Static variable in class jspecview.java.FileDropperJmol
 
fdup(String, int, int) - Static method in class javajs.util.PT
fdup duplicates p or q formats for formatCheck and the format() function.
ffAtomType - Variable in class org.jmol.minimize.MinAtom
 
fflistValue(T, int) - Static method in class org.jmol.script.SV
 
fformat(double, int, int) - Static method in class jme.JMEUtil
Truncate to dec digits after the decimal place and left-pad to length len.
FFParam - Class in org.jmol.minimize.forcefield
 
FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
 
ffParams - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
ffType - Variable in class org.jmol.minimize.MinAtom
 
fid - Variable in class org.jmol.util.Font
 
fids - Variable in class org.jmol.shape.Labels
 
fieldProperty(int) - Method in class org.jmol.adapter.readers.cif.CifReader
 
FIL - Enum Class in org.jmol.c
 
file - Static variable in class org.jmol.script.T
 
FILE_DROPPED - Static variable in interface org.jmol.api.JmolScriptManager
 
FILE_OPEN_ALREADY - Static variable in class jspecview.common.JSViewer
 
FILE_OPEN_ERROR - Static variable in class jspecview.common.JSViewer
 
FILE_OPEN_NO_DATA - Static variable in class jspecview.common.JSViewer
 
FILE_OPEN_OK - Static variable in class jspecview.common.JSViewer
 
FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
fileAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
filecachedirectory - Static variable in class org.jmol.script.T
 
filecaching - Static variable in class org.jmol.script.T
 
FileChooser - Class in org.jmol.dialog
JFileChooser with possibility to fix size and location
FileChooser() - Constructor for class org.jmol.dialog.FileChooser
 
FileDropper - Class in org.jmol.awt
A simple Dropping class to allow files to be dragged onto a target.
FileDropper(JmolStatusListener, Viewer, JmolDropEditor) - Constructor for class org.jmol.awt.FileDropper
 
FileDropperJmol - Class in jspecview.java
A simple Dropping class to allow files to be dragged onto a target.
FileDropperJmol(PlatformViewer) - Constructor for class jspecview.java.FileDropperJmol
 
fileFirstX - Variable in class jspecview.source.JDXDataObject
JDXReader only
fileHelper - Variable in class jspecview.common.JSViewer
 
fileLastX - Variable in class jspecview.source.JDXDataObject
JDXReader only
FileManager - Class in org.jmol.viewer
 
filename - Variable in class org.jmol.console.ScriptEditor
 
fileName - Variable in class jspecview.common.PanelNode
 
fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileName - Variable in class org.jmol.atomdata.AtomData
 
fileName - Variable in class org.jmol.export.___Exporter
 
fileName - Variable in class org.jmol.jvxl.readers.Parameters
 
fileNPoints - Variable in class jspecview.source.JDXDataObject
JDXReader only
fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filePath - Variable in class jspecview.source.AnIMLReader
 
filePath - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
FilePreview - Class in org.jmol.dialog
File previsualisation before opening
FilePreview(Viewer, JFileChooser, boolean, Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview
Constructor
FileReader - Class in org.jmol.io
 
FileReader(Viewer, String, String, String, String, Object, Map<String, Object>, boolean) - Constructor for class org.jmol.io.FileReader
 
fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filesData - Variable in class org.jmol.jvxl.readers.Parameters
 
FilesReader - Class in org.jmol.io
open a set of models residing in different files
FilesReader() - Constructor for class org.jmol.io.FilesReader
 
FileSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
fill - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
fill - Static variable in class org.jmol.script.T
 
fill() - Method in class com.jcraft.jzlib.InflaterInputStream
 
fill() - Method in class javajs.export.PDFCreator
 
fill3x3(String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills a double[3][3]
fillADa(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
 
fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
 
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelSet
 
fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
 
fillBackground(Object, GenericColor) - Method in class jspecview.common.PDFWriter
 
fillBackground(Object, GenericColor) - Method in class jspecview.java.AwtG2D
 
fillBackground(Object, GenericColor) - Method in class jspecview.js2d.JsG2D
 
fillBackground(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
 
fillBackground(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
 
fillBackground(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
 
fillCircle(Object, int, int, int) - Method in class jspecview.common.PDFWriter
 
fillCircle(Object, int, int, int) - Method in class jspecview.java.AwtG2D
 
fillCircle(Object, int, int, int) - Method in class jspecview.js2d.JsG2D
 
fillCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
fillCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
fillCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.export.Export3D
 
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._PovrayExporter
 
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._TachyonExporter
 
fillCylinder(byte, int, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.export.Export3D
 
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinder(JmolRendererInterface, short, short, byte, int, int, int, int, int, int, int, boolean) - Static method in class org.jmol.render.FontLineShapeRenderer
 
fillCylinderBits(byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.export.Export3D
 
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.export.Export3D
 
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.Export3D
 
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
fillDataBlockFixed(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
Fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format.
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in interface org.jmol.api.JmolRendererInterface
 
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.export.Export3D
 
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.g3d.Graphics3D
 
fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills a float array with string data from a file
fillFloatArrays(V3[], float[]) - Method in interface javajs.api.EigenInterface
 
fillFloatArrays(V3[], float[]) - Method in class javajs.util.Eigen
Specifically for 3x3 systems, returns eigenVectors as V3[3] and values as float[3]; sorted from smallest to largest value.
fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int, String[][]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
Extracts a block of frequency data from a file.
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
 
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
 
fillParams(V3, V3, V3, float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
fillPolygon(Object, int[], int[], int) - Method in class jspecview.common.PDFWriter
 
fillPolygon(Object, int[], int[], int) - Method in class jspecview.java.AwtG2D
 
fillPolygon(Object, int[], int[], int) - Method in class jspecview.js2d.JsG2D
 
fillPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
 
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
 
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
 
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
 
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fillRect(Graphics) - Method in class jme.AtomDisplayLabel
 
fillRect(Object, int, int, int, int) - Method in class jspecview.common.PDFWriter
 
fillRect(Object, int, int, int, int) - Method in class jspecview.java.AwtG2D
 
fillRect(Object, int, int, int, int) - Method in class jspecview.js2d.JsG2D
 
fillRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
fillRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
fillRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
fillSphereBits(int, P3) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereBits(int, P3) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereBits(int, P3) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphereI(int, P3i) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillTextRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills background rectangle for label
fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
fills background rectangle for label
fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills background rectangle for label
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.___Exporter
 
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.__CartesianExporter
 
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export._PovrayExporter
 
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export._TachyonExporter
 
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.export.Export3D
 
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.export.Export3D
 
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle3f(P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
 
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.export.Export3D
 
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangles - Variable in class org.jmol.shape.Mesh
 
fillTriangleTwoSided(short, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.export.Export3D
 
fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filter - Static variable in class org.jmol.script.T
 
FILTER_LAST - Static variable in class javajs.img.PngEncoder
 
FILTER_NONE - Static variable in class javajs.img.PngEncoder
Constants for filters
FILTER_SUB - Static variable in class javajs.img.PngEncoder
 
FILTER_UP - Static variable in class javajs.img.PngEncoder
 
filterAllHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterCased - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterCIFAtom(Atom, String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
 
filteredPrecision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
check line for filter options
filterPDBAtom(Atom, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalize() - Method in class com.sparshui.server.GestureServer
 
finalize() - Method in class org.jmol.viewer.Viewer
 
finalizeAromatic(Lst<BS>) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
 
finalizeAtoms(BS, boolean) - Method in class org.jmol.viewer.ShapeManager
 
finalizeHydrogens() - Method in class org.jmol.modelsetbio.BioResolver
 
finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
finalizeMOData(Map<String, Object>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeModelSet() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.
finalizeModelSet() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeModulation() - Method in class org.jmol.adapter.readers.cif.MSRdr
Create a script that will run to turn modulation on and to display only atoms with modulated occupancy >= 0.5.
finalizeModulation() - Method in interface org.jmol.adapter.smarter.MSInterface
 
finalizeObject(int, int, float, int, boolean, Object, int, BS) - Method in class org.jmol.scriptext.ScriptExt
 
finalizeOutput() - Method in interface org.jmol.api.JmolRendererInterface
 
finalizeOutput() - Method in class org.jmol.export.___Exporter
 
finalizeOutput() - Method in class org.jmol.export._IdtfExporter
 
finalizeOutput() - Method in class org.jmol.export._ObjExporter
 
finalizeOutput() - Method in class org.jmol.export._PovrayExporter
 
finalizeOutput() - Method in class org.jmol.export._StlExporter
 
finalizeOutput() - Method in class org.jmol.export.Export3D
 
finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
 
finalizeOutput2() - Method in class org.jmol.export.___Exporter
 
finalizeOutput2() - Method in class org.jmol.export._PovrayExporter
 
finalizeOutput2() - Method in class org.jmol.export._TachyonExporter
 
finalizeReader() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
PRIOR to symmetry application, process all internal symop/translation aspects.
finalizeReaderASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeReaderMR() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
finalizeReaderPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
finalizeRingData() - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
 
finalizeRna3d(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
finalizeStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
 
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.BCIFReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.CifReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.P2nReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.InputReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
Fix connections to Fragments and Nicknames, adjust stereochemistry for wavy displays, flag invalid atoms, and adjust the scale to something more molecular.
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
Set final auxiliary info and symmetry, including "fileHeader", "magresUnits", and "interactionTensors"; note that print getProperty("auxiliaryInfo.models[1].magresUnits") should return a catalog of tensor types.
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
optional reader-specific method run first.
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
 
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
 
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
Symmetry has been applied.
finalizeTrajectoryAs(Lst<P3[]>, Lst<V3[]>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
 
finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
 
finalizeValidations(Viewer, Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
Create property_xxxx for each validation category.
find - Static variable in class org.jmol.script.T
 
find() - Method in class org.jmol.util.PatternMatcher.JSPattern
 
find(double) - Method in class jspecview.common.MeasurementData
 
find(String, int) - Method in class org.jmol.util.CommandHistory
 
find(String, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
 
find(String, String, int) - Method in class org.jmol.smiles.SmilesMatcher
Searches for all matches of a pattern within a SMILES string.
find(Lst<Measurement>, Measurement) - Static method in class org.jmol.modelset.Measurement
 
findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
 
findAtomsInRectangle(Rectangle) - Method in class org.jmol.modelset.ModelSet
 
findAtomsLike(String) - Method in class org.jmol.modelset.Atom
 
findAtomsLike(String) - Method in class org.jmol.smiles.SmilesAtom
 
findAtomsLike(String) - Method in interface org.jmol.util.Node
 
findAxis(P3[], int, P3, V3, V3) - Static method in class javajs.util.Measure
 
findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Have the vwr show a particular frame with frequencies if it can be found.
findLineSeparator(String) - Static method in class jme.JMEUtil
 
findMatchingPeakInfo(PeakInfo) - Method in class jspecview.common.PanelData
 
findMatchingPeakInfo(PeakInfo) - Method in class jspecview.common.Spectrum
 
findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
 
findMonomer(BS, boolean) - Method in class org.jmol.modelsetbio.ProteinStructure
 
findNearest2(int, int, Atom[], BS, int) - Method in class org.jmol.modelset.AtomCollection
 
findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
 
findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
 
findNearestAtomIndex(int, int, BS, int) - Method in class org.jmol.modelset.ModelSet
 
findNearestAtomIndex(int, int, Atom[], short[], int, BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shape.Shape
 
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShape
 
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
findNearestAtomIndexMovable(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
findNearestShapeAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.viewer.ShapeManager
 
findNode(String, int, P3) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
Called from TLink and TAtom to find a node with the given symmetry.
findNode(JSVPanel, Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
Returns the tree node that is associated with a panel
findNodeById(String, Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
 
findPeakByCoord(int, Coordinate) - Method in class jspecview.common.Spectrum
 
findSeparator(String) - Static method in class jme.JMEmol
 
findSourceByNameOrId(String, Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
 
findSpaceGroup(SymmetryInterface, BS, String, float[], T3, T3[], int) - Method in class org.jmol.viewer.Viewer
 
findSpaceGroup(Viewer, BS, String, float[], T3, T3[], int) - Method in interface org.jmol.api.SymmetryInterface
 
findSpaceGroup(Viewer, BS, String, float[], T3, T3[], int) - Method in class org.jmol.symmetry.Symmetry
 
findSpaceGroupFromXYZ(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
findX(Spectrum, double) - Method in class jspecview.common.PanelData
 
FINDX - Enum constant in enum class jspecview.common.ScriptToken
 
findXForPeakNearest(double) - Method in class jspecview.common.Spectrum
 
findXForPeakNearest(Coordinate[], double, boolean) - Static method in class jspecview.common.Coordinate
 
finish() - Method in class com.jcraft.jzlib.Deflater
 
finish() - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
finish(Object) - Method in class org.jmol.api.JmolAdapter
 
FINISH - Static variable in class org.jmol.thread.JmolThread
 
finished() - Method in class com.jcraft.jzlib.Deflater
 
finished() - Method in class com.jcraft.jzlib.Inflater
 
first - Variable in class org.jmol.modelset.TickInfo
 
first - Static variable in class org.jmol.script.T
 
firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
 
firstAtomIndex - Variable in class org.jmol.modelset.Group
 
firstAtomIndex - Variable in class org.jmol.modelset.Model
 
firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
 
firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
 
firstAtomToBond - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
firstChar - Variable in class org.jmol.adapter.readers.cif.CifReader
 
firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
 
firstIsotope - Static variable in class org.jmol.util.Elements
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
firstModelIndex - Variable in class org.jmol.atomdata.AtomData
 
firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
firstX - Variable in class jspecview.export.AMLExporter
 
firstX - Variable in class jspecview.export.CMLExporter
 
firstX - Variable in class jspecview.source.AnIMLReader
 
firstY - Variable in class jspecview.source.AnIMLReader
 
FIX - Enum constant in enum class jspecview.common.ExportType
 
fix2Stereo() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
fixAtoms(int, SV, BS, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
fixAtoms(int, SV, BS, int, int) - Method in class org.jmol.dssx.AnnotationParser
Adjusts _atoms bitset to account for added hydrogen atoms.
fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
 
fixD(float, boolean) - Method in class org.jmol.modelset.BondCollection
 
fixDataString(String) - Static method in class org.jmol.util.Parser
 
fixDOSName(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
fixDOSName(String) - Static method in class org.jmol.viewer.FileManager
Switch \ for / only for DOS names such as C:\temp\t.xyz, not names like http://cactus.nci.nih.gov/chemical/structure/CC/C=C\CC
fixDouble(double, double) - Static method in class javajs.util.PT
 
fixDoubleA(double[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fixDSSRJSONMap(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
 
fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
 
fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
kissingLoops and coaxStacks use index arrays instead of duplication;
fixed - Static variable in class org.jmol.script.T
 
fixedLattice - Variable in class org.jmol.jvxl.data.JvxlData
 
fixedOrigin - Variable in class org.jmol.shape.Axes
 
fixedOriginUC - Variable in class org.jmol.shape.Axes
 
fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationCenter - Variable in class org.jmol.export.___Exporter
 
fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
 
fixedtemp - Static variable in class org.jmol.script.T
 
FIXEDTEMP - Enum constant in enum class org.jmol.c.PAL
 
fixedTranslation - Variable in class org.jmol.viewer.TransformManager
 
fixedValue - Variable in class org.jmol.modelset.Measurement
 
fixedValue - Variable in class org.jmol.modelset.MeasurementData
 
fixFloat(float, double) - Static method in class javajs.util.PT
 
fixFloatA(float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fixFloatPt(P3, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fixFormalCharges(BS) - Method in class org.jmol.modelset.AtomCollection
 
fixIndices(int, int, BS) - Method in class org.jmol.modelset.Model
 
fixIndices(int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
 
fixIndices(int, BS) - Method in class org.jmol.modelset.Group
 
fixIndicesM(int, int, BS) - Method in class org.jmol.modelset.Model
 
fixInlineString(String, char) - Static method in class org.jmol.viewer.Viewer
 
fixJMEFormalCharges(BS, String) - Method in interface org.jmol.api.JmolPropertyManager
 
fixJMEFormalCharges(BS, String) - Method in class org.jmol.viewer.PropertyManager
Fix a JME string returned from NCI CIR to have the proper formal charges.
fixKey(String) - Method in interface javajs.api.GenericCifDataParser
 
fixKey(String) - Method in class javajs.util.CifDataParser
 
fixPropertyValue(BS, Object, boolean) - Method in class org.jmol.modelsetbio.BioResolver
 
fixPtFloats(T3, float) - Static method in class javajs.util.PT
 
fixRadius(float) - Static method in class org.jmol.adapter.readers.pdb.PdbReader
 
fixScreenZ(int) - Method in class org.jmol.export.___Exporter
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
fixTextImageRGB(int) - Static method in class org.jmol.g3d.Graphics3D
 
fixTitle(String) - Static method in class jspecview.dialog.DialogManager
 
fixUnitCell(float[]) - Method in interface org.jmol.api.SymmetryInterface
 
fixUnitCell(float[]) - Method in class org.jmol.symmetry.Symmetry
 
fixUnits(String) - Static method in class org.jmol.modelset.Measurement
 
fixUTF(byte[]) - Static method in class javajs.util.Rdr
 
fixUTF(byte[]) - Static method in class jspecview.common.JSVFileManager
 
fixValue(String, boolean) - Method in class org.jmol.modelset.Measurement
 
fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
flat - Static variable in class org.jmol.script.T
 
FLICK_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
FLICK_EVENT - Static variable in class com.sparshui.GestureType
 
FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
FLICK_GESTURE - Static variable in class com.sparshui.GestureType
 
FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
FlickEvent - Class in com.sparshui.common.messages.events
 
FlickEvent() - Constructor for class com.sparshui.common.messages.events.FlickEvent
 
FlickEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.FlickEvent
Constructs a flickEvent from a complete serialized version of the drag event.
FlickEvent(float, float) - Constructor for class com.sparshui.common.messages.events.FlickEvent
 
FlickEvent(int, int, int) - Constructor for class com.sparshui.common.messages.events.FlickEvent
 
flistValue(T, int) - Static method in class org.jmol.script.SV
 
FLOAT_MIN_SAFE - Static variable in class org.jmol.viewer.JC
 
floatifyJavaDouble - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
floatparam - Static variable in class org.jmol.script.T
 
floatParameter(int) - Method in class org.jmol.script.ScriptParam
 
floatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
 
floatParameterRange(int, float, float) - Method in class org.jmol.script.ScriptParam
 
floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptParam
process a general string or set of parameters as an array of floats, allowing for relatively free form input
floatproperty - Static variable in class org.jmol.script.T
 
floatToByteArray(byte[], int, float) - Static method in class com.sparshui.common.utils.Converter
 
floatToIntBits(float) - Static method in class javajs.util.T3
 
flowCommand - Static variable in class org.jmol.script.T
 
FlowLayout - Class in org.jmol.awtjs.swing
 
FlowLayout() - Constructor for class org.jmol.awtjs.swing.FlowLayout
 
flush() - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
flushBytes() - Method in class javajs.img.GifEncoder
 
flushImage(Object) - Method in class jspecview.java.AwtPlatform
 
flushImage(Object) - Method in class jspecview.js2d.JsPlatform
 
flushImage(Object) - Method in interface org.jmol.api.GenericPlatform
 
flushImage(Object) - Method in class org.jmol.awt.Platform
 
flushImage(Object) - Method in class org.jmol.awtjs2d.Platform
 
fm - Variable in class org.jmol.adapter.readers.spartan.SpartanUtil
 
fm - Variable in class org.jmol.viewer.Viewer
 
fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
foccupancy - Variable in class org.jmol.adapter.smarter.Atom
 
focusGained(FocusEvent) - Method in class jspecview.java.AwtDialogManager
 
focusLost(FocusEvent) - Method in class jspecview.java.AwtDialogManager
 
FoldingXyzReader - Class in org.jmol.adapter.readers.simple
This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
 
font - Variable in class jspecview.common.PrintLayout
The font of the elements
font - Variable in class org.jmol.modelset.Text
 
font - Static variable in class org.jmol.script.T
 
font - Variable in class org.jmol.util.Font
 
Font - Class in org.jmol.util
Provides font support using a int fid (Font ID) as an index into font table.
FONT - Static variable in class org.jmol.shapecgo.CGOMesh
 
FONT_AXES - Static variable in class org.jmol.shapecgo.CGOMesh
 
FONT_FACE_MONO - Static variable in class org.jmol.util.Font
 
FONT_FACE_SANS - Static variable in class org.jmol.util.Font
 
FONT_FACE_SERIF - Static variable in class org.jmol.util.Font
 
FONT_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
 
FONT_STYLE_BOLD - Static variable in class org.jmol.util.Font
 
FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.util.Font
 
FONT_STYLE_ITALIC - Static variable in class org.jmol.util.Font
 
FONT_STYLE_PLAIN - Static variable in class org.jmol.util.Font
 
FONT_VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
 
font3d - Variable in class org.jmol.render.FontLineShapeRenderer
 
font3d - Variable in class org.jmol.shape.FontLineShape
 
font3d - Variable in class org.jmol.shape.Frank
 
font3d - Variable in class org.jmol.shape.Measures
 
fontcaching - Static variable in class org.jmol.script.T
 
fontChild - Variable in class org.jmol.export._VrmlExporter
 
fontFace - Variable in class org.jmol.export._VrmlExporter
 
fontFace - Variable in class org.jmol.util.Font
 
fontID - Variable in class org.jmol.shapespecial.DrawMesh
 
FontLineShape - Class in org.jmol.shape
 
FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
 
FontLineShapeRenderer - Class in org.jmol.render
 
FontLineShapeRenderer() - Constructor for class org.jmol.render.FontLineShapeRenderer
 
FontManager - Interface in org.jmol.api
A generic interface for font queries.
fontScale - Variable in class org.jmol.modelset.Text
 
fontscaling - Static variable in class org.jmol.script.T
 
fontsize - Static variable in class org.jmol.script.T
 
fontSize - Variable in class org.jmol.export._VrmlExporter
 
fontSize - Variable in class org.jmol.util.Font
 
fontSizeNominal - Variable in class org.jmol.util.Font
 
fontStringWidth(Font, String) - Method in class jspecview.java.AwtPlatform
 
fontStringWidth(Font, String) - Method in class jspecview.js2d.JsPlatform
 
fontStringWidth(Font, String) - Method in interface org.jmol.api.FontManager
 
fontStringWidth(Font, String) - Method in class org.jmol.awt.Platform
 
fontStringWidth(Font, String) - Method in class org.jmol.awtjs2d.Platform
 
fontStyle - Variable in class org.jmol.export._VrmlExporter
 
fontStyle - Variable in class org.jmol.util.Font
 
force - Variable in class org.jmol.minimize.MinAtom
 
forceAsyncLoad(String) - Method in class jspecview.java.AwtPlatform
 
forceAsyncLoad(String) - Method in class jspecview.js2d.JsPlatform
 
forceAsyncLoad(String) - Method in interface org.jmol.api.GenericPlatform
 
forceAsyncLoad(String) - Method in class org.jmol.awt.Platform
 
forceAsyncLoad(String) - Method in class org.jmol.awtjs2d.Platform
 
forceautobond - Static variable in class org.jmol.script.T
 
forcefield - Static variable in class org.jmol.script.T
 
ForceField - Class in org.jmol.minimize.forcefield
 
ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
 
ForceFieldMMFF - Class in org.jmol.minimize.forcefield
MMFF94 implementation 5/14/2012 - fully validated for atom types and charges - reasonably well validated for energies (see below) - TODO: add UFF for preliminary/backup calculation
ForceFieldMMFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldMMFF
 
ForceFieldReader - Class in org.jmol.adapter.readers.more
 
ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
 
ForceFieldUFF - Class in org.jmol.minimize.forcefield
 
ForceFieldUFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
 
forceMOPAC - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
forcePacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
forceShowTriangles - Variable in class org.jmol.render.MeshRenderer
 
forceSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
forcmd - Static variable in class org.jmol.script.T
 
FORMAL_CHARGE - Enum constant in enum class org.jmol.c.PAL
 
FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
 
FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
 
FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber invalid input: '<'invalid input: '<' 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
formalcharge - Static variable in class org.jmol.script.T
 
formalCharge - Variable in class org.jmol.adapter.smarter.Atom
 
format - Static variable in class org.jmol.script.T
 
format(SV[], int) - Static method in class org.jmol.script.SV
Accepts arguments from the format() function First argument is a format string.
formatCheck(String) - Static method in class javajs.util.PT
formatCheck checks p and q formats and duplicates if necessary "%10.5p xxxx" ==> "%10.5p%10.5p%10.5p xxxx"
formatD(double, int, int, boolean, boolean) - Static method in class javajs.util.PT
 
formatDecimal(double, int) - Static method in class javajs.util.DF
a simple alternative to DecimalFormat (which Java2Script does not have and which is quite too complex for our use here.)
formatDecimalDbl(double, int) - Static method in class javajs.util.DF
 
formatDecimalTrimmed(double, int) - Static method in class javajs.util.DF
an alternative to DecimalFormat "0.#"
formatDecimalTrimmed0(double, int) - Static method in class javajs.util.DF
an alternative to DecimalFormat "0.0"
formatDistance(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
 
formatExpNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
 
formatF(float, int, int, boolean, boolean) - Static method in class javajs.util.PT
 
formatJ(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
 
formatLabel(Viewer, Atom, String, P3) - Method in class org.jmol.modelset.LabelToken
 
formatLabelAtomArray(Viewer, Atom, LabelToken[], char, int[], P3) - Static method in class org.jmol.modelset.LabelToken
returns a formatted string based on the precompiled label tokens
formatLabelBond(Viewer, Bond, LabelToken[], Map<String, Object>, int[], P3) - Static method in class org.jmol.modelset.LabelToken
 
formatLabelMeasure(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
 
formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
 
formatMeasurementAs(String, String, boolean) - Method in class org.jmol.modelset.Measurement
 
formatNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
 
formats - Variable in class org.jmol.shape.Labels
 
formatS(String, int, int, boolean, boolean) - Static method in class javajs.util.PT
 
formatStringF(String, String, float) - Static method in class javajs.util.PT
 
formatStringI(String, String, int) - Static method in class javajs.util.PT
 
formatStringS(String, String, String) - Static method in class javajs.util.PT
 
formatText(String) - Method in class org.jmol.viewer.Viewer
 
forThermalEllipsoid - Variable in class org.jmol.util.Tensor
 
foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
 
foundDistance2() - Method in class org.jmol.bspt.CubeIterator
After calling nextElement(), allows one to find out the value of the distance squared.
foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
foundDistance2() - Method in class org.jmol.symmetry.UnitCellIterator
 
fourdots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
fps - Static variable in class org.jmol.script.T
 
FRACTIONAL_PRECISION - Static variable in class javajs.util.PT
 
fractionalizeCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fractionalPoint - Variable in class org.jmol.script.ScriptParam
set in getPointOrPlane
fractionalrelative - Static variable in class org.jmol.script.T
 
fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
fracx - Static variable in class org.jmol.script.T
 
fracxyz - Static variable in class org.jmol.script.T
 
fracy - Static variable in class org.jmol.script.T
 
fracz - Static variable in class org.jmol.script.T
 
frame - Static variable in class org.jmol.script.T
 
frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
frameCounter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
FrameCounter - Class in org.openscience.jmol.app.janocchio
 
FrameCounter(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameCounter
Constructor
frameDelay - Variable in class org.jmol.modelset.Model
 
frameDeltaDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
FrameDeltaDisplay - Class in org.openscience.jmol.app.janocchio
 
FrameDeltaDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
Constructor
frameTitle - Variable in class jspecview.common.PanelNode
 
frameTitles - Variable in class org.jmol.modelset.ModelSet
 
frank - Static variable in class org.jmol.script.T
 
Frank - Class in org.jmol.shape
 
Frank() - Constructor for class org.jmol.shape.Frank
 
frankAscent - Variable in class org.jmol.shape.Frank
 
frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
 
frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
 
frankDescent - Variable in class org.jmol.shape.Frank
 
frankMargin - Static variable in class org.jmol.shape.Frank
 
frankOn - Variable in class org.jmol.viewer.Viewer
 
frankPopup - Variable in class org.jmol.popup.JmolGenericPopup
 
FrankRenderer - Class in org.jmol.render
 
FrankRenderer() - Constructor for class org.jmol.render.FrankRenderer
 
frankString - Static variable in class org.jmol.shape.Frank
 
frankWidth - Variable in class org.jmol.shape.Frank
 
freeBonds - Variable in class org.jmol.modelset.BondCollection
 
freeTempEnum(STR[]) - Method in class org.jmol.util.TempArray
 
freeTempEnum(STR[]) - Method in class org.jmol.viewer.Viewer
 
freeTempPoints(P3[]) - Method in class org.jmol.util.TempArray
 
freeTempPoints(P3[]) - Method in class org.jmol.viewer.Viewer
 
freeTempScreens(P3i[]) - Method in class org.jmol.util.TempArray
 
freeTempScreens(P3i[]) - Method in class org.jmol.viewer.Viewer
 
freeze() - Method in class org.jmol.modelset.Model
 
freeze() - Method in class org.jmol.modelsetbio.BioModel
 
freezeM() - Method in class org.jmol.modelset.Model
 
freq2dX - Variable in class jspecview.source.JDXDataObject
 
freq2dY - Variable in class jspecview.source.JDXDataObject
 
fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
FRIENDLY - Static variable in class org.jmol.util.ColorEncoder
 
from - Static variable in class org.jmol.script.T
 
from3D() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
fromASC(AtomSetCollection) - Static method in class org.jmol.adapter.writers.CDXMLWriter
 
fromCDX(GenericBinaryDocument) - Static method in class org.jmol.adapter.writers.CDXMLWriter
 
fromOABC(T3[], boolean) - Static method in class org.jmol.symmetry.UnitCell
A special constructor for spacially defined unit cells.
fromParams(float[], boolean, float) - Static method in class org.jmol.symmetry.UnitCell
 
fromString(Viewer, String, String) - Static method in class org.jmol.adapter.writers.CDXMLWriter
 
fromUnits(float, String) - Static method in class org.jmol.modelset.Measurement
 
front - Static variable in class org.jmol.script.T
 
frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
frontedges - Static variable in class org.jmol.script.T
 
frontlit - Static variable in class org.jmol.script.T
 
frontonly - Static variable in class org.jmol.script.T
 
frontOnly - Variable in class org.jmol.render.MeshRenderer
 
frontOnly - Variable in class org.jmol.shape.Mesh
 
FS - Static variable in class org.jmol.quantum.QS
 
fScrPt - Variable in class org.jmol.viewer.TransformManager
 
fslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
 
full - Static variable in class org.jmol.script.T
 
fullAtomWidthLabel - Variable in class jme.AtomDisplayLabel
 
fullCommand - Variable in class org.jmol.script.ScriptEval
 
fullCubeCorners - Static variable in class org.jmol.util.Triangulator
For each corner 0-7: {c c c t} where c c c are the connected corners, arranged clockwise and t is the bitset of triangles associated with faces intersecting at this corner.
fullCubePolygon - Static variable in class org.jmol.util.Triangulator
 
fullName - Variable in class jspecview.common.JSViewer
 
fullName - Variable in class org.jmol.util.GenericApplet
 
fullName - Variable in class org.jmol.viewer.Viewer
 
fullplane - Static variable in class org.jmol.script.T
 
fullTrim(Object) - Static method in class org.jmol.adapter.readers.cif.CifReader
 
fullTrim(String) - Method in interface javajs.api.GenericCifDataParser
 
fullTrim(String) - Method in class javajs.util.CifDataParser
Used especially for data that might be multi-line data that might have unwanted white space at start or end.
fullylit - Static variable in class org.jmol.script.T
 
fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
 
func - Variable in class org.jmol.jvxl.readers.Parameters
 
function - Static variable in class org.jmol.script.T
 
functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
 
functionName - Variable in class org.jmol.script.ScriptContext
 
functionName - Variable in class org.jmol.script.ScriptEval
 
functionxy - Static variable in class org.jmol.script.T
 
functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
for isosurface FUNCTIONXY
functionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
 
functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
fills an array with data -- if nX invalid input: '<' 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
functionXY(String, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
this is just a test method for isosurface FUNCTIONXY
functionxyz - Static variable in class org.jmol.script.T
 
functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
for isosurface FUNCTIONXYZ
functionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
 
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
 
functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
fux - Static variable in class org.jmol.script.T
 
fuxyz - Static variable in class org.jmol.script.T
 
fuy - Static variable in class org.jmol.script.T
 
fuz - Static variable in class org.jmol.script.T
 
fVal(String) - Static method in class javajs.util.PT
 
fValue(T) - Static method in class org.jmol.script.SV
 

G

g - Variable in class org.jmol.util.Rgb16
 
g - Variable in class org.jmol.viewer.Viewer
 
g(String) - Method in class javajs.export.PDFCreator
 
G_SIZE - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
g2d - Variable in class jspecview.common.JSViewer
 
g2d - Variable in class jspecview.common.PanelData
 
g2d0 - Variable in class jspecview.common.PanelData
 
g3d - Variable in class org.jmol.modelset.AtomCollection
 
g3d - Variable in class org.jmol.render.ShapeRenderer
could be vwr.gdata or an exporter
G3DRenderer - Interface in org.jmol.g3d
 
GamessReader - Class in org.jmol.adapter.readers.quantum
 
GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
 
GamessUKReader - Class in org.jmol.adapter.readers.quantum
 
GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
 
GamessUSReader - Class in org.jmol.adapter.readers.quantum
 
GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
 
gamma - Variable in class org.jmol.util.SimpleUnitCell
 
gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
GaussianAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
 
gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
 
GaussianDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
GaussianFchkReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
GaussianFchkReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
 
GaussianReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian 94/98/03/09 output files.
GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
 
gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
gaussians - Variable in class org.jmol.quantum.MOCalculation
 
GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian Wfn files -- not implemented yet
GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
 
GC - Static variable in class org.jmol.quantum.QS
 
gdata - Variable in class org.jmol.export.___Exporter
 
gdata - Variable in class org.jmol.viewer.Viewer
 
GData - Class in org.jmol.util
 
GData() - Constructor for class org.jmol.util.GData
It is possible to instantiate this class with no Graphics3D.
generate() - Method in class javajs.img.GifEncoder
 
generate() - Method in class javajs.img.ImageEncoder
 
generate() - Method in class javajs.img.Jpg64Encoder
 
generate() - Method in class javajs.img.JpgEncoder
 
generate() - Method in class javajs.img.PdfEncoder
 
generate() - Method in class javajs.img.PngEncoder
 
generate() - Method in class javajs.img.PpmEncoder
 
generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
generateCrystalClass(int, P3) - Method in class org.jmol.modelset.AtomCollection
 
generateCrystalClass(P3) - Method in interface org.jmol.api.SymmetryInterface
 
generateCrystalClass(P3) - Method in class org.jmol.symmetry.Symmetry
 
generateOutputForExport(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
for POV-Ray
generateOutputForExport(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
generatePrimes(int) - Static method in class jme.JMEUtil
 
generateScene(Map<String, Object>) - Method in interface org.jmol.api.JmolSceneGenerator
 
GenericApplet - Class in org.jmol.util
A collection of all methods necessary for initialization of and communication with the applet.
GenericApplet() - Constructor for class org.jmol.util.GenericApplet
 
GenericBinaryDocument - Interface in javajs.api
 
GenericBinaryDocumentReader - Interface in javajs.api
 
GenericCifDataParser - Interface in javajs.api
 
GenericColor - Interface in javajs.api
GenericColor allows both java.awt.Color and org.jmol.awtjs.swing.Color to be handled by methods that need not distinguish between them.
GenericConsole - Class in org.jmol.console
 
GenericConsole() - Constructor for class org.jmol.console.GenericConsole
 
GenericConsoleTextArea - Interface in org.jmol.api.js
 
GenericFileInterface - Interface in org.jmol.api
 
GenericGraphics - Interface in org.jmol.api
 
GenericImageDialog - Interface in org.jmol.api
 
GenericImageEncoder - Interface in javajs.api
 
GenericLineReader - Interface in javajs.api
 
GenericMenuInterface - Interface in org.jmol.api
 
GenericMouse - Class in jspecview.app
 
GenericMouse(JSVPanel) - Constructor for class jspecview.app.GenericMouse
 
GenericMouseInterface - Interface in org.jmol.api
 
GenericOutputChannel - Interface in javajs.api
 
GenericPlatform - Interface in org.jmol.api
 
GenericPopup - Class in org.jmol.popup
The overall parent of all popup classes in Jmol and JSmol.
GenericPopup() - Constructor for class org.jmol.popup.GenericPopup
 
GenericTextArea - Interface in org.jmol.console
 
GenericZipInputStream - Class in javajs.api
 
GenericZipInputStream(InputStream) - Constructor for class javajs.api.GenericZipInputStream
 
GenericZipTools - Interface in javajs.api
Class abandoned as unnecessary in SwingJS
GenNBOReader - Class in org.jmol.adapter.readers.quantum
NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structure
GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
 
Geodesic - Class in org.jmol.util
J2SRequireImport is needed because we use ArrayUtil in a static method
Geodesic() - Constructor for class org.jmol.util.Geodesic
 
geosurface - Static variable in class org.jmol.script.T
 
GeoSurface - Class in org.jmol.shapespecial
 
GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
 
GeoSurfaceRenderer - Class in org.jmol.renderspecial
 
GeoSurfaceRenderer() - Constructor for class org.jmol.renderspecial.GeoSurfaceRenderer
 
Gesture - Interface in com.sparshui.gestures
Defines the interface that all user-defined gestures must implement.
GestureServer - Class in com.sparshui.server
The main gesture server class.
GestureServer() - Constructor for class com.sparshui.server.GestureServer
 
GestureServer(int, GestureServer) - Constructor for class com.sparshui.server.GestureServer
 
gestureswipefactor - Static variable in class org.jmol.script.T
 
GestureType - Class in com.sparshui
This class is a place for the enum GestureType to stand.
GestureType(int) - Constructor for class com.sparshui.GestureType
 
GestureType(String) - Constructor for class com.sparshui.GestureType
 
get(int) - Method in class javajs.util.BS
Returns the value of the bit with the specified index.
get(int) - Method in class org.jmol.util.Int2IntHash
 
get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
GET_ALLOWED_GESTURES - Static variable in class com.sparshui.common.ClientProtocol.MessageType
 
GET_GROUP_ID - Static variable in class com.sparshui.common.ClientProtocol.MessageType
 
get1(int) - Static method in class org.jmol.awtjs.swing.Color
 
get2SidedNormix(V3, BS) - Static method in class org.jmol.util.Normix
 
get3(int, int, int) - Method in class jspecview.java.AwtColor
 
get3(int, int, int) - Method in class org.jmol.awt.AwtColor
 
get3(int, int, int) - Static method in class org.jmol.awtjs.swing.Color
 
get33(int, int) - Method in class javajs.util.M34
 
get3dProjection(V3) - Method in class javajs.util.Quat
 
get4(int, int, int, int) - Method in class jspecview.java.AwtColor
 
get4(int, int, int, int) - Method in class org.jmol.awt.AwtColor
 
get4(int, int, int, int) - Static method in class org.jmol.awtjs.swing.Color
 
getAbbrSimulationFileName(String) - Static method in class jspecview.common.JSVFileManager
In the case of applet-based simulations with file names that involve mol=..., we want to abbreviate those names for display
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Fetch the action that was created for the given command.
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
getActionCommand() - Method in interface org.jmol.api.SC
 
getActionCommand() - Method in class org.jmol.awt.AwtSwingComponent
 
getActionCommand() - Method in class org.jmol.awtjs.swing.JComponent
 
getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
 
getActionName(int) - Static method in class org.jmol.viewer.ActionManager
 
getActiveMenu() - Method in class org.jmol.modelkit.ModelKit
for the thin box on the top left of the window
getAdditionalHydrogens(BS, Lst<Atom>, int) - Method in class org.jmol.viewer.Viewer
 
getAdditionalOperations() - Method in interface org.jmol.api.SymmetryInterface
 
getAdditionalOperations() - Method in class org.jmol.symmetry.Symmetry
 
getAdditionalOperations(SymmetryOperation[]) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getAdditionalOperationsCount() - Method in interface org.jmol.api.SymmetryInterface
 
getAdditionalOperationsCount() - Method in class org.jmol.symmetry.Symmetry
 
getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
 
getAlignment(int) - Static method in class org.jmol.viewer.JC
 
getAllAtomInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getAllAtoms() - Method in class org.jmol.viewer.Viewer
 
getAllAtomTensors(String) - Method in class org.jmol.modelset.AtomCollection
 
getAllBondInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getAllChainInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getAllChimeInfo(SB) - Method in class org.jmol.viewer.ChimeMessenger
 
getAllChimeInfo(SB) - Method in interface org.jmol.viewer.JmolChimeMessenger
 
getAllCifData() - Method in interface javajs.api.GenericCifDataParser
 
getAllCifData() - Method in class javajs.util.CifDataParser
Parses all CIF data for a reader defined in the constructor into a standard Map structure and close the BufferedReader if it exists.
getAllCifDataType(String...) - Method in class javajs.util.CifDataParser
 
getAllData() - Method in class javajs.util.CompoundDocument
 
getAllDataFiles(String, String) - Method in interface javajs.api.GenericBinaryDocument
 
getAllDataFiles(String, String) - Method in class javajs.util.BinaryDocument
 
getAllDataFiles(String, String) - Method in class javajs.util.CompoundDocument
 
getAllDataMapped(String, String, Map<String, String>) - Method in interface javajs.api.GenericBinaryDocument
 
getAllDataMapped(String, String, Map<String, String>) - Method in class javajs.util.BinaryDocument
 
getAllDataMapped(String, String, Map<String, String>) - Method in class javajs.util.CompoundDocument
reads a compound document directory and saves all data in a Hashtable so that the files may be organized later in a different order.
getAllDefaultStructures(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAlleneAtoms(boolean, SmilesAtom, SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
 
getAllHeteroList(int) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAllOperators() - Method in class org.jmol.modelkit.ModelKit
 
getAllowedGestures(int) - Method in interface com.sparshui.client.SparshClient
This method must return the allowed Gestures for the specified group.
getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
 
getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
getAllowJSThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getAllowJSThreads() - Method in class org.jmol.script.ScriptEval
 
getAllPoints(int, int) - Method in class org.jmol.scriptext.ScriptExt
 
getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAllPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
 
getAllSequenceBits(String, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAllSettings(String) - Method in class org.jmol.viewer.Viewer
 
getAllStructures(String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
 
getAllZipData(InputStream, String[], String, String, String, Map<String, String>) - Method in interface javajs.api.GenericZipTools
 
getAllZipData(InputStream, String[], String, String, String, Map<String, String>) - Method in class javajs.util.ZipTools
Deprecated.
getAltLoc() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
 
getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getAmbientPercent() - Method in class org.jmol.util.GData
 
getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
 
getAndRegisterPlugin(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getAndSetNewVariable(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
 
getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
 
getAngles() - Method in class org.jmol.minimize.Minimizer
 
getAnnotationInfo(SV, String, int) - Method in class org.jmol.viewer.Viewer
 
getAnnotationInfo(Viewer, SV, String, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
getAnnotationInfo(Viewer, SV, String, int, int) - Method in class org.jmol.dssx.AnnotationParser
Get a string report of annotation data
getAnnotationParser(boolean) - Method in class org.jmol.viewer.Viewer
 
getApiPlatform() - Method in interface jspecview.api.JSVPanel
 
getApiPlatform() - Method in class jspecview.java.AwtPanel
 
getApiPlatform() - Method in class jspecview.js2d.JsPanel
 
getApp() - Method in interface jspecview.api.AppletFrame
 
getApp() - Method in class jspecview.appletjs.JSVApplet
 
getApplet() - Method in class jspecview.common.JSViewer
 
getAppletFrame() - Method in class jspecview.app.JSVApp
 
getAppletInfo() - Method in interface jspecview.api.AppletFrame
 
getAppletInfo() - Static method in class jspecview.app.JSVApp
 
getAppletInfo() - Method in class jspecview.appletjs.JSVApplet
Get Applet information
getAppletInfo() - Method in class jspecview.appletjs.JSVAppletPro
 
getAppletInfo() - Method in interface org.jmol.api.JmolAppletInterface
 
getAppletInfo() - Method in class org.jmol.util.GenericApplet
 
getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getArgb() - Method in class org.jmol.util.Rgb16
 
getArgb(float) - Method in class org.jmol.util.ColorEncoder
 
getArgb(short) - Static method in class org.jmol.util.C
 
getArgbFromPalette(float, float, float, int) - Method in class org.jmol.util.ColorEncoder
 
getArgbFromString(String) - Static method in class javajs.util.CU
accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or [red,green,blue] or a valid JavaScript color
getArgbGreyscale(short) - Static method in class org.jmol.util.C
 
getArgbHbondType(int) - Static method in class org.jmol.util.Edge
 
getArgbMinMax(float, float, float) - Method in class org.jmol.util.ColorEncoder
 
getArgbParam(int) - Method in class org.jmol.script.ScriptParam
 
getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptParam
 
getArgbParamOrNone(int, boolean) - Method in class org.jmol.script.ScriptParam
 
getArgbs(int) - Method in class org.jmol.modelsetbio.BioResolver
 
getArray() - Method in class javajs.util.Matrix
Access the internal two-dimensional array.
getArrayCopy() - Method in class javajs.util.Matrix
Copy the internal two-dimensional array.
getArrayDepth(T) - Static method in class org.jmol.script.SV
 
getArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
turn "[1,2,3]" into [1.0,2.0,3.0] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
getAscent() - Method in class org.jmol.util.Font
 
getAsciiFileOrNull(String) - Method in class org.jmol.viewer.Viewer
 
getAssocArray(int) - Method in class org.jmol.script.ScriptEval
 
getAssociatedAtoms(ModelSet) - Method in class org.jmol.modelset.BondSet
 
getAssociatedPeakInfo(int, Coordinate) - Method in class jspecview.common.Spectrum
 
getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtom(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtom(int) - Method in class org.jmol.modelset.Bond
 
getAtom(int) - Method in class org.jmol.modelset.Measurement
 
getAtom(int) - Method in class org.jmol.smiles.SmilesBond
 
getAtom(int) - Method in interface org.jmol.util.SimpleEdge
Get the respective atom, 0 or 1
getAtom1() - Method in class org.jmol.smiles.SmilesBond
 
getAtomAt(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getAtomBits(int, Object) - Method in class org.jmol.script.ScriptEval
 
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in interface org.jmol.api.JmolAnnotationParser
 
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.AnnotationParser
 
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.DSSR1
 
getAtomBitsBS(int, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAtomBitSet(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
 
getAtomBitSet(Object) - Method in class org.jmol.script.ScriptEval
A general method to evaluate a string representing an atom set.
getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in interface org.jmol.api.JmolScriptManager
 
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.script.ScriptManager
 
getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelSet
 
getAtomBitsMDa(int, Object, BS) - Method in class org.jmol.modelset.AtomCollection
general unqualified lookup of atom set type
getAtomBitsMDb(int, Object) - Method in class org.jmol.modelset.BondCollection
 
getAtomBitsStr(int, String, BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
getAtomCIPChiralityCode(Atom) - Method in class org.jmol.modelset.ModelSet
Determine the Cahn-Ingold-Prelog R/S chirality of an atom
getAtomCount() - Method in class jme.JMEmol
 
getAtomCount() - Method in class org.jmol.modelset.ModelLoader
 
getAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getAtomCount(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomCount(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the number of atoms contained in the file.
getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getAtomData(String, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
getAtomData(String, String, boolean) - Method in class org.jmol.viewer.PropertyManager
use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.
getAtomDefs(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
getAtomFromName(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
 
getAtomFromName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
 
getAtomGroupQuaternions(BS, int) - Method in class org.jmol.viewer.Viewer
 
getAtomGroupQuaternions(BS, int, char) - Method in class org.jmol.modelset.ModelSet
 
getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.Node
 
getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
 
getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
 
getAtomicDSSRData(float[], String) - Method in class org.jmol.modelsetbio.BioModel
 
getAtomicDSSRData(int) - Method in class org.jmol.modelset.ModelSet
 
getAtomicDSSRData(ModelSet, int, float[], String) - Method in interface org.jmol.api.JmolAnnotationParser
 
getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.AnnotationParser
 
getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.DSSR1
 
getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
Returns the atomic mass of the atom.
getAtomicMass(int) - Static method in class org.jmol.util.Elements
 
getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
 
getAtomIdentityInfo(int, Map<String, Object>, P3) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
 
getAtomIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomIndex(String, int) - Method in class org.jmol.modelset.Group
 
getAtomIndex(String, int) - Method in class org.jmol.modelsetbio.Monomer
 
getAtomIndex1() - Method in class org.jmol.modelset.Bond
 
getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
 
getAtomIndex1() - Method in class org.jmol.util.Edge
 
getAtomIndex2() - Method in class org.jmol.modelset.Bond
 
getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
 
getAtomIndex2() - Method in class org.jmol.util.Edge
 
getAtomIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getAtomIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getAtomIndices(BS) - Method in class org.jmol.modelset.AtomCollection
 
getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
 
getAtomInfo(int, String, P3) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get an AtomIterator for retrieval of all atoms in the file.
getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
getAtomName() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAtomName() - Method in class org.jmol.modelset.Atom
 
getAtomName() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomName() - Method in interface org.jmol.util.Node
 
getAtomName() - Method in interface org.jmol.util.SimpleNode
 
getAtomName(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getAtomNumber() - Method in class org.jmol.modelset.Atom
 
getAtomNumber() - Method in class org.jmol.smiles.SmilesAtom
Returns the Jmol atom number
getAtomNumber() - Method in interface org.jmol.util.Node
 
getAtomNumber(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
 
getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtomPointVector(BS) - Method in class org.jmol.modelset.AtomCollection
 
getAtomPropertiesLike(String) - Static method in class org.jmol.script.T
 
getAtoms() - Method in class jspecview.common.PeakInfo
 
getAtoms(int, Object) - Method in class org.jmol.modelset.ModelSet
general lookup for integer type -- from Eval
getAtoms(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getAtoms(String) - Method in class org.jmol.smiles.SmilesMatcher
 
getAtomsConnected(float, float, int, BS) - Method in class org.jmol.modelset.BondCollection
 
getAtomSetAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAtomIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for a particular atomSet.
getAtomSetAuxiliaryInfoValue(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetBondCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCenter(BS) - Method in class org.jmol.modelset.ModelSet
 
getAtomSetCollection() - Method in interface org.jmol.api.JmolFilesReaderInterface
 
getAtomSetCollection() - Method in class org.jmol.io.FileReader
 
getAtomSetCollection() - Method in class org.jmol.io.FilesReader
 
getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Create the AtomSetCollection and return it
getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for this atomSetCollection.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Direct DOM HTML4 page reading; Egon was interested in this at one point.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionFromReaderType(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
all in one -- for TestSmarterJmolAdapter
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
Get the name of the atom set collection, if known.
getAtomSetCollectionOrBufferedReaderFromZip(Viewer, InputStream, String, String[], Map<String, Object>, int, boolean) - Method in class org.jmol.io.JmolUtil
A rather complicated means of reading a ZIP file, which could be a single file, or it could be a manifest-organized file, or it could be a Spartan directory.
getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
Read an atomSetCollection object from a bufferedReader and close the reader.
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.api.JmolAdapter
Associate an atomSetCollection object with an array of BufferedReader.
getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
Get number of atomSets in the file or specific model index in file
getAtomSetIndex() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the name of an atomSet.
getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the number identifying each atomSet.
getAtomsFromAtomNumberInFrame(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.JmolStateCreator
 
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.StateCreator
 
getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
 
getAtomsInFrame(BS) - Method in class org.jmol.modelset.AtomCollection
 
getAtomSite() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAtomSite() - Method in class org.jmol.modelset.Atom
 
getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomSite() - Method in interface org.jmol.util.Node
 
getAtomsNearPlane(float, P4) - Method in class org.jmol.modelset.AtomCollection
 
getAtomsNearPt(float, P3, BS) - Method in class org.jmol.viewer.Viewer
 
getAtomsStartingAt(int) - Method in class org.jmol.script.ScriptParam
 
getAtomsWithin(float, T3, BS, int) - Method in class org.jmol.modelset.ModelSet
 
getAtomsWithinRadius(float, BS, boolean, RadiusData, BS) - Method in class org.jmol.modelset.ModelSet
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
getAtomSymmetry(Atom, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.readers.cif.MSRdr
When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.
getAtomSymmetry(Atom, XtalSymmetry.FileSymmetry) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getAtomTensor(int, String) - Method in class org.jmol.modelset.AtomCollection
 
getAtomTensorList(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomType() - Method in class org.jmol.modelset.Atom
 
getAtomType() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomType() - Method in interface org.jmol.util.Node
 
getAtomTypeDescriptions() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getAtomTypeDescs(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
 
getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getAtomValidation(String, Atom) - Method in class org.jmol.viewer.Viewer
 
getAtomValidation(Viewer, String, Atom) - Method in interface org.jmol.api.JmolAnnotationParser
 
getAtomValidation(Viewer, String, Atom) - Method in class org.jmol.dssx.AnnotationParser
Get all validation values corresponding to a specific validation type.
getAtropicStereoFlag(Node[]) - Static method in class org.jmol.smiles.SmilesStereo
 
getAtropismNode(int, Node, boolean) - Static method in class org.jmol.util.Edge
 
getAtropismOrder(int, int) - Static method in class org.jmol.util.Edge
 
getAtropismOrder12(int) - Static method in class org.jmol.util.Edge
 
getAtropisomerKeys(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
called by SmilesParser to get nn in ^nn- base on match to actual structure
getAttachedAtomForPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.
getAttribute(String, String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
getAttribute(String, String) - Method in class org.jmol.jsv.JDXMOLParser
 
getAttributeList() - Method in class jspecview.source.XMLParser
 
getAttrValue(String) - Method in class jspecview.source.XMLParser
 
getAttrValueLC(String) - Method in class jspecview.source.XMLParser
 
getAType() - Method in interface jspecview.api.AnnotationData
 
getAType() - Method in class jspecview.common.MeasurementData
 
getAType() - Method in class jspecview.dialog.JSVDialog
 
getAvailIn() - Method in class com.jcraft.jzlib.InflaterInputStream
 
getAvailIn() - Method in class com.jcraft.jzlib.ZStream
 
getAverageAtomPoint() - Method in class org.jmol.modelset.ModelSet
 
getAxesState(SB) - Method in class org.jmol.shape.Axes
 
getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getAxisLabel(boolean) - Method in class jspecview.common.Spectrum
checks in order: (1) Peaks tag attribute xUnits/yUnits, then (2) ##XLABEL/##YLABEL, then (3) ##XUNITS/##YUNITS
getAxisPoint(int, boolean, P3) - Method in class org.jmol.shape.Axes
get actual point or 1/2 vector from origin to this point
getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
 
getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
 
getBackgroundColor() - Method in class jspecview.java.AwtPanel
 
getBase64() - Method in class javajs.util.OC
 
getBase64(byte[]) - Static method in class javajs.util.Base64
 
getBaseModelBitSet() - Method in class org.jmol.viewer.Viewer
 
getBaseModelIndex(int) - Method in interface org.jmol.api.JmolJSpecView
 
getBaseModelIndex(int) - Method in class org.jmol.jsv.JSpecView
 
getBasePairs() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getBasePairs(Viewer, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
getBasePairs(Viewer, int) - Method in class org.jmol.dssx.AnnotationParser
 
getBasePairs(Viewer, int) - Method in class org.jmol.dssx.DSSR1
 
getBasePeakInfo() - Method in class jspecview.common.Spectrum
 
getBaseRing6Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getBaseSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
Get the symmetry that was in place prior to any supercell business.
getBasisAtom(int) - Method in class org.jmol.modelkit.ModelKit
 
getBasisAtom(int, boolean) - Method in class org.jmol.modelset.ModelSet
 
getBBoxVertices() - Method in class org.jmol.modelset.ModelSet
 
getBestLineThroughPoints(P3[], int) - Static method in class javajs.util.Measure
Get the endpoints of the best line through N points, where N >= 2
getBfactor() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getBfactor100() - Method in class org.jmol.modelset.Atom
 
getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
 
getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
 
getBFactors() - Method in class org.jmol.modelset.AtomCollection
 
getBgContrast(int) - Static method in class org.jmol.util.C
 
getBinaryType(InputStream) - Static method in class org.jmol.adapter.smarter.Resolver
 
getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
 
getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
 
getBindingInfo(String[], String[], String) - Method in class org.jmol.viewer.binding.Binding
 
getBindings() - Method in class org.jmol.viewer.binding.Binding
 
getBioBranches(Lst<BS>) - Method in class org.jmol.modelsetbio.BioModel
 
getBioModel(int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelsetbio.BioResolver
 
getBioModelSet(ModelSet) - Method in class org.jmol.modelsetbio.BioResolver
 
getBioPolymerCount() - Method in class org.jmol.modelsetbio.BioModel
 
getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getBioPolymerCountInModel(int) - Method in class org.jmol.modelsetbio.BioModelSet
 
getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
 
getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
 
getBioPolymerLength() - Method in class org.jmol.modelset.Group
 
getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
 
getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
 
getBioSmiles(BS) - Method in class org.jmol.viewer.Viewer
 
getBioSmilesType() - Method in class org.jmol.modelset.Atom
 
getBioSmilesType() - Method in class org.jmol.smiles.SmilesAtom
 
getBioSmilesType() - Method in interface org.jmol.util.Node
 
getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
 
getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
 
getBioStructureTypeName() - Method in interface org.jmol.util.Node
 
getBioStructureTypeName(boolean) - Method in enum class org.jmol.c.STR
 
getBIS(byte[]) - Static method in class javajs.util.Rdr
 
getBisectingPlane(P3, V3, T3, V3, P4) - Static method in class javajs.util.Measure
 
getBitSet() - Method in class jspecview.common.IntegralData
 
getBitSet(SV, boolean) - Static method in class org.jmol.script.SV
 
getBitSetForMF(Atom[], BS, String) - Static method in class org.jmol.util.JmolMolecule
 
getBitsetIdent(BS, String, Object, boolean, int, boolean) - Method in class org.jmol.scriptext.CmdExt
 
getBitsetIdentFull(BS, String, boolean, int, boolean, String[]) - Method in class org.jmol.scriptext.CmdExt
 
getBitsetProperty(BS, Lst<SV>, int, P3, P4, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptEval
 
getBitsetPropertyFloat(BS, int, String, float, float) - Method in class org.jmol.scriptext.CmdExt
 
getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
 
getBond(int) - Method in class org.jmol.smiles.SmilesAtom
Returns the bond at index number.
getBond(Atom) - Method in class org.jmol.modelset.Atom
 
getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
 
getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
 
getBondCount() - Method in class jme.JMEmol
 
getBondCount() - Method in class org.jmol.modelset.Atom
 
getBondCount() - Method in class org.jmol.modelset.Model
 
getBondCount() - Method in class org.jmol.smiles.SmilesAtom
 
getBondCount() - Method in interface org.jmol.util.SimpleNode
Get the total number of bonds, including hydrogen bonds.
getBondCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
for general use
getBondCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
 
getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
 
getBondedAtomIndex(int) - Method in interface org.jmol.util.Node
 
getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
 
getBondIndex(int) - Method in class org.jmol.minimize.MinAtom
 
getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
 
getBondingRadii() - Method in class org.jmol.modelset.AtomCollection
 
getBondingRadius() - Method in class org.jmol.modelset.Atom
 
getBondingRadius(int, int) - Static method in class org.jmol.api.JmolAdapter
 
getBondingRadius(int, int) - Static method in class org.jmol.util.Elements
This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two.
getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a BondIterator for retrieval of all bonds in the file.
getBondIterator(BS) - Method in class org.jmol.modelset.BondCollection
 
getBondIteratorForType(int, BS) - Method in class org.jmol.modelset.BondCollection
 
getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
 
getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getBondList(Object) - Method in class org.jmol.api.JmolAdapter
 
getBondOrder(String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
getBondOrderFromFloat(float) - Static method in class org.jmol.util.Edge
 
getBondOrderFromString(String) - Static method in class org.jmol.util.Edge
Encode name such as 1 2 3 2.1 3.1 single double triple atropisomer_12 or "partial 1.3"
getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.Edge
 
getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.Edge
used for formatting labels and in the connect PARTIAL command
getBondPickingMode() - Method in class org.jmol.viewer.ActionManager
 
getBondProperties(int) - Method in class jme.JMEmol
 
getBondRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getBondsForSelectedAtoms(BS) - Method in class org.jmol.viewer.Viewer
 
getBondsForSelectedAtoms(BS, boolean) - Method in class org.jmol.modelset.BondCollection
 
getBondTo(int) - Method in class org.jmol.minimize.MinAtom
 
getBondType() - Method in class org.jmol.util.Edge
 
getBondType() - Method in interface org.jmol.util.SimpleEdge
Get the order of the bond.
getBoolean(boolean) - Static method in class org.jmol.script.SV
 
getBoolean(int) - Method in class org.jmol.api.JmolViewer
 
getBoolean(int) - Method in class org.jmol.viewer.Viewer
 
getBoolean(ScriptToken) - Method in class jspecview.common.PanelData
 
getBoolean(ScriptToken) - Method in class jspecview.common.Parameters
 
getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
 
getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
 
getBooleans() - Method in class jspecview.common.Parameters
 
getBooleanValue(String, boolean) - Method in class org.jmol.util.GenericApplet
 
getBoolName(int) - Static method in class org.jmol.viewer.JC
 
getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
 
getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxCornerVector() - Method in class org.jmol.api.JmolViewer
 
getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxOrientation(int, BS, P3[]) - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
Return basic info on boundbox in the form of an array.
getBoundBoxVertices() - Method in class org.jmol.util.BoxInfo
 
getBoundingBox() - Method in class org.jmol.shape.Mesh
 
getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getBox(int) - Method in class org.jmol.shape.Labels
 
getBoxFacesFromOABC(P3[]) - Static method in class org.jmol.util.BoxInfo
 
getBoxInfo() - Method in class org.jmol.modelset.ModelSet
 
getBoxInfo(BS, float) - Method in class org.jmol.modelset.ModelSet
 
getBR(String) - Static method in class javajs.util.Rdr
 
getBranchBitSet(int, int, boolean) - Method in class org.jmol.viewer.Viewer
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.
getBranchBitSet(Node[], int, BS, Lst<BS>, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.
getBranchesForInversion(Node[], int, BS) - Static method in class org.jmol.util.JmolMolecule
 
getBSAll() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getBSAll() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getBSAtoms(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Create bsAtoms if it is null, and set bits if desired.
getBsBranches(float[]) - Method in class org.jmol.modelset.ModelSet
 
getBSSideChain() - Method in class org.jmol.modelset.Group
 
getBSSideChain() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getBsSurfaceClone() - Method in interface org.jmol.api.JmolEnvCalc
 
getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getBufferData() - Method in class jspecview.source.XMLParser
 
getBufferedFileInputStream(String) - Method in class jspecview.java.AwtPlatform
 
getBufferedFileInputStream(String) - Method in class jspecview.js2d.JsPlatform
 
getBufferedFileInputStream(String) - Method in interface org.jmol.api.GenericPlatform
 
getBufferedFileInputStream(String) - Method in class org.jmol.awt.Platform
 
getBufferedFileInputStream(String) - Method in class org.jmol.awtjs2d.Platform
 
getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
 
getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
 
getBufferedInputStreamOrErrorMessageFromName(String, String, boolean, boolean, byte[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getBufferedReader() - Method in class javajs.util.DataReader
 
getBufferedReader(BufferedInputStream, String) - Static method in class javajs.util.Rdr
Read an input stream fully, saving a byte array, then return a buffered reader to those bytes converted to string form.
getBufferedReader(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
getBufferedReaderForInputStream(InputStream) - Static method in class jspecview.common.JSVFileManager
 
getBufferedReaderForResource(Viewer, Object, String, String) - Static method in class org.jmol.viewer.FileManager
 
getBufferedReaderForStringOrBytes(Object) - Static method in class jspecview.common.JSVFileManager
 
getBufferedReaderFromName(String, String) - Static method in class jspecview.common.JSVFileManager
 
getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
 
getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.io.FilesReader
called by SmartJmolAdapter to request another buffered reader or binary document, rather than opening all the readers at once.
getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getBundle(String) - Method in class org.jmol.modelkit.ModelKitPopup
 
getBundle(String) - Method in class org.jmol.popup.JmolGenericPopup
 
getBundle(String) - Method in class org.jmol.popup.JmolPopup
 
getButtonCount() - Method in class org.jmol.awtjs.swing.ButtonGroup
 
getButtonGroup() - Method in class org.jmol.awt.AwtPopupHelper
 
getButtonGroup() - Method in class org.jmol.awtjs2d.JSPopupHelper
 
getButtonGroup() - Method in interface org.jmol.popup.PopupHelper
 
getButtonMods(int) - Static method in class org.jmol.viewer.binding.Binding
 
getByteCount() - Method in class javajs.util.OC
 
getByteCount() - Method in class org.jmol.export.___Exporter
 
getBytes() - Method in class javajs.img.PngEncoder
 
getBytes(String) - Static method in class com.jcraft.jzlib.ZStream
added by Bob Hanson
getBytes64(byte[]) - Static method in class javajs.util.Base64
 
getBytesFromSB(SB) - Static method in class javajs.util.Rdr
Allow for base64-encoding check.
getBytesRead() - Method in class com.jcraft.jzlib.Deflate
 
getBytesRead() - Method in class com.jcraft.jzlib.Deflater
 
getBytesWritten() - Method in class com.jcraft.jzlib.Deflate
 
getBytesWritten() - Method in class com.jcraft.jzlib.Deflater
 
getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getCachedPngjBytes(FileManager, String) - Method in class org.jmol.io.JmolUtil
 
getCalcType(Atom[], String[], int) - Static method in class org.jmol.quantum.NMRCalculation
 
getCalcValue() - Method in class org.openscience.jmol.app.janocchio.Measure
 
getCallback(String) - Static method in enum class org.jmol.c.CBK
 
getCallbackParameter(int) - Method in class org.jmol.script.ScriptParam
 
getCameraDepth() - Method in class org.jmol.viewer.TransformManager
 
getCameraFactors() - Method in class org.jmol.viewer.TransformManager
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.
getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
 
getCanonicalCopy(float, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getCanonicalCopy(P3[], float) - Static method in class org.jmol.util.BoxInfo
Change points references to canonical form used in Triangulator, while also scaling.
getCanonicalCopyTrimmed(P3, float) - Method in class org.jmol.symmetry.UnitCell
 
getCanonicalName(String) - Method in class org.jmol.viewer.FileManager
 
getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
 
getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
 
getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCaretPosition() - Method in interface org.jmol.api.js.GenericConsoleTextArea
 
getCaretPosition() - Method in interface org.jmol.console.GenericTextArea
 
getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
 
getCartoonType(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getCartoonType(int) - Method in interface org.jmol.api.PymolAtomReader
 
getCel() - Method in class org.jmol.util.GData
 
getCellRange() - Method in interface org.jmol.api.SymmetryInterface
 
getCellRange() - Method in class org.jmol.symmetry.Symmetry
 
getCellRange(T3, P3[]) - Static method in class org.jmol.util.SimpleUnitCell
 
getCellStyle(int, int, GridBagConstraints) - Method in interface org.jmol.awtjs.swing.TableCellRenderer
 
getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
getCellWeight(P3) - Method in interface org.jmol.api.SymmetryInterface
 
getCellWeight(P3) - Method in class org.jmol.symmetry.Symmetry
 
getCellWeights(BS) - Method in class org.jmol.modelset.ModelSet
 
getCelPower() - Method in class org.jmol.util.GData
 
getCenter() - Method in class com.sparshui.common.messages.events.RotateEvent
 
getCenter() - Method in class com.sparshui.common.messages.events.ZoomEvent
 
getCenter(Location, Location) - Static method in class com.sparshui.common.Location
 
getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.modelset.ModelSet
 
getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.viewer.Viewer
 
getCenterAndPoints(Lst<P3>) - Static method in class javajs.util.Measure
from a list of points, create an array that includes the center point as the first point.
getCenterText() - Method in class org.jmol.modelkit.ModelKit
 
getCentroid(Location, Location, float) - Static method in class com.sparshui.common.Location
get weighted average location.
getChainAt(int) - Method in class org.jmol.modelset.Model
 
getChainBits(int) - Method in class org.jmol.modelset.AtomCollection
 
getChainCount(boolean) - Method in class org.jmol.modelset.Model
 
getChainCountInModelWater(int, boolean) - Method in class org.jmol.modelset.ModelSet
 
getChainID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getChainID() - Method in class org.jmol.modelset.Atom
 
getChainID() - Method in class org.jmol.smiles.SmilesAtom
 
getChainID() - Method in interface org.jmol.util.Node
 
getChainID(String, boolean) - Method in class org.jmol.viewer.Viewer
Create a unique integer for any chain string.
getChainIDStr() - Method in class org.jmol.modelset.Atom
 
getChainIDStr() - Method in class org.jmol.smiles.SmilesAtom
 
getChainIDStr() - Method in interface org.jmol.util.Node
 
getChainIDStr(int) - Method in class org.jmol.viewer.Viewer
 
getChangeableColix(int, int) - Method in class org.jmol.util.GData
 
getChangeableColixIndex(short) - Static method in class org.jmol.util.C
 
getChangeInX() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
 
getChangeInY() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
 
getCharacters() - Method in class jspecview.source.XMLParser
 
getCharge() - Method in class org.jmol.smiles.SmilesAtom
Returns the charge of the atom.
getCharge(int) - Method in class jme.JMEmol
 
getCheckBox(String) - Method in class org.jmol.awt.AwtPopupHelper
 
getCheckBox(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
getCheckBox(String) - Method in interface org.jmol.popup.PopupHelper
 
getChemicalInfo(String, String, BS) - Method in class org.jmol.viewer.Viewer
 
getChemicalShift(Atom) - Method in interface org.jmol.api.JmolNMRInterface
If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding
getChemicalShift(Atom) - Method in class org.jmol.quantum.NMRCalculation
 
getChildCount() - Method in interface jspecview.api.JSVTreeNode
 
getChildCount() - Method in class jspecview.tree.SimpleTreeNode
 
getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
 
getChimeInfo(int, BS) - Method in interface org.jmol.api.JmolPropertyManager
 
getChimeInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
 
getChimeMessenger() - Method in class org.jmol.viewer.Viewer
 
getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
 
getChiralClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
 
getChiralityForAtoms(CIPData) - Method in class org.jmol.symmetry.CIPChirality
A general determination of chirality that involves ultimately all of Rules 1-6.
getCifData(int) - Method in class org.jmol.viewer.Viewer
 
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.BCIFReader
 
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.Cif2Reader
 
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.CifReader
 
getCIPChirality(boolean) - Method in class org.jmol.modelset.Atom
Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags
getCIPChirality(boolean) - Method in class org.jmol.modelset.Bond
Not implemented.
getCIPChirality(boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getCIPChirality(boolean) - Method in class org.jmol.util.Edge
 
getCIPChirality(boolean) - Method in interface org.jmol.util.Node
 
getCIPChiralityCode() - Method in class org.jmol.modelset.Atom
 
getCIPChiralityCode() - Method in class org.jmol.smiles.SmilesAtom
 
getCIPChiralityCode() - Method in interface org.jmol.util.Node
 
getCIPChiralityCode(char) - Static method in class org.jmol.viewer.JC
 
getCIPChiralityName(int) - Static method in class org.jmol.viewer.JC
 
getCIPChiralityRule() - Method in class org.jmol.modelset.Atom
 
getCIPRuleName(int) - Static method in class org.jmol.viewer.JC
 
getClegId() - Method in interface org.jmol.api.SymmetryInterface
 
getClegId() - Method in class org.jmol.symmetry.Symmetry
 
getClickableSet(boolean) - Method in class org.jmol.modelset.AtomCollection
 
getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
 
getClickedCoordinate() - Method in class jspecview.common.PanelData
Returns the spectrum coordinate of the point on the display that was clicked
getClipboardText() - Static method in class jspecview.java.AwtClipboard
Get the String residing on the clipboard.
getClipboardText() - Method in class org.jmol.api.JmolViewer
 
getClipboardText() - Static method in class org.jmol.awt.AwtClipboard
Get the String residing on the clipboard.
getClipboardText() - Method in class org.jmol.viewer.Viewer
 
getClone() - Method in class org.jmol.adapter.smarter.Atom
 
getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
 
getCmdExt() - Method in class org.jmol.script.ScriptEval
 
getCmlBondOrder(int) - Static method in class org.jmol.util.Edge
 
getCode() - Method in enum class org.jmol.c.FIL
 
getCode() - Method in class org.jmol.symmetry.SymmetryOperation
 
getColix() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getColix(int) - Static method in class org.jmol.util.C
 
getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
 
getColix2(int, Atom, boolean) - Method in class org.jmol.shape.Labels
 
getColixA(short, byte, Atom) - Method in class org.jmol.shape.Shape
 
getColixArray(String) - Static method in class org.jmol.util.C
 
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
 
getColixB(short, int, Bond) - Method in class org.jmol.shape.Shape
 
getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
 
getColixI(short, byte, int) - Method in class org.jmol.shape.Shape
 
getColixInherited(short, short) - Static method in class org.jmol.util.C
 
getColixO(Object) - Static method in class org.jmol.util.C
 
getColixS(String) - Static method in class org.jmol.util.C
 
getColixTranslucencyFractional(short) - Static method in class org.jmol.util.C
 
getColixTranslucencyLabel(short) - Static method in class org.jmol.util.C
 
getColixTranslucencyLevel(short) - Static method in class org.jmol.util.C
 
getColixTranslucent(int) - Static method in class org.jmol.util.C
 
getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.C
 
getColor() - Method in class jme.JME
 
getColor() - Method in class jspecview.common.ColoredAnnotation
 
getColor() - Method in enum class org.jmol.c.STR
 
getColor(ScriptToken) - Method in class jspecview.common.PanelData
 
getColor1(int) - Method in class jspecview.common.ColorParameters
 
getColor1(int) - Method in class jspecview.common.PDFWriter
 
getColor1(int) - Method in class jspecview.java.AwtG2D
 
getColor1(int) - Method in class jspecview.java.AwtParameters
 
getColor1(int) - Method in class jspecview.js2d.JsG2D
 
getColor1(int) - Method in class jspecview.js2d.JsParameters
 
getColor1(int) - Method in interface org.jmol.api.GenericGraphics
 
getColor1(int) - Method in class org.jmol.awt.AwtG2D
 
getColor1(int) - Method in class org.jmol.awtjs2d.JsG2D
 
getColor3(int, int, int) - Method in class jspecview.common.ColorParameters
 
getColor3(int, int, int) - Method in class jspecview.common.PDFWriter
 
getColor3(int, int, int) - Method in class jspecview.java.AwtG2D
 
getColor3(int, int, int) - Method in class jspecview.java.AwtParameters
 
getColor3(int, int, int) - Method in class jspecview.js2d.JsG2D
 
getColor3(int, int, int) - Method in class jspecview.js2d.JsParameters
 
getColor3(int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
getColor3(int, int, int) - Method in class org.jmol.awt.AwtG2D
 
getColor3(int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
getColor4(int, int, int, int) - Method in class jspecview.common.PDFWriter
 
getColor4(int, int, int, int) - Method in class jspecview.java.AwtG2D
 
getColor4(int, int, int, int) - Method in class jspecview.js2d.JsG2D
 
getColor4(int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
getColor4(int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
getColor4(int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
getColorArgbOrGray(short) - Method in class org.jmol.util.GData
 
getColorCommand(String, byte, short, boolean) - Static method in class org.jmol.shape.Shape
 
getColorCommandUnk(String, short, boolean) - Static method in class org.jmol.shape.Shape
 
getColoredAnnotation(GenericGraphics, Spectrum, Lst<String>, Annotation) - Static method in class jspecview.common.Annotation
 
getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
 
getColorFromString(String) - Method in class jspecview.common.ColorParameters
 
getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
 
getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
 
getColorKey() - Method in class org.jmol.util.ColorEncoder
 
getColorList(int, short[], int, BS, Map<Short, Integer>) - Method in class org.jmol.export.___Exporter
input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index
getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
 
getColorRange(int) - Method in class org.jmol.script.ScriptEval
 
getColorScheme() - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
 
getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
 
getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
 
getColorTrans(ScriptEval, int, boolean, int[]) - Method in class org.jmol.scriptext.ScriptExt
Checks color, translucent, opaque parameters.
getColour(Spectrum, boolean) - Method in interface jspecview.api.VisibleInterface
 
getColour(Spectrum, boolean) - Method in class jspecview.common.Visible
Returns the integer color of a solution based on its visible spectrum.
getColumn(int) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
 
getColumn(int) - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
 
getColumn(int) - Method in class org.jmol.awtjs.swing.JTable
 
getColumn(int, float[]) - Method in class javajs.util.M3
Copies the matrix values in the specified column into the array parameter.
getColumn(int, float[]) - Method in class javajs.util.M4
Copies the matrix values in the specified column into the array parameter.
getColumn33(int, float[]) - Method in class javajs.util.M34
 
getColumnCentering(int) - Method in class jspecview.java.AwtDialog
 
getColumnCentering(int) - Method in class jspecview.js2d.JsDialog
 
getColumnClass(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getColumnCount() - Method in interface javajs.api.GenericCifDataParser
 
getColumnCount() - Method in class javajs.util.CifDataParser
 
getColumnCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getColumnData(int) - Method in interface javajs.api.GenericCifDataParser
 
getColumnData(int) - Method in class javajs.util.CifDataParser
 
getColumnDimension() - Method in class javajs.util.Matrix
Get column dimension.
getColumnModel() - Method in class org.jmol.awtjs.swing.JTable
 
getColumnName(int) - Method in interface javajs.api.GenericCifDataParser
 
getColumnName(int) - Method in class javajs.util.CifDataParser
 
getColumnName(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getColumnV(int, T3) - Method in class javajs.util.M3
Copies the matrix values in the specified column into the vector parameter.
getCommand(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
getCommandDown() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the top of the list, updates list position.
getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Generates a commandline from the options set for povray path etc and sets in the textField.
getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.Viewer
 
getCommandSet(String) - Static method in class org.jmol.script.T
retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
getCommandUp() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the bottom of the list, updates list position.
getComment() - Method in class com.jcraft.jzlib.GZIPHeader
 
getComparator(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getComponent(int) - Method in interface org.jmol.api.SC
 
getComponent(int) - Method in class org.jmol.awt.AwtSwingComponent
 
getComponent(int) - Method in class org.jmol.awtjs.swing.Container
 
getComponentCount() - Method in interface org.jmol.api.SC
 
getComponentCount() - Method in class org.jmol.awt.AwtSwingComponent
 
getComponentCount() - Method in class org.jmol.awtjs.swing.Container
 
getComponents() - Method in interface org.jmol.api.SC
 
getComponents() - Method in class org.jmol.awt.AwtSwingComponent
 
getComponents() - Method in class org.jmol.awtjs.swing.Container
 
getConeMesh(P3, M3, short) - Static method in class org.jmol.export.___Exporter
 
getConformation(int, boolean, BS, BS) - Method in class org.jmol.modelsetbio.BioModel
 
getConformation(int, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
 
getConnectingAtoms(BS, BS) - Method in class org.jmol.modelset.ModelSet
 
getConsole() - Method in class org.jmol.viewer.Viewer
 
getConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getConsoleFontScale() - Method in class org.jmol.viewer.Viewer
 
getContentPane() - Method in class org.jmol.awtjs.swing.JDialog
 
getContents() - Method in class javajs.util.AjaxURLConnection
 
getContext(String) - Method in class org.jmol.viewer.StateManager
 
getContextVariableAsVariable(String, boolean) - Method in class org.jmol.script.ScriptParam
 
getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
create a set of contour data.
getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
NWCHEM only
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.BioPolymer
 
getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
getConventionalUnitCell(String, M3) - Method in class org.jmol.symmetry.UnitCell
return a conventional lattice from a primitive
getConversionFactor(Map<String, Object>, String, String) - Static method in class org.qcschema.QCSchemaUnits
Get the necessary conversion factor to the desired units from a key_units or atomic units
getConversionFactorTo(ArrayList<Object>, String) - Static method in class org.qcschema.QCSchemaUnits
For a reader, use the JSON [units, factor] along with a desired unit to get the conversion factor from file values to desired units.
getConvertedSpectrum() - Method in class jspecview.common.Spectrum
 
getCoord() - Method in class jspecview.common.PeakPickEvent
 
getCoordinate() - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript to return the coordinate of clicked point in the plot area of the JSVPanel
getCoordinate() - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript to return the coordinate of clicked point in the plot area of the JSVPanel
getCoordinate() - Method in class jspecview.appletjs.JSVApplet
 
getCoordinate() - Method in class jspecview.application.MainFrame
 
getCoordinate() - Method in class jspecview.common.JSViewer
 
getCoordinateMap(T3[], int[], BS) - Method in class org.jmol.export.__CartesianExporter
 
getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
 
getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
 
getCoordinateState(BS) - Method in class org.jmol.viewer.Viewer
 
getCorrelationMaps(String, Node[], int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getCorrelationMaps(String, Node[], int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
getCorrelationTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
get the correlation time in seconds
getCorrelationTimeTauPS() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
get the correlation time in picoseconds
getCouples() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
getCoupleWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
 
getCovalentBondCount() - Method in class org.jmol.modelset.Atom
 
getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of bonds of this atom.
getCovalentBondCount() - Method in interface org.jmol.util.Node
 
getCovalentBondCount() - Method in interface org.jmol.util.SimpleNode
Get the total number of covalent bonds, thus not including hydrogen bonds.
getCovalentBondCountPlusMissingH() - Method in class org.jmol.modelset.Atom
 
getCovalentBondCountPlusMissingH() - Method in class org.jmol.smiles.SmilesAtom
 
getCovalentBondCountPlusMissingH() - Method in interface org.jmol.util.Node
includes actual + missing
getCovalentBondOrder(int) - Static method in class org.jmol.util.Edge
 
getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getCovalentHydrogenCount() - Method in interface org.jmol.util.Node
 
getCovalentOrder() - Method in class org.jmol.modelset.Bond
 
getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
 
getCovalentOrder() - Method in class org.jmol.util.Edge
 
getCovalentOrder() - Method in interface org.jmol.util.SimpleEdge
 
getCovalentOrPartialBondCount() - Method in class org.jmol.modelset.Atom
 
getCovalentRadius(int) - Static method in class org.jmol.util.Elements
Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODR
getCRC() - Method in class com.jcraft.jzlib.GZIPHeader
 
getCrcValue(byte[]) - Method in interface javajs.api.GenericZipTools
 
getCrcValue(byte[]) - Method in class javajs.util.ZipTools
 
getCrossLinkGroup(int, Lst<Integer>, Group, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
 
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Atom
Used by SMILES to get vector of cross-links
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Group
 
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
 
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in interface org.jmol.util.Node
 
getCSSstyle(int, int) - Method in class org.jmol.awtjs.swing.Component
 
getCSVString(String, int[]) - Static method in class javajs.util.PT
CSV format -- escaped quote is "" WITHIN "..."
getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
 
getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
 
getCurrentColorSchemeName() - Method in class org.jmol.util.ColorEncoder
 
getCurrentFileAsString(String) - Method in class org.jmol.viewer.Viewer
 
getCurrentGraphSet() - Method in class jspecview.common.PanelData
 
getCurrentModelAuxInfo() - Method in class org.jmol.viewer.Viewer
 
getCurrentModelFileAsString(String) - Method in class org.jmol.script.ScriptEval
 
getCurrentModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getCurrentPanelIndex() - Method in interface jspecview.api.JSVMainPanel
 
getCurrentPanelIndex() - Method in class jspecview.java.AwtMainPanel
 
getCurrentPanelIndex() - Method in class jspecview.js2d.JsMainPanel
 
getCurrentPlotColor(int) - Method in class jspecview.common.PanelData
 
getCurrentSpectrumIndex() - Method in class jspecview.common.PanelData
 
getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
 
getCurrentStructureFile() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getCurrentSubSpectrum() - Method in class jspecview.common.Spectrum
 
getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
 
getCursorX() - Method in class org.jmol.viewer.Viewer
 
getCursorY() - Method in class org.jmol.viewer.Viewer
 
getCutoff() - Method in class org.openscience.jmol.app.janocchio.NoeTable
get the cutoff distance
getCutoffAng() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
get the cutoff distance
getCutoffField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
 
getData() - Method in interface javajs.api.GenericCifDataParser
 
getData() - Method in class javajs.util.CifDataParser
The work horse; a general reader for loop data.
getData() - Method in interface jspecview.api.AnnotationData
 
getData() - Method in class jspecview.common.MeasurementData
 
getData() - Method in class jspecview.dialog.JSVDialog
 
getData(InputStream, String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
called by SmarterJmolAdapter via JmolUtil to open a Spartan directory and get all the needed data as a string.
getData(String, String) - Method in class org.jmol.api.JmolViewer
 
getData(String, String) - Method in class org.jmol.viewer.Viewer
 
getData(String, BS, int) - Method in interface org.jmol.api.JmolDataManager
 
getData(String, BS, int) - Method in class org.jmol.viewer.DataManager
 
getDataClass() - Method in class jspecview.source.JDXHeader
Returns the data class spectrum only
getDataHeader() - Method in class jspecview.common.IntegralData
 
getDataHeader() - Method in class jspecview.common.MeasurementData
 
getDataHeader() - Method in class jspecview.common.PeakData
 
getDataObj(String, BS, int) - Method in class org.jmol.viewer.Viewer
Retrieve a data object
getDataState(JmolStateCreator, SB) - Method in interface org.jmol.api.JmolDataManager
 
getDataState(JmolStateCreator, SB) - Method in class org.jmol.viewer.DataManager
 
getDataType() - Method in class jspecview.source.JDXHeader
Getter for property dataType.
getDate() - Method in class jspecview.source.JDXHeader
Getter for property date.
getDateFormat(String) - Method in class jspecview.java.AwtPlatform
 
getDateFormat(String) - Method in class jspecview.js2d.JsPlatform
 
getDateFormat(String) - Method in interface org.jmol.api.GenericPlatform
 
getDateFormat(String) - Method in class org.jmol.awt.Platform
 
getDateFormat(String) - Method in class org.jmol.awtjs2d.Platform
 
getDef(String) - Method in class org.jmol.export._VrmlExporter
 
getDefaultAnnotationInfo(Annotation.AType) - Method in class jspecview.source.JDXDataObject
 
getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
 
getDefaultLargePDBRendering(SB, int) - Method in class org.jmol.modelsetbio.BioModel
 
getDefaultLattice() - Method in class org.jmol.viewer.Viewer
 
getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
When creating a new bond, determine bond diameter from order
getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
 
getDefaultModel() - Method in class org.jmol.modelkit.ModelKit
 
getDefaultPropertyParam(int) - Method in interface org.jmol.api.JmolPropertyManager
 
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.PropertyManager
 
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.Viewer
 
getDefaultScheme() - Method in class jspecview.application.DisplaySchemesProcessor
 
getDefaultStructure(BS, BS) - Method in class org.jmol.modelset.ModelSet
 
getDefaultUnitPrecision() - Method in class jspecview.source.JDXDataObject
 
getDefaultVdwNameOrData(int, VDW, BS) - Method in class org.jmol.viewer.Viewer
 
getDefaultVdwNameOrData(VDW, BS) - Method in interface org.jmol.api.JmolDataManager
 
getDefaultVdwNameOrData(VDW, BS) - Method in class org.jmol.viewer.DataManager
 
getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelSet
 
getDefinedAtomSet(String) - Method in class org.jmol.viewer.Viewer
 
getDeflater() - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
getDegrees(float, boolean) - Method in class org.jmol.multitouch.ActionManagerMT
 
getDegrees(float, boolean) - Method in class org.jmol.viewer.ActionManager
Transform a screen pixel change to an angular change such that a full sweep of the dimension (up to 500 pixels) corresponds to 180 degrees of rotation.
getDelayMaximumMs() - Method in class org.jmol.viewer.Viewer
 
getDeltaX() - Method in class jspecview.source.JDXDataObject
Returns the delta X
getDescent() - Method in class org.jmol.util.Font
 
getDescription() - Method in enum class jspecview.common.ScriptToken
 
getDescription() - Method in class jspecview.java.AwtDialogFileFilter
Returns the JSpecViewFileFilter description
getDescription() - Method in class org.jmol.dialog.Dialog.TypeFilter
 
getDescription() - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
 
getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getDFMap(String, String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
finds the position in the Jmol-required list of function types.
getDialog() - Method in class org.jmol.dialog.FileChooser
 
getDialog(Annotation.AType) - Method in class jspecview.common.PanelData
 
getDialog(Annotation.AType, Spectrum) - Method in class jspecview.common.JSViewer
 
getDialog(JSVDialog) - Method in class jspecview.dialog.DialogManager
 
getDialog(JSVDialog) - Method in class jspecview.java.AwtDialogManager
 
getDialog(JSVDialog) - Method in class jspecview.js2d.JsDialogManager
 
getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.dialog.DialogManager
 
getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.java.AwtDialogManager
 
getDialogInput(Object, String, String, int, Object, Object[], String) - Method in class jspecview.js2d.JsDialogManager
 
getDialogManager() - Method in class jspecview.common.JSViewer
 
getDialogPrint(boolean) - Method in class jspecview.common.JSViewer
 
getDialogs() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getDiameter(int, int) - Method in class org.jmol.render.FontLineShapeRenderer
 
getDiff() - Method in class org.openscience.jmol.app.janocchio.Measure
 
getDiffusePercent() - Method in class org.jmol.util.GData
 
getDihedralCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
getDihedralMap(int[]) - Method in class org.jmol.modelset.ModelSet
 
getDimensionFromParams(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
getDimensionValue(int) - Method in class org.jmol.modelset.Atom
 
getDipolarConstantHz(Atom, Atom) - Method in interface org.jmol.api.JmolNMRInterface
 
getDipolarConstantHz(Atom, Atom) - Method in class org.jmol.quantum.NMRCalculation
 
getDipolarCouplingHz(Atom, Atom, V3) - Method in interface org.jmol.api.JmolNMRInterface
 
getDipolarCouplingHz(Atom, Atom, V3) - Method in class org.jmol.quantum.NMRCalculation
 
getDirectedNormalThroughPoints(T3, T3, T3, T3, V3, V3) - Static method in class javajs.util.Measure
 
getDirectory() - Method in class javajs.util.CompoundDocument
 
getDirectoryListing(String) - Method in class javajs.util.CompoundDocument
 
getDisplay1D() - Method in class jspecview.common.PanelData
 
getDisplayModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getDisplayName() - Method in class org.jmol.symmetry.SpaceGroup
 
getDisplaySchemes() - Method in class jspecview.application.DisplaySchemesProcessor
Returns the list of DisplaySchemes that were loaded
getDisplaySchemesProcessor(JSVInterface) - Method in class jspecview.application.JSpecView
 
getDistance(Location) - Method in class com.sparshui.common.Location
 
getDistanceFormatForState() - Method in class org.jmol.modelset.Measurement
 
getDistances() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
getDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
 
getDocument() - Method in class org.jmol.awtjs.swing.JTextPane
 
getDocumentBase() - Method in interface jspecview.api.AppletFrame
 
getDocumentBase() - Method in class jspecview.appletjs.JSVApplet
 
getDoTranslate() - Static method in class org.jmol.i18n.GT
 
getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDouble(Map<String, Object>, String) - Method in class org.molecularplayground.MPJmolApp
 
getDouble(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
getDouble(Map<String, Object>, String, String) - Static method in class org.qcschema.QCSchemaUnits
Reads a value from an associative array, converting it to the desired units.
getDoubleArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
Retrieve a double array, possibly unpacking it if it is run-length encoded.
getDrawHover() - Method in class org.jmol.viewer.Viewer
 
getDrawTitle(boolean) - Method in class jspecview.common.PanelData
 
getDSSRFrame(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
 
getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
 
getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
 
getDSSRFrame(Viewer) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getDx() - Method in class com.sparshui.common.messages.events.DragEvent
 
getDy() - Method in class com.sparshui.common.messages.events.DragEvent
 
getEchoName(int) - Static method in class org.jmol.viewer.JC
 
getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
 
getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getEdgePoints(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getEdges() - Method in class org.jmol.modelset.Atom
 
getEdges() - Method in class org.jmol.smiles.SmilesAtom
 
getEdges() - Method in interface org.jmol.util.Node
 
getEdges() - Method in interface org.jmol.util.SimpleNode
Get the bond array, including hydrogen bonds.
getEigenvalues() - Method in interface javajs.api.EigenInterface
 
getEigenvalues() - Method in class javajs.util.Eigen
return values sorted from smallest to largest value.
getEigenvectorsFloatTransposed() - Method in interface javajs.api.EigenInterface
 
getEigenvectorsFloatTransposed() - Method in class javajs.util.Eigen
Transpose V and turn into floats; sorted from smallest to largest value.
getElement() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getElement(int, int) - Method in class javajs.util.M3
Retrieves the value at the specified row and column of this matrix.
getElement(int, int) - Method in class javajs.util.M4
Retrieves the value at the specified row and column of this matrix.
getElement(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
allow for any number of characters, for which the first one or two are an element symbol.
getElementColix(int) - Method in class org.jmol.viewer.ColorManager
 
getElementColor(ScriptToken) - Method in class jspecview.common.ColorParameters
Gets the color of an element in the scheme
getElementFromUser() - Method in class org.jmol.modelkit.ModelKit
 
getElementKey(int) - Static method in class org.jmol.modelkit.ModelKit
 
getElementName(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getElementNumber() - Method in class org.jmol.modelset.Atom
 
getElementNumber() - Method in class org.jmol.smiles.SmilesAtom
Returns the atomic number of the element or 0
getElementNumber() - Method in interface org.jmol.util.Node
 
getElementNumber() - Method in interface org.jmol.util.SimpleNode
 
getElementNumber(int) - Static method in class org.jmol.util.Elements
 
getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
 
getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
 
getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelSet
 
getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
 
getElementSymbol() - Method in class org.jmol.modelset.Atom
 
getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
 
getElementSymbol(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
 
getElementSymbolIso(boolean) - Method in class org.jmol.modelset.Atom
 
getElemNos(boolean) - Method in class org.jmol.shapespecial.Polyhedron
 
getEllipsoidForAtomTensor(Tensor, Atom) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getEllipsoidShade(float, float, float, int, M4) - Method in class org.jmol.util.Shader
 
getEmbeddedFileState(String, boolean, String) - Method in class org.jmol.viewer.FileManager
Get the specified SPT file of a Jmol zip collection or the embedded script for any other file that is embeddable.
getEmbeddedScript(String) - Static method in class org.jmol.viewer.FileManager
Extract a Jmol script embedded using JC.EMBEDDED_SCRIPT_TAG.
getEmptyEllipsoid(String, int) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getEmptyPanel(JSViewer) - Static method in class jspecview.java.AwtPanel
Constructs a new JSVPanel
getEmptyPanel(JSViewer) - Static method in class jspecview.js2d.JsPanel
Constructs a new JSVPanel
getEncodedOrder() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within element
getEndChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getEndChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getEndingPointIndex(int) - Method in class jspecview.common.PanelData
 
getEndingPointIndex(int) - Method in class jspecview.common.ViewData
in some cases, there is only one scaleData, but there are more than that number of spectra this is no problem -- we just use mod to set this to 0
getEndInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getEndInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getEndTag() - Method in class jspecview.source.XMLParser
 
getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergy() - Method in class org.jmol.modelset.Bond
 
getEnergy() - Method in class org.jmol.modelset.HBond
 
getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEntryIcon(String[]) - Method in class org.jmol.popup.GenericPopup
 
getEquationForQuadricWithCenter(float, float, float, M3, V3, M3, double[], M4) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getEquivPointList(Lst<P3>, int, String, M4[]) - Method in interface org.jmol.api.SymmetryInterface
 
getEquivPointList(Lst<P3>, int, String, M4[]) - Method in class org.jmol.symmetry.Symmetry
 
getEquivPoints(Lst<P3>, P3, String) - Method in interface org.jmol.api.SymmetryInterface
 
getEquivPoints(Lst<P3>, P3, String) - Method in class org.jmol.symmetry.Symmetry
 
getErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptError
 
getErrorLineMessage2() - Method in class org.jmol.script.ScriptEval
 
getErrorLog() - Method in class jspecview.source.JDXSource
Returns the error log for this source
getErrorMessage() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getErrorMessage() - Method in class org.jmol.api.JmolViewer
 
getErrorMessage() - Method in class org.jmol.script.ScriptError
 
getErrorMessage() - Method in class org.jmol.viewer.Viewer
 
getErrorMessageUn() - Method in class org.jmol.api.JmolViewer
 
getErrorMessageUn() - Method in class org.jmol.viewer.Viewer
 
getErrorMessageUntranslated() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptError
 
getErrorMessageUntranslated() - Method in exception class org.jmol.script.ScriptException
 
getEulerZXZ() - Method in class javajs.util.Quat
 
getEulerZYZ() - Method in class javajs.util.Quat
 
getEvalContextAndHoldQueue(JmolScriptEvaluator) - Method in class org.jmol.viewer.Viewer
 
getEventType() - Method in interface com.sparshui.common.Event
Returns the integer value of this event type.
getEventType() - Method in class com.sparshui.common.messages.events.DragEvent
 
getEventType() - Method in class com.sparshui.common.messages.events.FlickEvent
 
getEventType() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
 
getEventType() - Method in class com.sparshui.common.messages.events.RotateEvent
 
getEventType() - Method in class com.sparshui.common.messages.events.SpinEvent
 
getEventType() - Method in class com.sparshui.common.messages.events.TouchEvent
 
getEventType() - Method in class com.sparshui.common.messages.events.ZoomEvent
 
getExecutor() - Method in interface org.jmol.api.JmolParallelProcessor
 
getExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
 
getExpCouple(int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
getExpDist(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getExplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getExplicitHydrogenCount() - Method in interface org.jmol.util.Node
[CH2] for example
getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getExpNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getExportDate() - Method in class org.jmol.export.___Exporter
 
getExportDriverList() - Method in class org.jmol.viewer.Viewer
 
getExportName() - Method in interface org.jmol.api.JmolRendererInterface
 
getExportName() - Method in class org.jmol.export.Export3D
 
getExportName() - Method in class org.jmol.g3d.Graphics3D
 
getExportType() - Method in interface org.jmol.api.JmolRendererInterface
 
getExportType() - Method in class org.jmol.export.Export3D
 
getExportType() - Method in class org.jmol.g3d.Graphics3D
 
getExpValue() - Method in class org.openscience.jmol.app.janocchio.Measure
 
getExtension(File) - Method in class jspecview.java.AwtDialogFileFilter
Returns the extension of a file
getF2C() - Method in class org.jmol.symmetry.UnitCell
 
getFaces() - Method in class org.jmol.util.MeshSurface
 
getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
 
getFactoredValue(int) - Method in class org.jmol.util.Tensor
Returns a factored eigenvalue; thermal ellipsoids use sqrt(abs(eigenvalue)) for ellipsoid axes; others use just use abs(eigenvalue); all cases get factored by typeFactor
getFactorToAU(String) - Static method in class org.qcschema.QCSchemaUnits
Get the standard conversion factor to atomic units for this unit.
getFieldString(byte) - Method in class org.jmol.adapter.readers.cif.CifReader
 
getFile() - Method in class org.openscience.jmol.app.HistoryFile
 
getFile(String, Object, boolean) - Method in interface jspecview.api.JSVFileHelper
 
getFile(String, Object, boolean) - Method in class jspecview.java.AwtFileHelper
 
getFile(String, Object, boolean) - Method in class jspecview.js2d.JsFileHelper
 
getFileAsBytes(String, OC) - Method in class org.jmol.viewer.FileManager
 
getFileAsMap(String, String, boolean) - Method in class org.jmol.viewer.FileManager
create a PNG or ZIP file and return it as a map or, optionally, as a byte[]
getFileAsString(String) - Method in class javajs.util.CompoundDocument
 
getFileAsString(String) - Static method in class jspecview.common.JSVFileManager
 
getFileAsString(String) - Method in class org.jmol.viewer.Viewer
 
getFileAsString3(String, boolean, String) - Method in class org.jmol.viewer.Viewer
 
getFileAsString4(String, int, boolean, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
 
getFileData(int) - Method in class org.jmol.modelset.ModelSet
 
getFileDataAsString(String[], int, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getFileHeader() - Method in interface javajs.api.GenericCifDataParser
 
getFileHeader() - Method in class javajs.util.CifDataParser
 
getFileHeader(int) - Method in class org.jmol.modelset.ModelSet
 
getFileInfo() - Method in class org.jmol.viewer.FileManager
 
getFileList(String, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
get a complete critical file list for a spartan file Mac directory based on file extension ".spardir.zip" or ".spardir"
getFileName() - Method in class javajs.util.OC
 
getFileName() - Method in class org.jmol.viewer.FileManager
 
getFileName() - Method in exception class org.jmol.viewer.JmolAsyncException
 
getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
 
getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
 
getFilePath() - Method in class jspecview.common.PeakInfo
 
getFilePath() - Method in class jspecview.source.JDXDataObject
The path to the file
getFilePath() - Method in class jspecview.source.JDXSource
 
getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getFilePathForwardSlash() - Method in class jspecview.source.JDXDataObject
 
getFileReferences(String, Lst<String>, Lst<String>) - Static method in class org.jmol.viewer.FileManager
 
getFileType() - Method in class org.jmol.viewer.FileManager
 
getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
getFileTypefromFilter(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Just get the resolved file type; if a file, does NOT close the reader
getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
Get the type of this file or molecular model, if known.
getFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getFilterWithCase(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getFinalOperationCount() - Method in interface org.jmol.api.SymmetryInterface
 
getFinalOperationCount() - Method in class org.jmol.symmetry.Symmetry
 
getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
 
getFirstAtomIndexFromAtomNumber(int, BS) - Method in class org.jmol.modelset.AtomCollection
 
getFirstX() - Method in class jspecview.source.JDXDataObject
Returns the first X value
getFirstY() - Method in class jspecview.source.JDXDataObject
Returns the first Y value
getFlexFitList(BS, BS, String, boolean) - Method in class org.jmol.scriptext.SmilesExt
 
getFloat(int) - Method in class org.jmol.api.JmolViewer
 
getFloat(int) - Method in class org.jmol.shapecgo.CGOMesh
 
getFloat(int) - Method in class org.jmol.viewer.Viewer
 
getFloatColumnData(int) - Method in class org.jmol.adapter.readers.cif.BCIFReader
Called by processAtomSites to retrieve individual matrix elements and set them by name.
getFloatColumnData(int) - Method in class org.jmol.adapter.readers.cif.CifReader
 
getFloatEncodedInt(String) - Static method in class org.jmol.util.Edge
Encodes a string such as "2.10" as an integer instead of a double so as to distinguish "2.1" from "2.10".
getFloatProperty(String) - Method in class org.jmol.modelset.Atom
 
getFloatProperty(String) - Method in class org.jmol.smiles.SmilesAtom
 
getFloatProperty(String) - Method in interface org.jmol.util.Node
 
getFloats(byte[], int, float) - Static method in class javajs.util.MessagePackReader
mmtf type 1 and 11 byte[4] to float32
getFocusNow(boolean) - Method in interface jspecview.api.JSVPanel
 
getFocusNow(boolean) - Method in class jspecview.java.AwtPanel
 
getFocusNow(boolean) - Method in class jspecview.js2d.JsPanel
 
getFont(float) - Method in class org.jmol.shape.Frank
 
getFont3D(float) - Method in class org.jmol.util.GData
 
getFont3D(int) - Static method in class org.jmol.util.Font
 
getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
 
getFont3DCurrent() - Method in class org.jmol.util.GData
 
getFont3DFS(String, float) - Method in class org.jmol.util.GData
 
getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
 
getFont3DScaled(Font, float) - Method in class org.jmol.util.GData
 
getFontAscent(Object) - Method in class jspecview.java.AwtPlatform
 
getFontAscent(Object) - Method in class jspecview.js2d.JsPlatform
 
getFontAscent(Object) - Method in interface org.jmol.api.FontManager
 
getFontAscent(Object) - Method in class org.jmol.awt.Platform
 
getFontAscent(Object) - Method in class org.jmol.awtjs2d.Platform
 
getFontCommand(String, Font) - Static method in class org.jmol.shape.Shape
 
getFontDescent(Object) - Method in class jspecview.java.AwtPlatform
 
getFontDescent(Object) - Method in class jspecview.js2d.JsPlatform
 
getFontDescent(Object) - Method in interface org.jmol.api.FontManager
 
getFontDescent(Object) - Method in class org.jmol.awt.Platform
 
getFontDescent(Object) - Method in class org.jmol.awtjs2d.Platform
 
getFontFaceID(String) - Method in interface jspecview.api.JSVPanel
 
getFontFaceID(String) - Method in class jspecview.java.AwtPanel
 
getFontFaceID(String) - Method in class jspecview.js2d.JsPanel
 
getFontFaceID(String) - Static method in class org.jmol.util.Font
 
getFontFidFS(String, float) - Method in class org.jmol.util.GData
 
getFontFidI(float) - Method in class org.jmol.util.GData
 
getFontMetrics() - Method in class org.jmol.util.Font
 
getFontMetrics(Font, Object) - Method in class jspecview.java.AwtPlatform
 
getFontMetrics(Font, Object) - Method in class jspecview.js2d.JsPlatform
 
getFontMetrics(Font, Object) - Method in interface org.jmol.api.FontManager
 
getFontMetrics(Font, Object) - Method in class org.jmol.awt.Platform
 
getFontMetrics(Font, Object) - Method in class org.jmol.awtjs2d.Platform
 
getFontName(ScriptToken, String) - Method in class jspecview.common.ColorParameters
 
getFontStyleID(String) - Static method in class org.jmol.util.Font
 
getForceField(String) - Method in class org.jmol.minimize.Minimizer
 
getForceFieldUsed() - Method in class org.jmol.minimize.Minimizer
 
getFormalCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getFormalCharge() - Method in class org.jmol.modelset.Atom
 
getFormalCharge() - Method in class org.jmol.smiles.SmilesAtom
 
getFormalCharge() - Method in interface org.jmol.util.Node
 
getFormalCharge() - Method in interface org.jmol.util.SimpleNode
 
getFormatType(String) - Static method in class org.jmol.script.SV
 
getFormulaForAtoms(BS, String, boolean) - Method in class org.jmol.viewer.Viewer
Get formula -- MF or CELLFORMULA, possibly empirical
getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
get all integers after letters negative entries are spaces (1Xn)
getFractional(Atom, P3) - Method in class org.jmol.modelset.Trajectory
 
getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
 
getFractionalCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
 
getFractionalOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getFractionalOffset() - Method in class org.jmol.symmetry.Symmetry
 
getFractionalOrigin() - Method in interface org.jmol.api.SymmetryInterface
 
getFractionalOrigin() - Method in class org.jmol.symmetry.Symmetry
 
getFractionalOrigin() - Method in class org.jmol.util.SimpleUnitCell
Get the fractional origin for the UccageRenderer.
getFractionalPoint(int) - Method in class org.jmol.script.ScriptParam
Could return a P4 for large 1100100100 type indicators
getFrame() - Method in interface jspecview.java.JmolFrame
 
getFrame() - Method in interface org.jmol.awt.JmolFrame
 
getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
getFrameActions() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getFrameActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getFrameAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getFrameAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getFrameAtoms() - Method in class org.jmol.viewer.Viewer
 
getFrameBase(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getFrameCount() - Method in class org.jmol.viewer.AnimationManager
 
getFrameDelayMs(int) - Method in class org.jmol.modelset.ModelSet
 
getFrameModelInfo(String) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.FrameCounter
 
getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
 
getFrameOffsets(BS, boolean) - Method in class org.jmol.modelset.ModelSet
 
getFrameTitle() - Method in class org.jmol.viewer.Viewer
 
getFrameTitle(int) - Method in class org.jmol.modelset.ModelSet
 
getFreqField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
 
getFullMap() - Method in class org.jmol.script.ScriptContext
 
getFullName() - Method in interface javajs.api.JSInterface
 
getFullName() - Method in class jspecview.appletjs.JSVApplet
 
getFullName() - Method in class org.jmol.util.GenericApplet
 
getFullPath() - Method in interface org.jmol.api.GenericFileInterface
 
getFullPathName(boolean) - Method in class org.jmol.script.ScriptEval
 
getFullPathName(boolean) - Method in class org.jmol.viewer.FileManager
 
getFullPathName(String) - Static method in class jspecview.common.JSVFileManager
FileManager.classifyName follow this with .replace('\\','/') and Escape.escape() to match Jmol's file name in
getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
 
getFullPDBHeader() - Method in class org.jmol.modelsetbio.BioModel
 
getFullProteinStructureState(BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
 
getFullScreenDimensions(Object, int[]) - Method in class jspecview.java.AwtPlatform
 
getFullScreenDimensions(Object, int[]) - Method in class jspecview.js2d.JsPlatform
 
getFullScreenDimensions(Object, int[]) - Method in interface org.jmol.api.GenericPlatform
 
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
 
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awtjs2d.Platform
 
getFunction(String) - Method in class org.jmol.script.ScriptEval
 
getFunction(String) - Method in class org.jmol.viewer.Viewer
 
getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
 
getFunctions(boolean) - Method in class org.jmol.viewer.Viewer
 
getGestures(int) - Method in class com.sparshui.server.ServerToClientProtocol
Retrieve a list of allowed gestures for the provided group id.
getGestureType() - Method in interface com.sparshui.gestures.Gesture
Get the integer value of this gesture type.
getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
getGlideFromTrans(T3, T3) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getGLmolView() - Method in class org.jmol.util.GenericApplet
This method is only called by JmolGLmol applet._refresh();
getGLmolView() - Method in class org.jmol.viewer.Viewer
This method is only called by JmolGLmol applet._refresh();
getGraphics(Object) - Method in class jspecview.java.AwtPlatform
 
getGraphics(Object) - Method in class jspecview.js2d.JsPlatform
 
getGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
 
getGraphics(Object) - Method in class org.jmol.awt.Platform
 
getGraphics(Object) - Method in class org.jmol.awtjs.Platform
 
getGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
 
getGraphSetKey() - Method in interface jspecview.api.AnnotationData
 
getGraphSetKey() - Method in class jspecview.common.MeasurementData
 
getGraphSetKey() - Method in class jspecview.dialog.JSVDialog
 
getGroup1() - Method in class org.jmol.modelset.Group
 
getGroup1() - Method in class org.jmol.modelsetbio.Monomer
 
getGroup1(char) - Method in class org.jmol.modelset.Atom
 
getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
 
getGroup1(char) - Method in interface org.jmol.util.Node
 
getGroup1b() - Method in class org.jmol.modelsetbio.Monomer
 
getGroup1b() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getGroup3() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getGroup3() - Method in class org.jmol.modelset.Group
 
getGroup3(boolean) - Method in class org.jmol.modelset.Atom
 
getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getGroup3(boolean) - Method in interface org.jmol.util.Node
 
getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
 
getGroupBits(BS) - Method in class org.jmol.modelset.Atom
 
getGroupBits(BS) - Method in class org.jmol.smiles.SmilesAtom
 
getGroupBits(BS) - Method in interface org.jmol.util.Node
 
getGroupCount() - Method in class org.jmol.modelset.Model
 
getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
 
getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
getGroupID(Location) - Method in interface com.sparshui.client.SparshClient
This method must return an ID for a group of points that should be processed together.
getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
getGroupID(TouchPoint) - Method in class com.sparshui.server.ServerToClientProtocol
Retrieve a list of allowed gestures for the provided group id.
getGroupID(String) - Method in class org.jmol.modelsetbio.BioResolver
 
getGroupInfo(int, P3) - Method in class org.jmol.modelset.Group
 
getGroupParameter(int) - Method in class org.jmol.modelset.Group
Monomers only
getGroupParameter(int) - Method in class org.jmol.modelsetbio.Monomer
 
getGroups() - Method in class org.jmol.modelset.ModelSet
In versions earlier than 12.1.51, groups[] was a field of ModelCollection.
getGroupsWithin(int, BS) - Method in class org.jmol.modelset.ModelSet
 
getGroupsWithin(int, BS) - Method in class org.jmol.viewer.Viewer
 
getGroupsWithinAll(int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
getGyromagneticRatio(String) - Static method in class jspecview.source.JDXDataObject
 
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in interface org.jmol.api.JmolAnnotationParser
 
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.DSSR1
 
getHCount() - Method in class org.jmol.minimize.MinAtom
 
getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getHeader(int) - Method in class javajs.util.LimitedLineReader
 
getHeaderMap(InputStream, Map<String, String>) - Static method in class jspecview.source.JDXReader
 
getHeaderMapS(InputStream, Map<String, String>, String) - Static method in class jspecview.source.JDXReader
 
getHeaderRendererIcon(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getHeaderRowDataAsArray() - Method in class jspecview.source.JDXDataObject
 
getHeaderRowDataAsArray(boolean, int) - Method in class jspecview.source.JDXHeader
 
getHeaderRowDataAsArray(boolean, String[][]) - Method in class jspecview.source.JDXSource
 
getHeaderTable() - Method in class jspecview.source.JDXHeader
Returns the table of headers
getHeight() - Method in interface jspecview.api.JSVViewPanel
 
getHeight() - Method in class jspecview.common.JSViewer
 
getHeight() - Method in class jspecview.js2d.JsMainPanel
 
getHeight() - Method in class jspecview.js2d.JsPanel
 
getHeight() - Method in class org.jmol.awtjs.swing.Component
 
getHeight() - Method in class org.jmol.util.Font
 
getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
 
getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
 
getHelp(String) - Method in class org.jmol.viewer.Viewer
 
getHermiteLevel() - Method in class org.jmol.viewer.Viewer
 
getHermiteList(int, T3, T3, T3, T3, T3, T3[], int, int, boolean) - Static method in class org.jmol.util.GData
Used by Navigator, BioShapeRenderer, and DrawRenderer
getHeteroList(int) - Method in class org.jmol.modelset.ModelSet
 
getHexCode(short) - Static method in class org.jmol.util.C
 
getHexCodes(short[]) - Static method in class org.jmol.util.C
 
getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
 
getHexitValue(char) - Static method in class org.jmol.util.Escape
 
getHiddenCanvas(JSAppletObject, String, int, int) - Method in interface javajs.api.js.J2SObjectInterface
 
getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
 
getHistoryWindowPosition(String) - Method in interface org.jmol.api.JmolAppAPI
 
getHistoryWindowPosition(String) - Method in class org.openscience.jmol.app.JmolApp
 
getHistoryWindowSize(String) - Method in interface org.jmol.api.JmolAppAPI
 
getHistoryWindowSize(String) - Method in class org.openscience.jmol.app.JmolApp
 
getHklPlane(T3, float, Lst<P3>) - Method in class org.jmol.script.ScriptParam
 
getHorizAlignmentName(int) - Static method in class org.jmol.viewer.JC
 
getHoverDelay() - Method in class org.jmol.viewer.Viewer
 
getHtmlDisabled() - Method in class org.jmol.awtjs.swing.AbstractButton
 
getHtmlDisabled() - Method in class org.jmol.awtjs.swing.JMenuItem
 
getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getHybridizationAndAxes(int, int, V3, V3, String, boolean, boolean, boolean, T3) - Method in class org.jmol.modelset.AtomCollection
 
getHybridizationAndAxes(int, V3, V3, String) - Method in class org.jmol.viewer.Viewer
 
getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
Get the hydrogen atom count -- for ligand files
getHydrogenCount() - Method in class jspecview.source.JDXDataObject
 
getHydrogenCount(int) - Method in class jme.JMEmol
 
getHydrophobicity() - Method in class org.jmol.modelset.Atom
 
getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
 
getHydrophobicity(int) - Static method in class org.jmol.util.Elements
 
getIcon() - Method in interface org.jmol.api.SC
 
getIcon() - Method in class org.jmol.awt.AwtSwingComponent
 
getIcon() - Method in class org.jmol.awtjs.swing.AbstractButton
 
getIconX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getIconX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
 
getIconX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getId() - Method in enum class org.jmol.c.STR
 
getID() - Method in class com.sparshui.server.Group
 
getID() - Method in class com.sparshui.server.TouchPoint
Get the touch point ID.
getIdentifierOrNull(String) - Method in class org.jmol.modelsetbio.BioModelSet
 
getIdentity() - Method in class org.jmol.minimize.MinAtom
 
getIdentity() - Method in class org.jmol.modelset.Bond
 
getIdentityXYZ(P3, int) - Method in class org.jmol.modelset.Atom
 
getIDStr() - Method in class org.jmol.modelset.Chain
 
getImage(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
getImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
 
getImage(Viewer, Object, String, boolean) - Method in class org.jmol.io.JmolUtil
 
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.api.JmolViewer
 
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
 
getImageDialog(String, Map<String, GenericImageDialog>) - Method in class jspecview.java.AwtPlatform
 
getImageDialog(String, Map<String, GenericImageDialog>) - Method in class jspecview.js2d.JsPlatform
 
getImageDialog(String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.GenericPlatform
 
getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awt.Platform
 
getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awtjs2d.Platform
 
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
 
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in class org.jmol.dialog.Dialog
 
getImageHeight(Object) - Method in class jspecview.java.AwtPlatform
 
getImageHeight(Object) - Method in class jspecview.js2d.JsPlatform
 
getImageHeight(Object) - Method in interface org.jmol.api.GenericPlatform
 
getImageHeight(Object) - Method in class org.jmol.awt.Platform
 
getImageHeight(Object) - Method in class org.jmol.awtjs2d.Platform
 
getImageIcon(String) - Method in class jspecview.java.AwtPopup
 
getImageIcon(String) - Method in class jspecview.js2d.JsPopup
 
getImageIcon(String) - Method in class org.jmol.awt.AwtJmolPopup
 
getImageIcon(String) - Method in class org.jmol.awt.AwtModelKitPopup
 
getImageIcon(String) - Method in class org.jmol.awtjs2d.JSJmolPopup
 
getImageIcon(String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
getImageIcon(String) - Method in class org.jmol.popup.GenericPopup
 
getImagEigenvalues() - Method in class javajs.util.Eigen
Return the imaginary parts of the eigenvalues
getImageURL(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getImageWidth(Object) - Method in class jspecview.java.AwtPlatform
 
getImageWidth(Object) - Method in class jspecview.js2d.JsPlatform
 
getImageWidth(Object) - Method in interface org.jmol.api.GenericPlatform
 
getImageWidth(Object) - Method in class org.jmol.awt.Platform
 
getImageWidth(Object) - Method in class org.jmol.awtjs2d.Platform
 
getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getImplicitHydrogenCount() - Method in interface org.jmol.util.Node
can be > 0 for PDB model with no H atoms or for SMILES string CCC
getInchi(BS, Object, String) - Method in class org.jmol.viewer.Viewer
Get an InChI or InChIKey for a set of atoms or MOL data.
getInchi(Viewer, BS, Object, String) - Method in interface org.jmol.api.JmolInChI
 
getInchi(Viewer, BS, Object, String) - Method in class org.jmol.inchi.InChIJNI
 
getInchi(Viewer, BS, Object, String) - Method in class org.jmol.inchi.InChIJS
 
getInChI() - Method in class jspecview.java.AwtPlatform
 
getInChI() - Method in class jspecview.js2d.JsPlatform
 
getInChI() - Method in interface org.jmol.api.GenericPlatform
 
getInChI() - Method in class org.jmol.awt.Platform
 
getInChI() - Method in class org.jmol.awtjs2d.Platform
 
getIndex() - Method in interface jspecview.api.JSVTreeNode
 
getIndex() - Method in class jspecview.application.AwtTreeNode
 
getIndex() - Method in class jspecview.common.PeakInfo
 
getIndex() - Method in class jspecview.tree.SimpleTreeNode
 
getIndex() - Method in class org.jmol.modelset.Atom
 
getIndex() - Method in class org.jmol.smiles.SmilesAtom
Returns the atom index of the atom.
getIndex() - Method in class org.jmol.symmetry.SpaceGroup
 
getIndex() - Method in interface org.jmol.util.Node
 
getIndex() - Method in interface org.jmol.util.SimpleNode
 
getIndex(int, int, int, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
 
getIndexFromName(String) - Method in class org.jmol.shape.Shape
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Polyhedra
 
getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
 
getInflater() - Method in class com.jcraft.jzlib.InflaterInputStream
 
getInfo() - Method in class org.jmol.modelset.Atom
 
getInfo() - Method in class org.jmol.symmetry.SymmetryOperation
 
getInfo() - Method in class org.jmol.util.Font
 
getInfo() - Method in class org.jmol.util.Modulation
 
getInfo(boolean) - Method in class org.jmol.shape.Mesh
 
getInfo(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getInfo(boolean, String) - Method in class jspecview.common.PanelData
 
getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
 
getInfo(int, String) - Method in class org.jmol.modelset.ModelSet
 
getInfo(String) - Method in class jspecview.common.Spectrum
 
getInfo(String) - Method in interface org.jmol.api.JmolNMRInterface
 
getInfo(String) - Method in class org.jmol.quantum.NMRCalculation
 
getInfo(String) - Method in class org.jmol.util.BoxInfo
for {*}.boundbox("info"|"volume"|"center"|null)
getInfo(String) - Method in class org.jmol.util.Tensor
returns an object of the specified type, including "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
getInfo(Map<String, Object>) - Method in class jspecview.common.IntegralData
 
getInfo(Map<String, Object>) - Method in class jspecview.common.PeakData
 
getInfo(Map<String, Object>) - Method in class org.jmol.util.ModulationSet
 
getInfo(Map<String, Object>) - Method in class org.jmol.util.Vibration
 
getInfoAsString(int) - Method in class org.jmol.shape.Measures
 
getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
 
getInfoB(int, String) - Method in class org.jmol.modelset.ModelSet
 
getInfoI(int, String) - Method in class org.jmol.modelset.ModelSet
 
getInfoM(String) - Method in class org.jmol.modelset.ModelSet
 
getInfoXYZ(Atom) - Method in class org.jmol.viewer.ChimeMessenger
called when an atom is picked
getInfoXYZ(Atom) - Method in interface org.jmol.viewer.JmolChimeMessenger
 
getInlineChar() - Method in class org.jmol.viewer.Viewer
 
getInlineData() - Method in class jspecview.source.JDXDataObject
 
getInlineData(int) - Method in class org.jmol.modelset.ModelSet
 
getInlineData(SB, String, boolean, Integer, String) - Method in class org.jmol.viewer.StateCreator
 
getInMotion(boolean) - Method in class org.jmol.viewer.Viewer
 
getInput(String, String, String) - Method in interface jspecview.api.JSVPanel
 
getInput(String, String, String) - Method in class jspecview.java.AwtPanel
 
getInput(String, String, String) - Method in class jspecview.js2d.JsPanel
 
getInputStream() - Method in interface javajs.api.GenericBinaryDocument
 
getInputStream() - Method in class javajs.util.AjaxURLConnection
 
getInputStream() - Method in class javajs.util.BinaryDocument
 
getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
getInputStream(String, boolean, byte[]) - Static method in class jspecview.common.JSVFileManager
 
getInsCode() - Method in class org.jmol.modelset.Group
 
getInsertedCommand() - Method in class org.jmol.viewer.Viewer
 
getInsertionCode() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getInsertionCode() - Method in class org.jmol.modelset.Atom
 
getInsertionCode() - Method in class org.jmol.modelset.Group
 
getInsertionCode() - Method in class org.jmol.smiles.SmilesAtom
 
getInsertionCode() - Method in interface org.jmol.util.Node
 
getInsertionCodeChar(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCodeFor(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
 
getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getInstance() - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
 
getInstanceWithParams(String, Class<?>[], Object...) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getInt(int) - Method in class org.jmol.api.JmolViewer
 
getInt(int) - Method in class org.jmol.shapecgo.CGOMesh
 
getInt(int) - Method in class org.jmol.viewer.Viewer
 
getInt(Map<String, Object>, String) - Method in class org.molecularplayground.MPJmolApp
 
getInt(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
getInt4(int, byte[]) - Static method in class javajs.img.PngEncoder
 
getIntArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
Retrieve an int array, possibly unpacking it if it is run-length encoded.
getIntArray2(int) - Method in class org.jmol.scriptext.ScriptExt
 
getIntArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
turn "[1,2,3]" into [1,2,3] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
getIntegralFactor() - Method in class jspecview.common.IntegralData
 
getIntegration() - Method in class org.jmol.quantum.QuantumCalculation
 
getIntegrationRatiosFromString(Spectrum, String) - Static method in class jspecview.common.IntegralData
Parses x-coordinates and values from a string and returns them as IntegrationRatio objects
getInterface(String) - Static method in class javajs.api.Interface
 
getInterface(String) - Static method in class jspecview.common.JSViewer
 
getInterface(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getInterface(String, Viewer, String) - Static method in class org.jmol.api.Interface
 
getIntersection(float, P4, P3[], Lst<P3[]>, float[], BS, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSlicer
 
getIntersection(P3, V3, P4, P3, V3, V3) - Static method in class javajs.util.Measure
Calculate the intersection of a line with a plane.
getIntersectionPP(P4, P4) - Static method in class javajs.util.Measure
Calculate the line that is the intersection of two planes.
getInts(byte[], int) - Static method in class javajs.util.MessagePackReader
mmtf types 2-4 Decode a byte array into a byte, short, or int array.
getIntTableIndex() - Method in interface org.jmol.api.SymmetryInterface
 
getIntTableIndex() - Method in class org.jmol.symmetry.Symmetry
 
getIntTableNumber() - Method in interface org.jmol.api.SymmetryInterface
 
getIntTableNumber() - Method in class org.jmol.symmetry.Symmetry
 
getIntTableNumberFull() - Method in interface org.jmol.api.SymmetryInterface
 
getIntTableNumberFull() - Method in class org.jmol.symmetry.Symmetry
 
getIntTableTransform() - Method in interface org.jmol.api.SymmetryInterface
 
getIntTableTransform() - Method in class org.jmol.symmetry.Symmetry
 
getInvariantSymops(P3, int[]) - Method in interface org.jmol.api.SymmetryInterface
 
getInvariantSymops(P3, int[]) - Method in class org.jmol.symmetry.Symmetry
 
getInverseNormix(short) - Static method in class org.jmol.util.Normix
 
getIsHetero() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getIsoExt() - Method in class org.jmol.script.ScriptEval
 
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in interface org.jmol.api.JmolNMRInterface
If t is null, then a1, a2, and type are used to find the appropriate tensor.
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
 
getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
 
getIsotope() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
 
getIsotopeNumber() - Method in interface org.jmol.util.Node
 
getIsotopeNumber() - Method in interface org.jmol.util.SimpleNode
 
getIsotopeNumber(int) - Static method in class org.jmol.util.Elements
 
getItaIndex() - Method in class org.jmol.symmetry.SpaceGroup
 
getITASettingValue(Viewer, String, String) - Method in interface org.jmol.api.SymmetryInterface
 
getITASettingValue(Viewer, String, String) - Method in class org.jmol.symmetry.Symmetry
 
getItem(int) - Method in class org.jmol.awtjs.swing.JMenu
 
getItem(int) - Static method in class org.jmol.quantum.QS
 
getItemCount() - Method in class org.jmol.awtjs.swing.JMenu
 
getItemType(SC) - Method in class org.jmol.awt.AwtPopupHelper
 
getItemType(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
getItemType(SC) - Method in interface org.jmol.popup.PopupHelper
 
getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelSet
only some models can be iterated through.
getIterator(Viewer, Atom, BS, float) - Method in interface org.jmol.api.SymmetryInterface
 
getIterator(Viewer, Atom, BS, float) - Method in class org.jmol.symmetry.Symmetry
 
getJavaConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getJavaConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Deprecated.
getJBR() - Method in class org.jmol.viewer.Viewer
 
getJcampdx() - Method in class jspecview.source.JDXHeader
Getter for property jcampdx.
getJCouplingHz(Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
 
getJDXBaseModelIndex(int) - Method in class org.jmol.viewer.Viewer
get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file.
getJDXSpectrum(int) - Method in class jspecview.source.JDXSource
Returns the Spectrum at a given index in the list
getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
 
getJmol(JFrame, int, int, Map<String, Object>) - Static method in class org.openscience.jmol.app.Jmol
 
getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.Jmol
 
getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelSet
 
getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelSet
 
getJmolDistance(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
 
getJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
Calc using Jmol atom index
getJmolFilePath(String) - Static method in class jspecview.common.JSVFileManager
 
getJmolFrameType(int) - Method in class org.jmol.modelset.ModelSet
 
getJmolNoe(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
 
getJmolNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
getJmolParameter(String) - Method in class org.jmol.util.GenericApplet
 
getJmolPerspective() - Method in class org.jmol.export.___Exporter
 
getJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJmolValueAsString(Viewer, String) - Static method in class org.molecularplayground.MPJmolApp
 
getJmolVersion() - Static method in class org.jmol.api.JmolViewer
 
getJmolVersion() - Static method in class org.jmol.viewer.Viewer
 
getJmolVersionNoDate() - Static method in class org.jmol.api.JmolViewer
 
getJsObjectInfo(Object[], String, Object[]) - Method in class jspecview.java.AwtPlatform
 
getJsObjectInfo(Object[], String, Object[]) - Method in class jspecview.js2d.JsPlatform
 
getJsObjectInfo(Object[], String, Object[]) - Method in interface org.jmol.api.GenericPlatform
 
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awt.Platform
 
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awtjs2d.Platform
 
getJsonNioServer() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJspecViewProperties(Object) - Method in class org.jmol.viewer.Viewer
 
getJSpecViewProperty(String) - Method in class jspecview.application.MainFrame
 
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolStatusListener
 
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolSyncInterface
 
getJSpecViewProperty(String) - Method in class org.jmol.util.GenericApplet
JSpecView shares the JmolSyncInterface; used to get JSpecView
getJSpecViewProperty(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
getJSVPanel(JSViewer, Lst<Spectrum>) - Method in interface jspecview.api.AppletFrame
 
getJSVPanel(JSViewer, Lst<Spectrum>) - Method in class jspecview.appletjs.JSVApplet
 
getJVXLCutoff() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getJVXLCutoff() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getJzt() - Method in class org.jmol.viewer.Viewer
 
getJzu() - Method in class org.jmol.viewer.FileManager
 
getKey() - Method in interface org.jmol.api.JmolAbstractButton
 
getKey() - Method in class org.jmol.console.JmolButton
 
getKey() - Method in class org.jmol.console.JmolLabel
 
getKey() - Method in class org.jmol.console.JmolToggleButton
 
getKey() - Method in class org.jmol.console.KeyJCheckBox
 
getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
 
getKey() - Method in class org.jmol.console.KeyJMenu
 
getKey() - Method in class org.jmol.console.KeyJMenuItem
 
getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
 
getKey(int, int, int, int, int) - Static method in class org.jmol.minimize.MinObject
 
getKey(ScriptTokenizer) - Static method in enum class jspecview.common.ScriptToken
 
getKeyMap() - Static method in class org.jmol.shapecgo.CGOMesh
 
getKeys(boolean) - Method in class org.jmol.script.SV
 
getLabel(int) - Method in class org.jmol.shape.Labels
 
getLabel(int, boolean, boolean) - Method in class org.jmol.modelset.Measurement
 
getLabel(String) - Static method in class org.jmol.console.GenericConsole
 
getLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
 
getLabel1() - Method in class org.jmol.console.AppletConsole
 
getLabel1() - Method in class org.jmol.console.GenericConsole
 
getLabelArray() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
 
getLabeler() - Method in class org.jmol.modelset.AtomCollection
 
getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.GenericConsole
 
getLanguage() - Static method in class org.jmol.i18n.GT
 
getLanguageList() - Static method in class org.jmol.i18n.Language
This is the place to put the list of supported languages.
getLanguageList(GT) - Static method in class org.jmol.i18n.GT
 
getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastError() - Static method in exception class org.jmol.smiles.InvalidSmilesException
 
getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
 
getLastException() - Method in class org.jmol.smiles.SmilesMatcher
 
getLastFileFirstNode(Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
 
getLastIndex() - Method in class org.jmol.modelset.Measurement
 
getLastPathComponent() - Method in interface jspecview.api.JSVTreePath
 
getLastPathComponent() - Method in class jspecview.tree.SimpleTreePath
 
getLastVibrationVector(int, int) - Method in class org.jmol.modelset.ModelSet
 
getLastX() - Method in class jspecview.source.JDXDataObject
Returns the last X value
getLastY() - Method in class jspecview.source.JDXDataObject
Returns the last Y value
getLatticeCentering() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeCentering() - Method in class org.jmol.symmetry.Symmetry
 
getLatticeCentering(SymmetryOperation[]) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
 
getLatticeOp() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeOp() - Method in class org.jmol.symmetry.Symmetry
 
getLatticePoints(Lst<P3>, int, int, int) - Static method in class javajs.util.Measure
Based on a set of centering points, creates a list of lattice points in place.
getLatticeType() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeType() - Method in class org.jmol.symmetry.Symmetry
 
getLeadAtom() - Method in class org.jmol.modelset.Group
 
getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadAtomOr(Atom) - Method in class org.jmol.modelset.Group
 
getLeadColix(int) - Method in class org.jmol.renderbio.BackboneRenderer
 
getLeadColix(int) - Method in class org.jmol.renderbio.CartoonRenderer
 
getLeadColix(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
getLeadColix(int) - Method in class org.jmol.renderbio.RibbonsRenderer
 
getLeadColix(int) - Method in class org.jmol.renderbio.RocketsRenderer
 
getLeadColix(int) - Method in class org.jmol.renderbio.StrandsRenderer
 
getLeadColix(int) - Method in class org.jmol.renderbio.TraceRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.BackboneRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.CartoonRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.RibbonsRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.RocketsRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.StrandsRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.TraceRenderer
 
getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLength(int) - Method in class org.jmol.shapespecial.Ellipsoid
 
getLength(Object) - Static method in class javajs.util.AU
 
getLevel(int) - Static method in class org.jmol.util.Logger
Returns the text corresponding to a level.
getlexpNoes() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getLigandInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
 
getLigandInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getLigandModel(String, String, String, String) - Method in class org.jmol.viewer.Viewer
obtain CIF data for a ligand for purposes of adding hydrogens or for any other purpose in terms of saving a data set for a file in a state
getLightingState() - Method in class org.jmol.viewer.Viewer
 
getLightSource() - Method in class org.jmol.util.GData
 
getLimitedStreamBytes(InputStream, long) - Static method in class javajs.util.Rdr
Read a possibly limited number of bytes (when n > 0) from a stream, leaving the stream open.
getLine() - Method in class org.jmol.jvxl.readers.XmlReader
 
getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEval
 
getList() - Method in class org.jmol.script.SV
 
getList(Object, String) - Static method in class org.qcschema.QCSchemaUnits
Retrieve an array of any sort as a list of objects, possibly unpacking it if it is run-length encoded.
getList(String) - Method in class org.jmol.symmetry.CIPData
Retrieve an array of bit sets that match a given SMARTS
getList(String) - Method in class org.jmol.symmetry.CIPDataSmiles
 
getLoadSymmetryParams(int, SB, Map<String, Object>) - Method in class org.jmol.scriptext.CmdExt
 
getLocalDirectory(Viewer, boolean) - Static method in class org.jmol.viewer.FileManager
 
getLocalPathForWritingFile(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
 
getLocalUrl(String) - Method in class jspecview.java.AwtPlatform
 
getLocalUrl(String) - Method in class jspecview.js2d.JsPlatform
 
getLocalUrl(String) - Method in interface org.jmol.api.GenericPlatform
 
getLocalUrl(String) - Method in class org.jmol.awt.Platform
 
getLocalUrl(String) - Method in class org.jmol.awtjs2d.Platform
 
getLocalUrl(String) - Method in class org.jmol.viewer.Viewer
 
getLocation() - Method in class com.sparshui.server.TouchPoint
Get the touch point location.
getLocationOnScreen(Object) - Method in class jspecview.dialog.DialogManager
 
getLocationOnScreen(Object) - Method in class jspecview.java.AwtDialogManager
 
getLocationOnScreen(Object) - Method in class jspecview.js2d.JsDialogManager
 
getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
 
getLogFileName() - Method in class org.jmol.viewer.Viewer
 
getLogLevel() - Static method in class org.jmol.util.Logger
 
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerAwt
 
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerJS
 
getLong(Map<String, Object>, String) - Method in class org.molecularplayground.MPJmolApp
 
getLong(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
getLongDate() - Method in class jspecview.source.JDXHeader
Getter for property longDate.
getMacro(String) - Method in class org.jmol.viewer.Viewer
retrieve macros.json from the directory
getMadBond() - Method in class org.jmol.api.JmolViewer
 
getMadBond() - Method in class org.jmol.viewer.Viewer
 
getMadParameter() - Method in class org.jmol.script.ScriptParam
 
getMagic(InputStream, int) - Static method in class javajs.util.Rdr
 
getMagneticShielding(Atom) - Method in interface org.jmol.api.JmolNMRInterface
 
getMagneticShielding(Atom) - Method in class org.jmol.quantum.NMRCalculation
 
getManifestScriptPath(String) - Static method in class org.jmol.viewer.FileManager
check a JmolManifest for a reference to a script file (.spt)
getMap() - Method in class org.jmol.script.SV
 
getMapForJME(String, Atom[], BS) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getMapForJME(String, Atom[], BS) - Method in class org.jmol.smiles.SmilesMatcher
 
getMapForStream(BufferedInputStream) - Method in class javajs.util.MessagePackReader
 
getMapKeys(int, boolean) - Method in class org.jmol.script.SV
 
getMapValueNoCase(Map<String, ?>, String) - Static method in class javajs.util.PT
 
getMass() - Method in class org.jmol.modelset.Atom
 
getMass() - Method in class org.jmol.smiles.SmilesAtom
 
getMass() - Method in interface org.jmol.util.Node
 
getMass() - Method in interface org.jmol.util.SimpleNode
 
getMatch() - Method in class jspecview.common.PeakInfo
 
getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
Returns the matching atom or null.
getMatchingAtomIndex() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of a matching atom in a molecule.
getMatchingBond() - Method in class org.jmol.smiles.SmilesBond
 
getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
 
getMathExt() - Method in class org.jmol.script.ScriptEval
 
getMatrix() - Method in class javajs.util.Quat
 
getMatrix4f(M3, T3) - Static method in class org.jmol.script.ScriptMathProcessor
 
getMatrixAndUnitCell(SimpleUnitCell, Object, M4) - Static method in class org.jmol.symmetry.UnitCell
 
getMatrixFromString(String, float[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
MMCifReader only
getMatrixFromString(SymmetryOperation, String, float[], boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format
getMatrixFromXYZ(String, float[], boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getMatrixSelected(int[], int) - Method in class javajs.util.Matrix
Get a submatrix for a give number of columns and selected row set.
getMaxDim() - Method in class org.jmol.util.BoxInfo
 
getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
 
getMaxX() - Method in class jspecview.source.JDXDataObject
Calculates and returns the maximum x value in the list of coordinates Fairly expensive operation
getMaxX(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
Returns the maximum x value value from an array of arrays of Coordinates.
getMaxX(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
Returns the minimum x value of an array of Coordinates
getMaxY() - Method in class jspecview.source.JDXDataObject
Calculates and returns the maximum y value in the list of coordinates Fairly expensive operation
getMaxY() - Method in class jspecview.source.JDXDecompressor
 
getMaxY(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
Returns the maximum y value of an array of Coordinates
getMaxYUser(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
Returns the maximum y value value from an array of arrays of Coordinates.
getMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
getMeasurementCount() - Method in class org.jmol.api.JmolViewer
 
getMeasurementCount() - Method in class org.jmol.viewer.Viewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
 
getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getMeasurementListArray(String) - Method in class jspecview.common.IntegralData
 
getMeasurementListArray(String) - Method in class jspecview.common.MeasurementData
 
getMeasurementListArray(String) - Method in class jspecview.common.PeakData
 
getMeasurementListArrayReal(String) - Method in class jspecview.common.IntegralData
 
getMeasurementListArrayReal(String) - Method in class jspecview.common.PeakData
 
getMeasurements(boolean, boolean) - Method in class org.jmol.modelset.MeasurementData
if this is the client, then this method can be called to get the result vector, either as a string or as an array.
getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
Used by MouseManager and Picking Manager to build the script
getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
 
getMeasurementTable() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getMenu(String) - Method in class org.jmol.awt.AwtPopupHelper
 
getMenu(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
getMenu(String) - Method in interface org.jmol.popup.PopupHelper
 
getMenu(String) - Method in class org.jmol.viewer.Viewer
 
getMenuAsText(String) - Method in class jspecview.popup.JSVPopupResourceBundle
 
getMenuAsText(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
getMenuAsText(String) - Method in class org.jmol.popup.MainPopupResourceBundle
 
getMenuAsText(String) - Method in class org.jmol.popup.PopupResource
 
getMenuHTML() - Method in class org.jmol.awtjs.swing.AbstractButton
 
getMenuIcon() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
getMenuIcon() - Method in interface org.openscience.jmol.app.JmolPlugin
 
getMenuItem(String) - Method in class org.jmol.awt.AwtPopupHelper
 
getMenuItem(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
getMenuItem(String) - Method in interface org.jmol.popup.PopupHelper
 
getMenuItem(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Fetch the menu item that was created for the given command.
getMenuName() - Method in class jspecview.popup.JSVPopupResourceBundle
 
getMenuName() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
getMenuName() - Method in class org.jmol.popup.MainPopupResourceBundle
 
getMenuName() - Method in class org.jmol.popup.PopupResource
 
getMenuPopup(String, char) - Method in class jspecview.java.AwtPlatform
 
getMenuPopup(String, char) - Method in class jspecview.js2d.JsPlatform
 
getMenuPopup(String, char) - Method in interface org.jmol.api.GenericPlatform
 
getMenuPopup(String, char) - Method in class org.jmol.awt.Platform
 
getMenuPopup(String, char) - Method in class org.jmol.awtjs2d.Platform
 
getMenuScript(String) - Static method in class org.jmol.viewer.JC
 
getMenuText() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
getMenuText() - Method in interface org.openscience.jmol.app.JmolPlugin
 
getMesh(String) - Method in class org.jmol.shape.MeshCollection
 
getMeshList(String, boolean) - Method in class org.jmol.shape.MeshCollection
Get matching list of meshes, order reversed
getMeshSlicer() - Method in class org.jmol.util.MeshSurface
 
getMessage() - Method in exception class org.jmol.script.ScriptException
 
getMessage() - Method in exception class org.jmol.smiles.InvalidSmilesException
 
getMFArray(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
 
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shape.Mesh
 
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getMinDistances(MeasurementData) - Method in interface org.jmol.api.JmolNMRInterface
 
getMinDistances(MeasurementData) - Method in class org.jmol.quantum.NMRCalculation
 
getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
 
getMinimizer(boolean) - Method in class org.jmol.viewer.Viewer
 
getMinindex() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
 
getMinindex() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getMinMax() - Method in class jme.JMEmol
 
getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getMinMax(Object, int, boolean) - Method in class org.jmol.scriptext.MathExt
 
getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getMinX() - Method in class jspecview.source.JDXDataObject
Calculates and returns the minimum x value in the list of coordinates Fairly expensive operation
getMinX(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
Returns the minimum x value value from an array of arrays of Coordinates.
getMinX(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
Returns the minimum x value of an array of Coordinates
getMinY() - Method in class jspecview.source.JDXDataObject
Calculates and returns the minimum y value in the list of coordinates Fairly expensive operation
getMinY() - Method in class jspecview.source.JDXDecompressor
 
getMinY(Coordinate[], int, int) - Static method in class jspecview.common.Coordinate
Returns the minimum y value of an array of Coordinates
getMinYUser(Lst<Spectrum>, ViewData) - Static method in class jspecview.common.Coordinate
Returns the minimum y value value from an array of arrays of Coordinates.
getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
 
getMissingHydrogenCount(Atom, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getMixingTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
get the mixing time
getMixingTimeSec() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
get the mixing time
getMKState() - Method in class org.jmol.modelkit.ModelKit
 
getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in class org.jmol.smiles.SmilesMatcher
called by ForceFieldMMFF.setAtomTypes only
getMod(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
Modulation data keys are keyed by model number as well as type using [at]n, where n is the model number, starting with 0.
getMod(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getMode(String) - Static method in enum class jspecview.common.PanelData.LinkMode
 
getMode(String) - Static method in enum class jspecview.common.Spectrum.IRMode
 
getModel() - Method in class jspecview.common.PeakInfo
 
getModel() - Method in class org.jmol.modelset.Group
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelAdapter() - Method in class org.jmol.api.JmolViewer
 
getModelAdapter() - Method in class org.jmol.viewer.Viewer
 
getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelSet
Note that this method returns all atoms, included deleted ones.
getModelAtomBitSetIncludingDeletedBs(BS) - Method in class org.jmol.modelset.ModelSet
note -- this method returns ALL atoms, including deleted.
getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelSet
 
getModelBS(int, BS) - Method in class org.jmol.modelset.Trajectory
set bits for all trajectories associated with this model
getModelBS(BS, boolean) - Method in class org.jmol.modelset.ModelSet
Get the set of models associated with a set of atoms.
getModelCellRange(int) - Method in class org.jmol.modelset.ModelSet
 
getModelCenter() - Method in class org.jmol.export.__CartesianExporter
 
getModelCml(BS, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelCml(BS, int, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelCml(BS, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
 
getModelCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getModelDataBaseName(BS) - Method in class org.jmol.modelset.ModelSet
 
getModelDipole() - Method in class org.jmol.viewer.Viewer
 
getModelDipole(int) - Method in class org.jmol.modelset.ModelSet
 
getModelExtract(Object, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
getModelExtract(BS, boolean, boolean, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelExtract(BS, boolean, boolean, String, boolean) - Method in class org.jmol.viewer.PropertyManager
V3000, SDF, MOL, JSON, CD (ChemDoodle), XYZ, XYZVIB, XYZRN, CML, PDB, PQR, QCJSON, PWMAT, XSF MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)
getModelFileData(String, String, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelFileInfo() - Method in class org.jmol.viewer.Viewer
 
getModelFileInfo(BS) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelFileInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
 
getModelFileName(int) - Method in class org.jmol.modelset.ModelSet
 
getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelFileType(int) - Method in class org.jmol.modelset.ModelSet
 
getModelForAtomIndex(int) - Method in class org.jmol.viewer.Viewer
 
getModelIndex() - Method in class org.jmol.modelset.Atom
SMILES only
getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
 
getModelIndex() - Method in interface org.jmol.util.Node
 
getModelIndexForAtom(int) - Method in class org.jmol.viewer.Viewer
 
getModelIndexFromId(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getModelIndexFromId(String) - Method in class org.jmol.api.JmolViewer
 
getModelIndexFromId(String) - Method in class org.jmol.modelset.ModelSet
 
getModelIndexFromId(String) - Method in class org.jmol.util.GenericApplet
 
getModelIndexFromId(String) - Method in class org.jmol.viewer.Viewer
 
getModelIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getModelIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getModelInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getModelInfo(String) - Method in class org.jmol.viewer.Viewer
get a value from the current model's Model.auxiliaryInfo
getModelInfoAsString() - Method in class org.jmol.modelset.ModelSet
 
getModelkit(boolean) - Method in class org.jmol.viewer.Viewer
 
getModelkitPropertySafely(String) - Method in class org.jmol.viewer.Viewer
Get a ModelKit property, but only if the modelkit exists already.
getModelName(int) - Method in class org.jmol.api.JmolViewer
 
getModelName(int) - Method in class org.jmol.modelset.ModelSet
 
getModelName(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumber() - Method in class org.jmol.modelset.Atom
 
getModelNumber(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumber(int) - Method in class org.jmol.modelset.ModelSet
 
getModelNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelSet
 
getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
 
getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
 
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
getModelOrientation(int) - Method in class org.jmol.modelset.ModelSet
 
getModelPeakInfoForAutoSelectOnLoad() - Method in class jspecview.common.Spectrum
 
getModelProperties(int) - Method in class org.jmol.api.JmolViewer
 
getModelProperties(int) - Method in class org.jmol.viewer.Viewer
 
getModelProperty(int, String) - Method in class org.jmol.modelset.ModelSet
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
 
getModelSetAuxiliaryInfo(BS) - Method in class org.jmol.modelset.ModelSet
Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.
getModelSetAuxiliaryInfoForAtoms(Object) - Method in class org.jmol.viewer.Viewer
 
getModelSetFileName() - Method in class org.jmol.api.JmolViewer
 
getModelSetFileName() - Method in class org.jmol.viewer.Viewer
 
getModelSetPathName() - Method in class org.jmol.api.JmolViewer
 
getModelSetPathName() - Method in class org.jmol.viewer.Viewer
 
getModelSetProperties() - Method in class org.jmol.api.JmolViewer
 
getModelSetProperties() - Method in class org.jmol.viewer.Viewer
 
getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
 
getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelSet
 
getModelTitle(int) - Method in class org.jmol.modelset.ModelSet
 
getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getModelUndeletedAtomsBitSetBs(BS) - Method in class org.jmol.viewer.Viewer
 
getModifiedTime() - Method in class com.jcraft.jzlib.GZIPHeader
 
getModPoint(boolean) - Method in interface org.jmol.api.JmolModulationSet
 
getModPoint(boolean) - Method in class org.jmol.util.ModulationSet
 
getModType(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getModType(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getModulation() - Method in class org.jmol.modelset.Atom
 
getModulation(char, T3, boolean) - Method in interface org.jmol.api.JmolModulationSet
 
getModulation(char, T3, boolean) - Method in class org.jmol.util.ModulationSet
 
getModulation(int) - Method in class org.jmol.modelset.AtomCollection
 
getModulationList(BS, char, P3) - Method in class org.jmol.modelset.ModelSet
 
getModulationMap() - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getModulationMap() - Method in interface org.jmol.adapter.smarter.MSInterface
 
getMOHeader(int, String[], Map<String, Object>[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getMoInfo(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getMolecularFormula(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
 
getMolecularFormula(String, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getMolecularFormula(String, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
 
getMolecularFormulaAtoms(Node[], BS, float[], boolean) - Static method in class org.jmol.util.JmolMolecule
 
getMoleculeBitSet(BS) - Method in class org.jmol.modelset.ModelSet
return cumulative sum of all atoms in molecules containing these atoms
getMoleculeBitSetForAtom(int) - Method in class org.jmol.modelset.ModelSet
 
getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getMoleculeIndex(int, boolean) - Method in class org.jmol.modelset.ModelSet
 
getMoleculeInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getMoleculeNumber(boolean) - Method in class org.jmol.modelset.Atom
 
getMoleculeNumber(boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getMoleculeNumber(boolean) - Method in interface org.jmol.util.Node
 
getMolecules() - Method in class org.jmol.modelset.ModelSet
 
getMolecules(Node[], BS[], Lst<BS>, BS) - Static method in class org.jmol.util.JmolMolecule
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.
getMonomerIndex() - Method in class org.jmol.modelset.Group
 
getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
getMoreInfo() - Method in interface org.jmol.api.SymmetryInterface
 
getMoreInfo() - Method in class org.jmol.symmetry.Symmetry
 
getMOString(float[]) - Static method in class org.jmol.quantum.QS
 
getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
 
getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
 
getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
 
getMotionFixedAtoms(SymmetryInterface, BS) - Method in class org.jmol.viewer.Viewer
For the current SINGLE model only.
getMouseAction(int, int, int) - Static method in class org.jmol.viewer.binding.Binding
 
getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
 
getMouseActionStr(String) - Static method in class org.jmol.viewer.binding.Binding
create an action code from a string such as "CTRL-LEFT-double click"
getMouseEnabled() - Method in class org.jmol.viewer.Viewer
 
getMouseManager(double, Object) - Method in class jspecview.java.AwtPlatform
 
getMouseManager(double, Object) - Method in class jspecview.js2d.JsPlatform
 
getMouseManager(double, Object) - Method in interface org.jmol.api.GenericPlatform
 
getMouseManager(double, Object) - Method in class org.jmol.awt.Platform
 
getMouseManager(double, Object) - Method in class org.jmol.awtjs2d.Platform
 
getMoveToText(boolean) - Method in class org.jmol.modelset.Orientation
 
getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
getMSInfoB(String) - Method in class org.jmol.modelset.ModelSet
 
getMyInfo(P3) - Method in class org.jmol.modelsetbio.Monomer
 
getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getName() - Method in class com.jcraft.jzlib.GZIPHeader
 
getName() - Method in interface com.sparshui.gestures.Gesture
Get the name of this gesture.
getName() - Method in class javajs.util.OC
 
getName() - Method in interface org.jmol.api.GenericFileInterface
 
getName() - Method in interface org.jmol.api.JmolAbstractButton
 
getName() - Method in interface org.jmol.api.JmolScriptFunction
 
getName() - Method in interface org.jmol.api.SC
 
getName() - Method in class org.jmol.awt.AwtSwingComponent
 
getName() - Method in class org.jmol.awtjs.swing.Component
 
getName() - Method in enum class org.jmol.c.STER
 
getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
getName() - Method in class org.jmol.script.ScriptFunction
 
getName() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
getName() - Method in interface org.openscience.jmol.app.JmolPlugin
 
getNameList() - Static method in enum class org.jmol.c.CBK
 
getNameList(Lst<ScriptToken>) - Static method in enum class jspecview.common.ScriptToken
 
getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
 
getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
 
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
 
getNavigationState() - Method in interface org.jmol.api.JmolNavigatorInterface
 
getNavigationState() - Method in class org.jmol.navigate.Navigator
 
getNavigationState() - Method in class org.jmol.viewer.TransformManager
 
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getNavPtHeight() - Method in class org.jmol.viewer.TransformManager
 
getNBOAtomLabel(Atom) - Method in class org.jmol.adapter.readers.quantum.NBOParser
get the
getNBOAtomLabel(Atom) - Method in class org.jmol.viewer.Viewer
 
getNBOTypeFromName(String) - Static method in class org.jmol.viewer.JC
 
getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getNearestIndexForX(Coordinate[], double) - Static method in class jspecview.common.Coordinate
 
getNearestXWithYAbove(Coordinate[], double, double, boolean, boolean) - Static method in class jspecview.common.Coordinate
discovers nearest peak left or right of x that is above threshold y
getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
 
getNetByID(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
Find or create a net with this netID, giving it a default name "Net"+id
getNetFor(String, String, boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
Find or create a TNet for this id and label.
getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
 
getNewDfCoefMap() - Static method in class org.jmol.quantum.QS
 
getNewScales(int, boolean, double, double) - Method in class jspecview.common.ViewData
 
getNext(Object, int) - Method in class javajs.util.MessagePackReader
 
getNextDataToken() - Method in interface javajs.api.GenericCifDataParser
 
getNextDataToken() - Method in class javajs.util.CifDataParser
first checks to see if the next token is an unquoted control code, and if so, returns null
getNextStatement() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getNextStatement() - Method in class org.jmol.script.ScriptEval
when paused, indicates what statement will be next
getNextToken() - Method in interface javajs.api.GenericCifDataParser
 
getNextToken() - Method in class javajs.util.CifDataParser
Get a token as a String value (for the reader)
getNextTokenObject() - Method in class javajs.util.CifDataParser
Get the token as a Java Object
getNextTokenProtected() - Method in class javajs.util.CifDataParser
Just makes sure
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.JvxlReader
 
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getNHPoint(P3, V3, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenAtom() - Method in class org.jmol.modelset.Group
 
getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNMRCalculation() - Method in class org.jmol.viewer.Viewer
 
getNmrDataJSON() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
getNMRfreq() - Method in class org.openscience.jmol.app.janocchio.NoeTable
gets the NMR frequency
getNMRfreqMHz() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
gets the NMR frequency
getNMRPredict(String) - Method in class org.jmol.viewer.Viewer
 
getNoeExprefValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getnoeNPrefIndices() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getNOEorJHH(Atom[], int) - Method in interface org.jmol.api.JmolNMRInterface
 
getNOEorJHH(Atom[], int) - Method in class org.jmol.quantum.NMRCalculation
 
getNoesy() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
get if NOESY or ROESY was used for simulation
getNoesy() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getNoeWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
 
getNominalMass() - Method in class org.jmol.modelset.Atom
 
getNominalSpecFreq(String, double) - Static method in class jspecview.source.JDXDataObject
 
getNormal() - Method in class javajs.util.Quat
 
getNormalDirected(V3) - Method in class javajs.util.Quat
 
getNormalFromCenter(P3, P3, P3, P3, boolean, V3, V3) - Static method in class javajs.util.Measure
 
getNormalMap(T3[], int, BS, Lst<String>) - Method in class org.jmol.export.__CartesianExporter
 
getNormals(T3[], P4) - Method in class org.jmol.shape.Mesh
 
getNormalsTemp() - Method in class org.jmol.shape.Mesh
 
getNormalThroughPoints(T3, T3, T3, T3, T3) - Static method in class javajs.util.Measure
 
getNormalToLine(P3, P3, V3) - Static method in class javajs.util.Measure
 
getNormixCount() - Static method in class org.jmol.util.Normix
 
getNormixes() - Method in class org.jmol.shapespecial.Polyhedron
 
getNormixV(V3, BS) - Static method in class org.jmol.util.Normix
 
getNoValue() - Method in class org.jmol.quantum.NciCalculation
 
getNoValue() - Method in class org.jmol.quantum.QuantumPlaneCalculation
Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
getNPoints() - Method in class com.sparshui.common.messages.events.DragEvent
 
getNPointsFound() - Method in class jspecview.source.JDXDecompressor
Report out the number of points found (for error reporting)
getNumberOfGraphSets() - Method in class jspecview.common.PanelData
Returns the Number of Graph sets
getNumberOfSpectra() - Method in class jspecview.source.JDXSource
Returns the number of Spectra in this Source
getNumberOfSpectraInCurrentSet() - Method in class jspecview.common.PanelData
 
getNumDim() - Method in class jspecview.source.JDXDataObject
 
getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEval
 
getObjectColix(int) - Method in class org.jmol.viewer.Viewer
 
getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
 
getObjectMad10(int) - Method in class org.jmol.viewer.Viewer
 
getObjectMap(Map<String, ?>, char) - Method in class org.jmol.viewer.Viewer
used in autocompletion in console using TAB
getObservedFreq() - Method in class jspecview.source.JDXDataObject
Returns the observed frequency (for NMR Spectra)
getObservedNucleus() - Method in class jspecview.source.JDXDataObject
^1H, ^13C, for example
getOccupancy() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getOccupancy100() - Method in class org.jmol.modelset.Atom
 
getOccupancy100(boolean) - Method in class org.jmol.util.ModulationSet
 
getOccupancy100(boolean) - Method in class org.jmol.util.Vibration
 
getOccupancyFloat(int) - Method in class org.jmol.modelset.AtomCollection
 
getOffset(int, int, boolean) - Static method in class org.jmol.viewer.JC
Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered".
getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
 
getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
 
getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.Node
 
getOffsetVertices(P4) - Method in class org.jmol.shape.Mesh
 
geTokens() - Method in interface org.jmol.api.JmolScriptFunction
 
geTokens() - Method in class org.jmol.script.ScriptFunction
 
getOpacity255() - Method in interface javajs.api.GenericColor
 
getOpacity255() - Method in class jspecview.java.AwtColor
 
getOpacity255() - Method in class org.jmol.awt.AwtColor
 
getOpacity255() - Method in class org.jmol.awtjs.swing.Color
 
getOpAxis() - Method in class org.jmol.symmetry.SymmetryOperation
 
getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in class org.jmol.dialog.Dialog
 
getOpenSmiles(BS) - Method in class org.jmol.api.JmolViewer
 
getOpenSmiles(BS) - Method in class org.jmol.viewer.Viewer
 
getOperationRsVs(int) - Method in interface org.jmol.api.SymmetryInterface
 
getOperationRsVs(int) - Method in class org.jmol.symmetry.Symmetry
 
getOperativeSymmetry() - Method in class org.jmol.viewer.Viewer
Only return symmetry that has operators.
getOpIsCCW() - Method in class org.jmol.symmetry.SymmetryOperation
 
getOpOrder() - Method in class org.jmol.symmetry.SymmetryOperation
 
getOpPoint() - Method in class org.jmol.symmetry.SymmetryOperation
 
getOpPoint2() - Method in class org.jmol.symmetry.SymmetryOperation
 
getOption(String[], String, String) - Method in interface jspecview.api.js.JSVAppletObject
 
getOption(String, Viewer, String) - Static method in class org.jmol.api.Interface
Note! Do not use this method with "viewer." or "util." because when the JavaScript is built, "org.jmol.util" and "org.jmol.viewer" are condensed to "JU" and "JV" (javajs.util is also JU)
getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.dialog.DialogManager
 
getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.java.AwtDialogManager
 
getOptionFromDialog(Object, String[], JSVPanel, String, String) - Method in class jspecview.js2d.JsDialogManager
 
getOptionFromDialog(String[], String, String) - Method in class jspecview.common.JSViewer
 
getOpTrans() - Method in class org.jmol.symmetry.SymmetryOperation
 
getOpType() - Method in class org.jmol.symmetry.SymmetryOperation
 
getOrAddBond(Atom, Atom, int, short, BS, float, boolean) - Method in class org.jmol.modelset.BondCollection
 
getOrCalcPartialCharges(BS, BS) - Method in class org.jmol.viewer.Viewer
 
getOrientation(int, String, BS, P3[]) - Method in class org.jmol.viewer.Viewer
 
getOrigin() - Method in class jspecview.source.JDXHeader
Getter for property origin.
getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
 
getOriginVaVbVc() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getOS() - Method in class com.jcraft.jzlib.GZIPHeader
 
getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
 
getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
 
getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
getOtherNode(SimpleNode) - Method in class org.jmol.modelset.Bond
 
getOtherNode(SimpleNode) - Method in class org.jmol.smiles.SmilesBond
 
getOtherNode(SimpleNode) - Method in interface org.jmol.util.SimpleEdge
 
getOutputChannel(String, boolean) - Method in class jspecview.common.JSViewer
 
getOutputChannel(String, String[]) - Method in class org.jmol.viewer.Viewer
 
getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
getOverallSpan() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
getOverlayLegendData() - Method in class jspecview.common.PanelData
 
getOwner() - Method in class jspecview.source.JDXHeader
Getter for property owner.
getP(String) - Method in class org.jmol.viewer.Viewer
 
getPackingRangeValue(float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getPalette(String) - Static method in enum class org.jmol.c.PAL
 
getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
 
getPaletteID(String) - Static method in enum class org.jmol.c.PAL
 
getPaletteName(byte) - Static method in enum class org.jmol.c.PAL
 
getPane() - Method in class org.jmol.console.JmolConsole
 
getPanelData() - Method in interface jspecview.api.JSVPanel
 
getPanelData() - Method in class jspecview.java.AwtPanel
 
getPanelData() - Method in class jspecview.js2d.JsPanel
 
getPanelMany(JSViewer, Lst<Spectrum>) - Static method in class jspecview.java.AwtPanel
Constructs a JSVPanel with List of spectra and corresponding start and end indices of data points that should be displayed
getPanelMany(JSViewer, Lst<Spectrum>) - Static method in class jspecview.js2d.JsPanel
Constructs a JSVPanel with List of spectra and corresponding start and end indices of data points that should be displayed
getPanelNode() - Method in interface jspecview.api.JSVTreeNode
 
getPanelNode() - Method in class jspecview.application.AwtTreeNode
 
getPanelNode() - Method in class jspecview.tree.SimpleTreeNode
 
getPanelOne(JSViewer, Spectrum) - Static method in class jspecview.java.AwtPanel
Constructs a new JSVPanel
getParameter(String) - Method in interface jspecview.api.AppletFrame
 
getParameter(String) - Method in class jspecview.appletjs.JSVApplet
 
getParameter(String) - Method in class org.jmol.api.JmolViewer
 
getParameter(String) - Method in class org.jmol.viewer.Viewer
 
getParameter(String, int, boolean) - Method in class org.jmol.script.ScriptParam
 
getParameter(String, String) - Method in class jspecview.appletjs.JSVApplet
 
getParameters() - Method in interface jspecview.api.AnnotationData
 
getParameters() - Method in class jspecview.common.MeasurementData
 
getParameters() - Method in class jspecview.dialog.JSVDialog
 
getParameters(boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getParams() - Method in class org.jmol.quantum.NMRNoeMatrix
 
getParamType(int) - Static method in class org.jmol.script.T
 
getParent() - Method in interface org.jmol.api.SC
 
getParent() - Method in class org.jmol.awt.AwtSwingComponent
 
getParent() - Method in class org.jmol.awtjs.swing.Component
 
getParentAsFile() - Method in interface org.jmol.api.GenericFileInterface
 
getPartialBondDotted(int) - Static method in class org.jmol.util.Edge
 
getPartialBondOrder(int) - Static method in class org.jmol.util.Edge
 
getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.util.Edge
reads standard n.m double-as-integer (n*1000000 + m) and returns partial bond order as (n % 7) invalid input: '<'invalid input: '<' 5 + (m % 0x1F)
getPartialCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getPartialCharge() - Method in class org.jmol.modelset.Atom
 
getPartialCharges() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
 
getPartialCharges(BS) - Method in class org.jmol.script.ScriptEval
 
getPartnerAtom(NucleicMonomer) - Method in class org.jmol.modelsetbio.BasePair
 
getPath() - Method in interface jspecview.api.JSVTreeNode
 
getPath() - Method in class jspecview.tree.SimpleTreeNode
 
getPathForAllFiles() - Method in class org.jmol.viewer.FileManager
 
getPatternIndex() - Method in class org.jmol.smiles.SmilesAtom
 
getPdbAtomData(BS, OC, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
PDB or PQR only
getPdbData(int, String, BS, Object[], OC, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.PropertyManager
 
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.Viewer
 
getPdbData(String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioModel
 
getPDBHeader(int) - Method in class org.jmol.modelset.ModelSet
 
getPdbID() - Method in class org.jmol.viewer.Viewer
 
getPeakData() - Method in class jspecview.dialog.JSVDialog
 
getPeakInfo() - Method in class jspecview.common.PeakPickEvent
 
getPeakList() - Method in class jspecview.common.Spectrum
 
getPeakListArray(Measurement, double[], double) - Method in class jspecview.source.JDXDataObject
 
getPeakListing(Parameters, Boolean) - Method in class jspecview.common.PanelData
 
getPeakTitle() - Method in class jspecview.common.Spectrum
 
getPeakWidth() - Method in class jspecview.common.Spectrum
 
getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
 
getPercentMinimumY() - Method in class jspecview.common.IntegralData
 
getPercentOffset() - Method in class jspecview.common.IntegralData
 
getPercentYValueAt(double) - Method in class jspecview.common.IntegralData
 
getPercentYValueAt(double) - Method in class jspecview.common.Spectrum
 
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
 
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
calculate the perspective factor based on z
getPhiPsiForHelixType(String) - Method in class org.jmol.modelsetbio.BioExt
 
getPhongExponent() - Method in class org.jmol.util.GData
 
getPickedCoordinates(Coordinate, Coordinate) - Method in class jspecview.common.PanelData
click event processing
getPickedPoint(T3, int) - Method in class org.jmol.shape.MeshCollection
 
getPickingMode() - Method in class org.jmol.viewer.Viewer
 
getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
 
getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
 
getPickingState() - Method in class org.jmol.viewer.ActionManager
 
getPickingStyleIndex(String) - Static method in class org.jmol.viewer.ActionManager
 
getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
 
getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
 
getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
 
getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
 
getPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
 
getPlaneForObject(String, V3) - Method in class org.jmol.script.ScriptEval
 
getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.JvxlReader
Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneProjection(T3, P4, T3, V3) - Static method in class javajs.util.Measure
Project a point onto a plane, also returning the normal vector and the directed distance to the plane.
getPlaneSR(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getPlaneThroughPoint(T3, V3, P4) - Static method in class javajs.util.Measure
 
getPlaneThroughPoints(T3, T3, T3, V3, V3, P4) - Static method in class javajs.util.Measure
 
getPlatformInterface(String) - Method in class jspecview.common.JSViewer
 
getPlotColors(String) - Method in class jspecview.common.ColorParameters
 
getPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getPmeshData(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getPngZipStream(BufferedInputStream, boolean) - Static method in class javajs.util.Rdr
Either advance a PNGJ stream to its zip file data or pull out the ZIP data bytes and create a new stream for them from which a ZIP utility can start extracting files.
getPoint(int, P3) - Method in class org.jmol.jvxl.data.VolumeData
 
getPoint(int, T3) - Method in class org.jmol.shapecgo.CGOMesh
 
getPoint3f(int, boolean) - Method in class org.jmol.scriptext.ScriptExt
 
getPoint3f(int, boolean, boolean) - Method in class org.jmol.script.ScriptParam
Get an {x,y,z} value, possibly fractional, with option to throw an error.
getPoint4f(int) - Method in class org.jmol.script.ScriptParam
 
getPointArray(int, int, boolean) - Method in class org.jmol.script.ScriptParam
may return null values in some cases
getPointer(int) - Static method in class org.jmol.viewer.JC
 
getPointerName(int) - Static method in class org.jmol.viewer.JC
 
getPointGroupAsString(BS, String, int, float, P3[], P3, String) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupInfo(int, String, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupInfo(int, String, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
 
getPointGroupInfo(BS) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
getPointOrCenterVector(T) - Method in class org.jmol.script.ScriptParam
 
getPointOrPlane(int, int) - Method in class org.jmol.script.ScriptParam
Get the point or plane at an index
getPoints() - Method in interface org.jmol.api.JmolEnvCalc
 
getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getPointsOnPlane(P3[], P4) - Static method in class javajs.util.Measure
Based on a set of centering points, returns the list of points on a given plane.
getPointTransf(int, Atom, Quat, P3) - Method in class org.jmol.modelset.ModelSet
pick up the appropriate value for this atom
getPointVector(T, int) - Method in class org.jmol.script.ScriptParam
 
getPolygonColorData(int, short[], int[][], BS) - Static method in class org.jmol.shapesurface.Isosurface
 
getPolymerPointsAndVectors(int, BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPolymerPointsAndVectors(BS, Lst<P3[]>) - Method in class org.jmol.viewer.Viewer
 
getPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
getPolymerSequenceAtoms(int, int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPopulation() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
 
getPopupMenu() - Method in interface org.jmol.api.SC
 
getPopupMenu() - Method in class org.jmol.awt.AwtSwingComponent
 
getPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
 
getPopupMenu() - Method in class org.jmol.awtjs.swing.JMenu
 
getPOrNull(String) - Method in class org.jmol.viewer.Viewer
 
getPort() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
getPort() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
getPosition() - Method in interface javajs.api.GenericBinaryDocument
 
getPosition() - Method in class javajs.util.BinaryDocument
 
getPosition() - Method in interface org.jmol.api.AtomIndexIterator
 
getPosition() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
getPosition() - Method in class org.jmol.symmetry.UnitCellIterator
 
getPosXY() - Method in class jspecview.dialog.IntegrationDialog
 
getPosXY() - Method in class jspecview.dialog.JSVDialog
 
getPosXY() - Method in class jspecview.dialog.MeasurementsDialog
 
getPosXY() - Method in class jspecview.dialog.OverlayLegendDialog
 
getPosXY() - Method in class jspecview.dialog.PeakListDialog
 
getPosXY() - Method in class jspecview.dialog.ViewsDialog
 
getPrecision() - Method in interface org.jmol.api.SymmetryInterface
 
getPrecision() - Method in class org.jmol.symmetry.Symmetry
 
getPrecision() - Method in class org.jmol.util.SimpleUnitCell
 
getPreference(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getPreferences() - Method in class jspecview.application.PreferencesDialog
Returns the preferences (Properties Object)
getPreserveState() - Method in class org.jmol.viewer.Viewer
This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
getPreviousMolecule() - Method in class jme.JME
 
getPrintJobTitle(boolean) - Method in class jspecview.common.PanelData
 
getPrintLayout() - Method in interface jspecview.api.JSVPrintDialog
 
getPrintLayout() - Method in class jspecview.java.AwtPrintDialog
Returns the PrintLayout object
getPrivateKey() - Method in class org.jmol.export.Export3D
 
getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
 
getProjectedLineSegment(P3[], int, P3, V3, V3) - Static method in class javajs.util.Measure
 
getPropC(String, int) - Method in class org.jmol.shapesurface.Contact
 
getPropDataMC(String, Object[]) - Method in class org.jmol.shape.MeshCollection
 
getProperties() - Method in class org.openscience.jmol.app.HistoryFile
 
getproperty - Static variable in class org.jmol.script.T
 
getProperty(int, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
getProperty(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getProperty(String) - Method in class org.jmol.modelkit.ModelKit
Get a property of the modelkit.
getProperty(String) - Method in class org.jmol.util.GenericApplet
 
getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
only called from org.openscience.jvxl.Jvxl.main
getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
 
getProperty(String, int) - Method in class org.jmol.shape.Axes
 
getProperty(String, int) - Method in class org.jmol.shape.Labels
 
getProperty(String, int) - Method in class org.jmol.shape.Measures
 
getProperty(String, int) - Method in class org.jmol.shape.Shape
 
getProperty(String, int) - Method in class org.jmol.shape.Sticks
 
getProperty(String, int) - Method in class org.jmol.shapecgo.CGO
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Polyhedra
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
 
getProperty(String, int) - Method in class org.jmol.shapesurface.Contact
 
getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
 
getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getProperty(String, int) - Method in class org.jmol.shapesurface.Pmesh
 
getProperty(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getProperty(String, String) - Method in class org.jmol.util.GenericApplet
@XXXj2sOverride
getProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
Get the value of a property
getProperty(String, String, Object) - Method in interface org.jmol.api.JmolPropertyManager
 
getProperty(String, String, Object) - Method in class org.jmol.api.JmolViewer
 
getProperty(String, String, Object) - Method in class org.jmol.viewer.PropertyManager
 
getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
 
GETPROPERTY - Enum constant in enum class jspecview.common.ScriptToken
 
getPropertyAsJavaObject(String) - Method in interface jspecview.api.JSVAppletInterface
 
getPropertyAsJavaObject(String) - Method in class jspecview.app.JSVApp
 
getPropertyAsJavaObject(String) - Method in class jspecview.appletjs.JSVApplet
 
getPropertyAsJavaObject(String) - Method in class jspecview.application.MainFrame
 
getPropertyAsJavaObject(String) - Method in class jspecview.common.JSViewer
 
getPropertyAsJSON(String) - Method in interface jspecview.api.JSVAppletInterface
 
getPropertyAsJSON(String) - Method in class jspecview.app.JSVApp
 
getPropertyAsJSON(String) - Method in class jspecview.appletjs.JSVApplet
 
getPropertyAsJSON(String) - Method in class jspecview.application.MainFrame
 
getPropertyAsJSON(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsJSON(String) - Method in class org.jmol.util.GenericApplet
 
getPropertyAsJSON(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsJSON(String, String) - Method in class org.jmol.util.GenericApplet
@XXXj2sOverride
getPropertyAsString(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsString(String) - Method in class org.jmol.util.GenericApplet
 
getPropertyAsString(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsString(String, String) - Method in class org.jmol.util.GenericApplet
@XXXj2sOverride
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Echo
 
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Shape
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapecgo.CGO
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Draw
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Polyhedra
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
 
getPropertyNumber(String) - Method in interface org.jmol.api.JmolPropertyManager
 
getPropertyNumber(String) - Method in class org.jmol.viewer.PropertyManager
 
getPropertyNumber(String) - Method in class org.jmol.viewer.Viewer
 
getPropI(String, int) - Method in class org.jmol.shapesurface.Isosurface
 
getPropMC(String, int) - Method in class org.jmol.shape.MeshCollection
 
getPropMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
getPropShape(String, Object[]) - Method in class org.jmol.shape.Shape
 
getProteinStructure(int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getProteinStructureState(BS, int) - Method in class org.jmol.modelset.ModelSet
 
getProteinStructureSubType() - Method in class org.jmol.modelset.Group
 
getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureTag() - Method in class org.jmol.modelset.Group
 
getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getProteinStructureType() - Method in class org.jmol.modelset.Group
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getProteinStructureType(String) - Static method in enum class org.jmol.c.STR
In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
getPymolScreenOffset(P3, P3i, int, P3, double) - Method in class org.jmol.modelset.Text
PyMOL will use 1 here for pymolOffset[0] for relative, 0 or absolute.
getQCoefs(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getQCoefs(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getQuadrupolarConstant(Tensor) - Method in interface org.jmol.api.JmolNMRInterface
Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered
getQuadrupolarConstant(Tensor) - Method in class org.jmol.quantum.NMRCalculation
 
getQualifiedDataType() - Method in class jspecview.source.JDXHeader
 
getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
 
getQuality(String) - Method in class org.jmol.dialog.Dialog
 
getQuantumShellTag(int) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getQuantumShellTag(int) - Static method in class org.jmol.quantum.QS
 
getQuantumShellTagID(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getQuantumShellTagID(String) - Static method in class org.jmol.quantum.QS
 
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.quantum.QS
 
getQuaternion(char) - Method in class org.jmol.modelset.Group
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getQuaternionAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternionArray(Object, int) - Method in class org.jmol.script.ScriptEval
 
getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
 
getQuaternionFrame(P3, T3, T3) - Static method in class javajs.util.Quat
returns a quaternion frame based on three points (center, x, and any point in xy plane) or two vectors (vA, vB).
getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
 
getQuaternionFrameCenterAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternionFrameV(V3, V3, V3, boolean) - Static method in class javajs.util.Quat
Create a quaternion based on a frame
getQuaternionP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuaternionParameter(int, BS, boolean) - Method in class org.jmol.script.ScriptParam
 
getQuaternionRotation(String) - Method in interface org.jmol.api.SymmetryInterface
 
getQuaternionRotation(String) - Method in class org.jmol.symmetry.Symmetry
 
getQuotedAttribute(String, String) - Static method in class javajs.util.PT
 
getQuotedOrUnquotedAttribute(String, String) - Static method in class javajs.util.PT
single- or double-quoted string or up to the first space -- like HTML5 not case-sensitive
getQuotedStringAt(String, int) - Static method in class javajs.util.PT
 
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.JvxlReader
 
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getQuotedStringNext(String, int[]) - Static method in class javajs.util.PT
 
getQuotedStringOrObject(char) - Method in class javajs.util.CifDataParser
CIF 1.0 only.
getQuotedStringOrObject(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
final get for quoted object
getRadio(String) - Method in class org.jmol.awt.AwtPopupHelper
 
getRadio(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
getRadio(String) - Method in interface org.jmol.popup.PopupHelper
 
getRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getRadius() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getRadius() - Method in class org.jmol.modelset.Atom
 
getRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
 
getRange(BS, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
getRangeGroups(int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
getRasMolRadius() - Method in class org.jmol.modelset.Atom
 
getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
 
getReader(String, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
Get a reader based on its name.
getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getRealCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
 
getRealEigenvalues() - Method in class javajs.util.Eigen
Return the real parts of the eigenvalues
getReciprocal(T3[], T3[], float) - Static method in class org.jmol.util.SimpleUnitCell
Generate the reciprocal unit cell, scaled as desired
getRecord(String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
getRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
 
getRedField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
 
getRedField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
 
getRedValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
getRedValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getRefreshing() - Method in class org.jmol.viewer.Viewer
 
getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
 
getRegistryInfo() - Method in class org.jmol.util.GenericApplet
 
getRegistryInfo() - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
 
getRemainingScript() - Method in class jspecview.common.ScriptTokenizer
 
getRendering() - Method in class org.jmol.shape.Mesh
 
getResno() - Method in class org.jmol.modelset.Atom
 
getResno() - Method in class org.jmol.modelset.Group
 
getResno() - Method in class org.jmol.smiles.SmilesAtom
 
getResno() - Method in interface org.jmol.util.Node
 
getResolution() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getResolution() - Method in class org.jmol.util.MeshSurface
 
getResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getResourceString(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getResourceString(Object, String, String[]) - Static method in class jspecview.common.JSVFileManager
 
getRGB() - Method in interface javajs.api.GenericColor
 
getRGB() - Method in class org.jmol.awtjs.swing.Color
 
getRhoStar() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getRhoStarField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
 
getRiboseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
 
getRmsd(P3[][], Quat) - Static method in class javajs.util.Measure
 
getRootNode() - Method in interface jspecview.api.JSVTree
 
getRootNode() - Method in class jspecview.application.AwtTree
 
getRootNode() - Method in class jspecview.tree.SimpleTree
 
getRotateBondIndex() - Method in class org.jmol.modelkit.ModelKit
 
getRotation() - Method in class com.sparshui.common.messages.events.RotateEvent
 
getRotation() - Method in class javajs.util.Matrix
similarly to M3/M4 standard rotation/translation matrix we set a rotationTranslation matrix to be: [ nxn rot nx1 trans 1xn 0 1x1 1 ]
getRotation(int) - Method in class javajs.export.PDFCreator
 
getRotation(M3) - Method in class org.jmol.viewer.TransformManager
 
getRotationMatrix(P3, P3, float) - Method in class org.jmol.export.___Exporter
 
getRotationMatrix(P3, P3, float, P3, P3) - Method in class org.jmol.export.___Exporter
 
getRotationQ() - Method in class org.jmol.viewer.TransformManager
 
getRotationScale(M3) - Method in class javajs.util.M4
Gets the upper 3x3 values of this matrix and places them into the matrix m1.
getRotationX() - Method in class com.sparshui.common.messages.events.SpinEvent
 
getRotationY() - Method in class com.sparshui.common.messages.events.SpinEvent
 
getRotationZ() - Method in class com.sparshui.common.messages.events.SpinEvent
 
getRow(int, float[]) - Method in class javajs.util.M3
Copies the matrix values in the specified row into the array parameter.
getRow(int, float[]) - Method in class javajs.util.M34
 
getRow(int, float[]) - Method in class javajs.util.M4
Copies the matrix values in the specified row into the array parameter.
getRow33(int, float[]) - Method in class javajs.util.M34
 
getRowCount() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
getRowCount() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getRowCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getRowDimension() - Method in class javajs.util.Matrix
Get row dimension.
getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
 
getRuleName(int) - Method in class org.jmol.symmetry.CIPChirality
 
getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
 
getSavedState(String) - Method in class org.jmol.viewer.StateManager
 
getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
 
getSavedUnitCell(String) - Method in class org.jmol.viewer.StateManager
 
getSaveFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
 
getSaveFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
 
getScale() - Method in class com.sparshui.common.messages.events.ZoomEvent
 
getScale() - Method in class jspecview.common.ViewData
 
getScale() - Method in interface org.jmol.api.JmolModulationSet
 
getScale() - Method in class org.jmol.util.ModulationSet
 
getScaleData() - Method in class jspecview.common.ViewData
 
getScalePixelsPerAngstrom(boolean) - Method in class org.jmol.viewer.Viewer
 
getScaleText(String, boolean, float, float[]) - Method in class org.jmol.viewer.Viewer
Depending upon the measure text, we need to indicate |-------| 1 A or 0.1 A for example.
getScreenDim() - Method in class org.jmol.viewer.Viewer
 
getScreenDimensions(Dimension) - Method in interface org.jmol.awtjs.swing.SwingController
Return the width and height of the window in d.
getScreenHeight() - Method in class org.jmol.api.JmolViewer
 
getScreenHeight() - Method in class org.jmol.viewer.Viewer
 
getScreenImage() - Method in class org.jmol.viewer.Viewer
 
getScreenImage() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
getScreenImage(boolean) - Method in class org.jmol.g3d.Graphics3D
 
getScreenImage(boolean) - Method in class org.jmol.util.GData
 
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.api.JmolViewer
 
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.viewer.Viewer
Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
getScreenNormal(T3, T3, float) - Method in class org.jmol.export._PovrayExporter
 
getScreenNormal(T3, T3, float) - Method in class org.jmol.export._TachyonExporter
 
getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager
 
getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager4D
 
getScreenWidth() - Method in class org.jmol.api.JmolViewer
 
getScreenWidth() - Method in class org.jmol.viewer.Viewer
 
getScript() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getScript() - Method in class org.jmol.script.ScriptEval
 
getScriptContext(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
getScriptContext(String) - Method in class org.jmol.script.ScriptEval
 
getScriptContext(String) - Method in class org.jmol.viewer.Viewer
 
getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
getScriptEditor() - Method in class org.jmol.console.GenericConsole
 
getScriptEditor() - Method in class org.jmol.console.JmolConsole
 
getScriptEditor() - Method in class org.jmol.consolejs.AppletConsole
 
getScriptForCallback(SC, String, String) - Method in class jspecview.popup.JSVGenericPopup
 
getScriptForCallback(SC, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
Secondary processing of menu item click
getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.GenericPopup
 
getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.JmolPopup
 
getScriptItem(boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
getScriptItem(boolean, boolean) - Method in class org.jmol.script.ScriptManager
 
getScriptQueue() - Method in interface jspecview.api.JSVAppInterface
 
getScriptQueue() - Method in class jspecview.app.JSVApp
 
getScriptQueue() - Method in class jspecview.application.MainFrame
 
getScriptQueue() - Method in interface org.jmol.api.JmolScriptManager
 
getScriptQueue() - Method in class org.jmol.script.ScriptManager
 
getScriptQueueInfo() - Method in class org.jmol.viewer.Viewer
 
getScriptToken(String) - Static method in enum class jspecview.common.ScriptToken
 
getScriptTokenList(String, boolean) - Static method in enum class jspecview.common.ScriptToken
 
getSDFDateLine(String) - Static method in class jme.JMEUtil
See CTFile -- this line is NOT optional.
getSDFDateLine(String, boolean) - Static method in class org.jmol.viewer.PropertyManager
 
getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getSelected() - Method in class org.jmol.shape.Measures
 
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
 
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getSelectedAtomIterator(BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
getSelectedDisplayScheme() - Method in class jspecview.application.PreferencesDialog
Retruns the current Display Scheme
getSelectedIndex() - Method in class org.jmol.awtjs.swing.JComboBox
 
getSelectedIndex(Object) - Method in interface jspecview.api.PlatformDialog
 
getSelectedIndex(Object) - Method in class jspecview.java.AwtDialog
 
getSelectedIndex(Object) - Method in class jspecview.js2d.JsDialog
 
getSelectedIntegral() - Method in class jspecview.common.PanelData
 
getSelectedItem() - Method in class org.jmol.awtjs.swing.JComboBox
 
getSelectedItem(Object) - Method in interface jspecview.api.PlatformDialog
 
getSelectedItem(Object) - Method in class jspecview.java.AwtDialog
 
getSelectedItem(Object) - Method in class jspecview.js2d.JsDialog
 
getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedPeak() - Method in class jspecview.common.Spectrum
 
getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
 
getSelectionHalosEnabled() - Method in class org.jmol.viewer.Viewer
 
getSelectionModel() - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
 
getSelectionModel() - Method in class org.jmol.awtjs.swing.JTable
 
getSelectorName(Object) - Method in class jspecview.dialog.DialogManager
 
getSeqCode(T) - Static method in class org.jmol.script.ScriptEval
 
getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSeqcodeFor(int, char) - Static method in class org.jmol.modelset.Group
 
getSeqcodeString() - Method in class org.jmol.modelset.Group
 
getSeqcodeStringFor(int) - Static method in class org.jmol.modelset.Group
 
getSeqID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getSeqID() - Method in class org.jmol.modelset.Atom
 
getSeqNumberFor(int) - Static method in class org.jmol.modelset.Group
 
getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
 
getSequenceBits(String, BS, BS) - Method in class org.jmol.modelset.ModelSet
 
getSequenceNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getSequenceNumber(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getSequenceNumber(int) - Method in interface org.jmol.api.PymolAtomReader
 
getSerial() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getServiceCommand(String) - Static method in class org.jmol.viewer.JC
 
getSetAxesTypeMad10(int) - Method in class org.jmol.script.ScriptEval
 
getSetHistory(int) - Method in class org.jmol.api.JmolViewer
 
getSetHistory(int) - Method in class org.jmol.util.CommandHistory
Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n invalid input: '<'= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
getSetHistory(int) - Method in class org.jmol.viewer.Viewer
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n invalid input: '<'= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
getSettableTokFromString(String) - Static method in class org.jmol.script.T
 
getShadeB(float, float, float) - Method in class org.jmol.util.Shader
 
getShadeFp8(float, float, float) - Method in class org.jmol.util.Shader
 
getShadeIndex(float, float, float) - Method in class org.jmol.util.Shader
 
getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
 
getShadeN(float, float, float, float) - Method in class org.jmol.util.Shader
 
getShades(short) - Method in class org.jmol.util.GData
 
getShape(int) - Method in class org.jmol.viewer.ShapeManager
 
getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JC
 
getShapeDetail() - Method in class org.jmol.shape.Echo
 
getShapeDetail() - Method in class org.jmol.shape.Shape
 
getShapeDetail() - Method in class org.jmol.shapecgo.CGO
 
getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeDetail() - Method in class org.jmol.shapespecial.Draw
 
getShapeDetail() - Method in class org.jmol.shapespecial.Polyhedra
 
getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
 
getShapeErrorState() - Method in class org.jmol.viewer.Viewer
 
getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
Returns the shape type index for a shape object given the object name.
getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEval
 
getShapeProperty(int, String) - Method in class org.jmol.scriptext.ScriptExt
 
getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
 
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.script.ScriptEval
 
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
 
getShapePropertyIndex(int, String, int) - Method in class org.jmol.viewer.ShapeManager
 
getShapeState() - Method in class org.jmol.shape.AtomShape
 
getShapeState() - Method in class org.jmol.shape.FontLineShape
 
getShapeState() - Method in class org.jmol.shape.Frank
 
getShapeState() - Method in class org.jmol.shape.Shape
 
getShapeState() - Method in class org.jmol.shape.Sticks
 
getShapeState() - Method in class org.jmol.shape.TextShape
 
getShapeState() - Method in class org.jmol.shapebio.BioShape
 
getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
 
getShapeState() - Method in class org.jmol.shapecgo.CGO
 
getShapeState() - Method in class org.jmol.shapespecial.Dipole
 
getShapeState() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeState() - Method in class org.jmol.shapespecial.Dots
 
getShapeState() - Method in class org.jmol.shapespecial.Draw
 
getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
 
getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
 
getShapeState() - Method in class org.jmol.shapesurface.Isosurface
 
getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
 
getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
 
getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JC
 
getShowAnnotation(Annotation.AType) - Method in class jspecview.common.PanelData
 
getShowAxes() - Method in class org.jmol.viewer.Viewer
 
getShowBbcage() - Method in class org.jmol.viewer.Viewer
 
getShowFrank() - Method in class org.jmol.viewer.Viewer
 
getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
 
getShowSelectedOnce() - Method in class org.jmol.viewer.Viewer
 
getShowUnitCell() - Method in class org.jmol.viewer.Viewer
 
getSignature() - Method in interface org.jmol.api.JmolScriptFunction
 
getSignature() - Method in class org.jmol.script.ScriptFunction
 
getSimpleXmlReader(BufferedReader) - Method in class jspecview.source.AnIMLReader
 
getSimulationFileData(String, String) - Static method in class jspecview.common.JSVFileManager
 
getSimulationType(String) - Static method in class jspecview.common.JSVFileManager
 
getSiteMultiplicity(P3) - Method in interface org.jmol.api.SymmetryInterface
 
getSiteMultiplicity(P3) - Method in class org.jmol.symmetry.Symmetry
 
getSize(int) - Method in class org.jmol.shape.AtomShape
 
getSize(int) - Method in class org.jmol.shape.Shape
overridden in Dots, CGOMesh, and AtomShape
getSize(int) - Method in class org.jmol.shapespecial.Dots
 
getSize(int, boolean) - Static method in class org.jmol.shapecgo.CGOMesh
 
getSizeG(Group) - Method in class org.jmol.shape.Shape
 
getSizeG(Group) - Method in class org.jmol.shapebio.BioShapeCollection
 
getSlabColor() - Method in class org.jmol.util.MeshSurface
 
getSlabObjectType(int, Object, boolean, Object) - Static method in class org.jmol.util.TempArray
 
getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
 
getSlabType() - Method in class org.jmol.util.MeshSurface
 
getSlabWithinRange(float, float) - Static method in class org.jmol.util.TempArray
 
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.AdfReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.AmsReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.CsfReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.DgridReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUKReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.GamessUSReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.MoldenReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.WebMOReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaters() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.AmsReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
 
getSlaters() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
getSmartsMap(String, BS, int) - Method in class org.jmol.viewer.Viewer
 
getSmartsMatch(String, BS) - Method in class org.jmol.api.JmolViewer
 
getSmartsMatch(String, BS) - Method in class org.jmol.viewer.Viewer
 
getSmartsMatchForNodes(String, Node[]) - Method in class org.jmol.viewer.Viewer
 
getSmiles(BS) - Method in class org.jmol.api.JmolViewer
 
getSmiles(BS) - Method in class org.jmol.viewer.Viewer
NOT getting aromatic smiles
getSmiles(Node[], int, BS, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSmiles(Node[], int, BS, String, int) - Method in class org.jmol.smiles.SmilesMatcher
internal to Jmol -- called by org.jmol.Viewer.getSmiles
getSmilesAtoms(String) - Method in class org.jmol.viewer.Viewer
 
getSmilesChiralityArray() - Method in class org.jmol.symmetry.CIPDataSmiles
 
getSmilesCorrelation(BS, BS, String, Lst<P3>, Lst<P3>, M4, Lst<BS>, boolean, int[][], P3, boolean, int) - Method in class org.jmol.scriptext.SmilesExt
The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
getSmilesExt() - Method in class org.jmol.script.ScriptEval
 
getSmilesFromJME(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSmilesFromJME(String) - Method in class org.jmol.smiles.SmilesMatcher
 
getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
 
getSmilesMatches(String, Object, BS, BS, int, boolean, boolean) - Method in class org.jmol.scriptext.SmilesExt
 
getSmilesOpt(BS, int, int, int, String) - Method in class org.jmol.viewer.Viewer
returns the SMILES string for a sequence or atom set does not include attached protons on groups
getSolnColour() - Method in interface jspecview.api.JSVAppletInterface
Returns the calculated colour of a visible spectrum (Transmittance)
getSolnColour() - Method in class jspecview.app.JSVApp
Returns the calculated colour of a visible spectrum (Transmittance)
getSolnColour() - Method in class jspecview.appletjs.JSVApplet
 
getSolnColour() - Method in class jspecview.application.MainFrame
 
getSolutionColor(boolean) - Method in class jspecview.common.JSViewer
 
GETSOLUTIONCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
getSolutionColorStr(boolean) - Method in class jspecview.common.JSViewer
 
getSortingStatus(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getSource(String, BufferedReader) - Method in interface jspecview.api.SourceReader
 
getSource(String, BufferedReader) - Method in class jspecview.source.AnIMLReader
 
getSourceID() - Method in class jspecview.common.PanelData
 
getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfoObj(String, Object, boolean, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupInfoObj(String, Object, boolean, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupJSON(Viewer, String, Object, int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupJSON(Viewer, String, Object, int) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupNameType(String) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupNameType(String) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperationCode(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupTitle() - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
getSpaceGroupXyz(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupXyz(int, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecialLabel(String, String) - Method in class org.jmol.popup.JmolPopup
menus or menu items with SPECIAL in their name are sent here for on-the-fly labeling
getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSpectra() - Method in class jspecview.source.JDXSource
Returns the Vector of Spectra
getSpectraAsArray() - Method in class jspecview.source.JDXSource
Used in Android
getSpectrum() - Method in interface jspecview.api.AnnotationData
 
getSpectrum() - Method in class jspecview.common.Measurement
 
getSpectrum() - Method in class jspecview.common.MeasurementData
 
getSpectrum() - Method in class jspecview.common.PanelData
 
getSpectrum() - Method in class jspecview.common.PanelNode
 
getSpectrum() - Method in class jspecview.dialog.JSVDialog
 
getSpectrumAt(int) - Method in class jspecview.common.PanelData
 
getSpectrumListAsString(Lst<PanelNode>) - Static method in class jspecview.common.PanelNode
 
getSpecular() - Method in class org.jmol.util.GData
 
getSpecularExponent() - Method in class org.jmol.util.GData
 
getSpecularPercent() - Method in class org.jmol.util.GData
 
getSpecularPower() - Method in class org.jmol.util.GData
 
getSpeedLevel() - Method in class com.sparshui.common.messages.events.FlickEvent
 
getSPF(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlReader
 
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getSphereData(int) - Static method in class org.jmol.util.MeshSurface
Calculates the data (faces, vertices, normals) for a sphere.
getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
 
getSpinOp(int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpinOp(int) - Method in class org.jmol.symmetry.Symmetry
 
getSpinState() - Method in class org.jmol.viewer.Viewer
 
getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
 
getStartChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStartChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStartingPointIndex(int) - Method in class jspecview.common.PanelData
 
getStartingPointIndex(int) - Method in class jspecview.common.ViewData
in some cases, there is only one scaleData, but there are more than that number of spectra this is no problem -- we just use mod to set this to 0
getStartInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStartInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getState() - Method in class com.sparshui.common.messages.events.TouchEvent
 
getState() - Method in class com.sparshui.server.GestureServer
 
getState() - Method in class com.sparshui.server.TouchPoint
Get the touch point state.
getState() - Method in interface jspecview.api.AnnotationData
 
getState() - Method in class jspecview.common.MeasurementData
 
getState() - Method in class jspecview.dialog.JSVDialog
 
getState() - Method in interface org.jmol.api.JmolGestureServerInterface
 
getState() - Method in interface org.jmol.api.JmolModulationSet
 
getState() - Method in class org.jmol.modelset.Trajectory
 
getState() - Method in class org.jmol.util.ModulationSet
 
getState(String) - Method in class org.jmol.shape.Mesh
 
getState(SB) - Method in interface org.jmol.api.JmolNMRInterface
 
getState(SB) - Method in class org.jmol.quantum.NMRCalculation
 
getState(ModelSet, int, SB) - Method in interface org.jmol.api.SymmetryInterface
 
getState(ModelSet, int, SB) - Method in class org.jmol.symmetry.Symmetry
 
getStateCreator() - Method in class org.jmol.viewer.Viewer
 
getStateInfo() - Method in class org.jmol.api.JmolViewer
 
getStateInfo() - Method in class org.jmol.viewer.Viewer
 
getStateInfo3(String, int, int) - Method in class org.jmol.viewer.Viewer
 
getStateText() - Method in class org.jmol.modelset.Text
 
getStaticGraphics(Object, boolean) - Method in class jspecview.java.AwtPlatform
 
getStaticGraphics(Object, boolean) - Method in class jspecview.js2d.JsPlatform
 
getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.GenericPlatform
 
getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
 
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs.Platform
 
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs2d.Platform
 
getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
 
getStereo() - Method in class org.jmol.smiles.SmilesAtom
 
getStereoAtAt(SimpleNode[]) - Method in class org.jmol.smiles.SmilesAtom
 
getStereoMode(String) - Static method in enum class org.jmol.c.STER
 
getStrandCount() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStrandCount() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStrandCount(int) - Method in class org.jmol.viewer.Viewer
 
getStrandID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStrandID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStream() - Method in class javajs.util.Rdr.StreamReader
 
getStream(InputStream) - Method in class org.apache.tools.bzip2.CBZip2InputStreamFactory
jsjava addition for reflection
getStreamAsBytes(BufferedInputStream, OC) - Static method in class javajs.util.Rdr
Read a an entire BufferedInputStream for its bytes, and either return them or leave them in the designated output channel.
getStreamAsBytes(BufferedInputStream, OC) - Static method in class jspecview.common.JSVFileManager
 
getStreamAsString(InputStream) - Static method in class javajs.util.ZipTools
 
getString() - Method in class org.jmol.modelset.Measurement
 
getString(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
getStringArray(Object, String) - Static method in class org.qcschema.QCSchemaUnits
Retrieve a String array, possibly unpacking it if it is run-length encoded.
getStringDetail() - Method in class org.jmol.modelset.Measurement
 
getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getStringX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getStringX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
 
getStringX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getStrucNo() - Method in class org.jmol.modelset.Group
 
getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getStructure() - Method in class org.jmol.modelset.Group
 
getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getStructuredModels() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStructuredModels() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStructureId() - Method in class org.jmol.modelset.Group
 
getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getStructureId() - Method in class org.jmol.modelsetbio.Monomer
 
getStructureID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStructureID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a StructureIterator.
getStructureList() - Method in class org.jmol.modelset.ModelSet
 
getStructureList() - Method in class org.jmol.viewer.GlobalSettings
 
getStructureList() - Method in class org.jmol.viewer.Viewer
 
getStructureMap(Lst<Object>, String, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure
getStructures(String, String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.
getStructures46(String[], String, Lst<Object>, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
getStructureState() - Method in class org.jmol.viewer.Viewer
 
getStructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStuctureAsText(String, String[][], String[][]) - Method in class org.jmol.popup.PopupResource
 
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Component
 
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Container
 
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.JSplitPane
 
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Component
 
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Container
 
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.JSplitPane
 
getSubgroupJSON(Viewer, int, int, int, int) - Method in interface org.jmol.api.SymmetryInterface
 
getSubgroupJSON(Viewer, int, int, int, int) - Method in class org.jmol.symmetry.Symmetry
Retrieve subgroup information for a space group.
getSubIndex() - Method in class jspecview.common.Spectrum
 
getSubIndex() - Method in class jspecview.common.SubSpecChangeEvent
 
getSubmatrix(int, int, int, int) - Method in class javajs.util.Matrix
Get a submatrix.
getSubSpectra() - Method in class jspecview.common.Spectrum
 
getSubstructureSet(Object, Object, int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSet(Object, Object, int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
Returns a bitset matching the pattern within a set of Jmol atoms.
getSubstructureSetArray(String, BS, int) - Method in class org.jmol.viewer.Viewer
 
getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
Returns a vector of bitsets indicating which atoms match the pattern.
getSubstructureSetArrayForNodes(String, Node[], int) - Method in class org.jmol.viewer.Viewer
 
getSubstructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getSubstructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getSubSystemUnitCell() - Method in interface org.jmol.api.JmolModulationSet
 
getSubSystemUnitCell() - Method in class org.jmol.util.ModulationSet
 
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
 
getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
 
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
 
getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
 
getSwingComponent(Object) - Method in class org.jmol.awt.AwtPopupHelper
 
getSwingComponent(Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
getSwingComponent(Object) - Method in interface org.jmol.popup.PopupHelper
 
getSym(int) - Method in class org.jmol.modelkit.ModelKit
 
getSymEditState() - Method in class org.jmol.modelkit.ModelKit
 
getSymMatrices(int) - Method in class org.jmol.modelset.ModelSet
 
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
getSymmetry() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getSymmetry(Viewer, String) - Static method in class org.jmol.api.Interface
 
getSymmetryEquivAtoms(BS, SymmetryInterface, BS) - Method in class org.jmol.modelset.ModelSet
Return a bitset of equivalent atoms
getSymmetryEquivAtomsForAtom(int, BS, BS, BS) - Method in class org.jmol.modelset.ModelSet
Set a bitset of the equivalent atoms of an atom.
getSymmetryEquivPointList(Lst<P3>, String) - Method in class org.jmol.viewer.Viewer
 
getSymmetryEquivPoints(P3, String) - Method in class org.jmol.viewer.Viewer
 
getSymmetryFromCode(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getSymmetryFromCode(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getSymmetryInfo(int, String, int, P3, P3, P3, int, String, float, int, int, int[]) - Method in class org.jmol.viewer.Viewer
A general method for retrieving symmetry information with full capability of the symop() scripting function.
getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelSet
 
getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int, int[]) - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int, int[]) - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryInfoStr() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfoStr() - Method in class org.jmol.symmetry.Symmetry
When information is desired about the space group, we use SymmetryInfo.
getSymmetryInvariant(int) - Method in class org.jmol.modelset.ModelSet
 
getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
getSymopText() - Method in class org.jmol.modelkit.ModelKit
 
getSymStatic() - Method in class org.jmol.viewer.Viewer
Retrieve the static Symmetry object, which should be used only statically
getSymTemp() - Method in class org.jmol.viewer.Viewer
Retrieve a new Symmetry object.
getSymViewState() - Method in class org.jmol.modelkit.ModelKit
 
getSyncFlush() - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
getSyncMode() - Method in class org.jmol.viewer.StatusManager
 
getTableHeader() - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getTableModel() - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
 
getTagName() - Method in class jspecview.source.XMLParser
 
getTagName(String) - Static method in class jspecview.common.JSVFileManager
Returns a name that can be used as a tag, possibly abbreviated.
getTagType() - Method in class jspecview.source.XMLParser
 
getTaintedAtoms(int) - Method in class org.jmol.modelset.AtomCollection
 
getTauField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
 
getTensor(Viewer, float[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.UnitCell
 
getTensorInfo(String, String, BS) - Method in interface org.jmol.api.JmolNMRInterface
 
getTensorInfo(String, String, BS) - Method in class org.jmol.quantum.NMRCalculation
 
getTensors() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getTensors() - Method in class org.jmol.modelset.Atom
 
getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
getText() - Method in interface org.jmol.api.js.GenericConsoleTextArea
 
getText() - Method in interface org.jmol.api.SC
 
getText() - Method in class org.jmol.awt.AwtSwingComponent
 
getText() - Method in class org.jmol.awtjs.swing.Component
 
getText() - Method in class org.jmol.console.GenericConsole
 
getText() - Method in interface org.jmol.console.GenericTextArea
 
getText() - Method in class org.jmol.console.ScriptEditor
 
getText() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
getText(Object) - Method in interface jspecview.api.PlatformDialog
 
getText(Object) - Method in class jspecview.java.AwtDialog
 
getText(Object) - Method in class jspecview.js2d.JsDialog
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class jspecview.java.AwtPlatform
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class jspecview.js2d.JsPlatform
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs.Platform
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
 
getTextPosition() - Method in class org.jmol.util.GData
 
getTFToggle(String) - Static method in class jspecview.common.Parameters
 
getThermalRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getTheta() - Method in class javajs.util.Quat
 
getThetaDirected(P4) - Method in class javajs.util.Quat
 
getThetaDirectedV(V3) - Method in class javajs.util.Quat
 
getThetaRadians() - Method in class javajs.util.Quat
 
getThisContext() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getThisContext() - Method in class org.jmol.script.ScriptEval
 
getThisModelAtoms() - Method in class org.jmol.viewer.Viewer
 
getThread() - Method in class org.jmol.minimize.Minimizer
 
getThresh() - Method in class jspecview.common.PeakData
 
getTime() - Method in class com.sparshui.common.messages.events.DragEvent
 
getTime() - Method in class com.sparshui.common.messages.events.RotateEvent
 
getTime() - Method in class com.sparshui.common.messages.events.TouchEvent
 
getTime() - Method in class com.sparshui.common.messages.events.ZoomEvent
 
getTime() - Method in class com.sparshui.server.TouchPoint
 
getTime() - Method in class jspecview.source.JDXHeader
Getter for property time.
getTimerMsg(String, int) - Static method in class org.jmol.util.Logger
 
getTip() - Method in enum class jspecview.common.ScriptToken
 
getTitle() - Method in interface jspecview.api.JSVViewPanel
 
getTitle() - Method in class jspecview.common.PanelData
Returns the title displayed on the graph
getTitle() - Method in class jspecview.common.PeakInfo
 
getTitle() - Method in class jspecview.java.AwtMainPanel
 
getTitle() - Method in class jspecview.java.AwtPanel
 
getTitle() - Method in class jspecview.js2d.JsMainPanel
 
getTitle() - Method in class jspecview.js2d.JsPanel
 
getTitle() - Method in class jspecview.source.JDXHeader
Getter for property title.
getTitleLabel() - Method in class jspecview.common.Spectrum
 
gettMixField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
 
getTok() - Method in interface org.jmol.api.JmolScriptFunction
 
getTok() - Method in class org.jmol.script.ScriptFunction
 
getToken(int) - Method in class org.jmol.script.ScriptContext
 
getToken(int) - Method in class org.jmol.script.ScriptParam
 
getToken(int) - Method in class org.jmol.scriptext.ScriptExt
 
getTokenCount() - Method in class org.jmol.script.ScriptContext
 
getTokenFromName(String) - Static method in class org.jmol.script.T
 
getTokenPeeked() - Method in interface javajs.api.GenericCifDataParser
 
getTokenPeeked() - Method in class javajs.util.CifDataParser
 
getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens() - Method in class org.jmol.jvxl.readers.JvxlReader
 
getTokens() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getTokens() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getTokens(String) - Static method in class javajs.util.PT
 
getTokens(String) - Static method in enum class jspecview.common.ScriptToken
read a string for possibly quoted tokens separated by space until // or # is reached.
getTokensAt(String, int) - Static method in class javajs.util.PT
 
getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokensLike(String) - Static method in class org.jmol.script.T
 
getTokensType(Map<String, Object>, int) - Static method in class org.jmol.script.T
 
getTokFromName(String) - Static method in class org.jmol.script.T
 
getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
 
getTopPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
 
getTorsionAngleRadians(double[], double[], double[], double[], V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
getTorsions(boolean) - Method in class org.jmol.minimize.Minimizer
 
getTotalHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getTotalHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getTotalHydrogenCount() - Method in interface org.jmol.util.Node
 
getTotalIn() - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
getTotalIn() - Method in class com.jcraft.jzlib.InflaterInputStream
 
getTotalIn() - Method in class com.jcraft.jzlib.ZStream
 
getTotalOut() - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
getTotalOut() - Method in class com.jcraft.jzlib.InflaterInputStream
 
getTotalOut() - Method in class com.jcraft.jzlib.ZStream
 
getTotalValence() - Method in class org.jmol.modelset.Atom
 
getTotalValence() - Method in class org.jmol.smiles.SmilesAtom
 
getTotalValence() - Method in interface org.jmol.util.Node
 
getTouchID() - Method in class com.sparshui.common.messages.events.TouchEvent
 
getTrajectoryState() - Method in class org.jmol.viewer.Viewer
 
getTransferData(DataFlavor) - Method in class jspecview.java.AwtClipboard
 
getTransferData(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
 
getTransferDataFlavors() - Method in class jspecview.java.AwtClipboard
 
getTransferDataFlavors() - Method in class org.jmol.awt.AwtClipboard
 
getTransform(P3, P3, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getTransform(P3, P3, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getTransform(UnitCell, SymmetryOperation[], P3, P3, boolean) - Method in class org.jmol.symmetry.SymmetryDesc
 
getTransformABC(Object, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getTransformedVertexVectors() - Method in class org.jmol.util.GData
 
getTransformMatrix4(Lst<P3>, Lst<P3>, M4, P3) - Static method in class javajs.util.Measure
Fills a 4x4 matrix with rotation-translation of mapped points A to B.
getTranslation() - Method in class javajs.util.Matrix
 
getTranslation(int) - Method in class org.jmol.modelset.ModelSet
 
getTranslation(T3) - Method in class javajs.util.M4
Retrieves the translational components of this matrix.
getTranslationScript() - Method in class org.jmol.viewer.TransformManager
 
getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
 
getTranslucentLevel(int) - Method in class org.jmol.script.ScriptEval
 
getTreeNode() - Method in class jspecview.common.PanelNode
 
getTriad(T3) - Method in class org.jmol.export.___Exporter
 
getTriad(T3) - Method in class org.jmol.export._PovrayExporter
 
getTriadC(T3) - Method in class org.jmol.export.___Exporter
 
getTriangulator() - Method in class org.jmol.viewer.Viewer
 
getTrueAtomCount() - Method in class org.jmol.modelset.Model
not actually accessed -- just pointing out what it is
getType() - Method in class javajs.util.OC
 
getType() - Method in class jspecview.common.PeakInfo
 
getType() - Method in interface org.jmol.api.JmolDialogInterface
 
getType() - Method in class org.jmol.dialog.Dialog
 
getType() - Method in class org.jmol.modelsetbio.BioPolymer
 
getType(int) - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
getType(String) - Static method in enum class jspecview.common.ExportType
 
getType(Atom) - Static method in enum class org.jmol.c.HB
 
getTypeLabel() - Method in class jspecview.source.JDXDataObject
 
getUndoInfo() - Method in class org.jmol.viewer.StateManager
 
getUndoMax() - Method in class org.jmol.viewer.StateManager
 
getUndoRedoState(int) - Method in class org.jmol.viewer.StateManager
 
getUnGzippedInputStream(byte[]) - Method in interface javajs.api.GenericZipTools
 
getUnGzippedInputStream(byte[]) - Method in class javajs.util.ZipTools
 
getUniqueID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getUniqueID() - Method in class org.jmol.modelsetbio.Monomer
 
getUniqueID(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getUniqueID(int) - Method in interface org.jmol.api.PymolAtomReader
 
getUniqueTensorSet(BS) - Method in interface org.jmol.api.JmolNMRInterface
An attempt to find unique atoms using tensors.
getUniqueTensorSet(BS) - Method in class org.jmol.quantum.NMRCalculation
 
getUnitCell() - Method in class org.jmol.shape.Mesh
 
getUnitCell() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getUnitCell(int) - Method in class org.jmol.modelset.ModelSet
 
getUnitCell(T3[], boolean, String) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCell(T3[], boolean, String) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
 
getUnitCellAtomIndex() - Method in class org.jmol.viewer.AnimationManager
 
getUnitCellCenter() - Method in class org.jmol.script.ScriptParam
 
getUnitCellDisplayName() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellDisplayName() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellForAtom(int) - Method in class org.jmol.modelset.ModelSet
 
getUnitCellInfo(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfo(boolean) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
 
getUnitCellInfoMap() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfoMap() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
 
getUnitCellInfoType(int) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfoType(int) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellMultiplied() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellMultiplied() - Method in class org.jmol.symmetry.Symmetry
Note, this has no origin shift.
getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellParams() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellParams() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellParams() - Method in class org.jmol.util.SimpleUnitCell
 
getUnitCellPointsWithin(float, BS, P3, boolean) - Method in class org.jmol.modelset.ModelSet
 
getUnitCellState() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellState() - Method in class org.jmol.modelkit.ModelKit
 
getUnitCellState() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellVectors() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellVectors() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellVerticesNoOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellVerticesNoOffset() - Method in class org.jmol.symmetry.Symmetry
 
getUnitConversion(String, String) - Static method in class org.qcschema.QCSchemaUnits
Calculate the unit conversion between two units, using a static unit-to-unit cache for efficiency.
getUnitID(int) - Method in class org.jmol.modelset.Atom
 
getUnitID(Atom, int) - Method in class org.jmol.modelsetbio.BioModel
Get a unitID.
getUnitIDFlags(String) - Static method in class org.jmol.viewer.JC
Get a unitID type
getUnitsJSON(String, boolean) - Static method in class org.qcschema.QCSchemaUnits
Get the [name, toAU] JSON code or just a new String[] {name, toAU}.
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class jspecview.java.AwtPopup
 
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class jspecview.popup.JSVGenericPopup
 
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
 
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
 
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
 
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
 
getUnlikely() - Static method in class javajs.util.P3
 
getUnzippedInputStream(GenericZipTools, BufferedInputStream) - Static method in class javajs.util.Rdr
Drill down into a GZIP stack until no more layers.
getUnzippedInputStreamBZip2(GenericZipTools, BufferedInputStream) - Static method in class javajs.util.Rdr
 
getUnzippedReaderOrStreamFromName(String, Object, boolean, boolean, boolean, boolean, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
 
getURLContents(URL, byte[], String, boolean) - Method in class jspecview.java.AwtPlatform
 
getURLContents(URL, byte[], String, boolean) - Method in class jspecview.js2d.JsPlatform
 
getURLContents(URL, byte[], String, boolean) - Method in interface org.jmol.api.GenericPlatform
 
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awt.Platform
 
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awtjs2d.Platform
 
getURLContentsStatic(URL, byte[], String, boolean) - Static method in class org.jmol.awtjs2d.Platform
In case this needs to be performed directly, without interface
getUrlFromDialog(String, String) - Method in interface jspecview.api.JSVFileHelper
 
getUrlFromDialog(String, String) - Method in class jspecview.java.AwtFileHelper
 
getUrlFromDialog(String, String) - Method in class jspecview.js2d.JsFileHelper
 
getUserDirectory() - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserFunctionResult(String, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
 
getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
 
getUserYFactor() - Method in class jspecview.common.Spectrum
 
getUtil(String, Viewer, String) - Static method in class org.jmol.api.Interface
 
getV0abc(int, Object) - Method in class org.jmol.viewer.Viewer
convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c.
getV0abc(Object, M4) - Method in interface org.jmol.api.SymmetryInterface
 
getV0abc(Object, M4) - Method in class org.jmol.symmetry.Symmetry
 
getV3() - Method in interface org.jmol.api.JmolModulationSet
 
getV3() - Method in class org.jmol.util.ModulationSet
 
getValence() - Method in class org.jmol.modelset.Atom
return the total bond order for this atom
getValence() - Method in class org.jmol.modelset.Bond
 
getValence() - Method in class org.jmol.smiles.SmilesAtom
 
getValence() - Method in class org.jmol.smiles.SmilesBond
 
getValence() - Method in interface org.jmol.util.Node
 
getValence() - Method in interface org.jmol.util.SimpleNode
 
getValidValues(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getValidVertices(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getValue() - Method in class com.jcraft.jzlib.Adler32
 
getValue() - Method in interface com.jcraft.jzlib.Checksum
 
getValue() - Method in class com.jcraft.jzlib.CRC32
 
getValue() - Method in class jspecview.common.Measurement
 
getValue() - Method in class jspecview.source.JDXSourceStreamTokenizer
 
getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
for readers only
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
 
getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
getValue(String, String) - Method in class org.jmol.util.GenericApplet
 
getValue(ScriptToken, ScriptTokenizer, String) - Static method in enum class jspecview.common.ScriptToken
tweak command options depending upon special cases
getValue2(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValueArray(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getValueAt(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
getValueAtPoint(P3) - Method in class org.jmol.quantum.MepCalculation
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValues(Mesh) - Method in class org.jmol.shape.MeshCollection
 
getValues(Mesh) - Method in class org.jmol.shapesurface.Isosurface
 
getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsMar(int, VDW) - Static method in class org.jmol.util.Elements
 
getVanderwaalsMarType(int, VDW) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsRadiusFloat(Viewer, VDW) - Method in class org.jmol.modelset.Atom
 
getVariable(Object) - Static method in class org.jmol.script.SV
 
getVariable(String) - Method in class org.jmol.script.ScriptContext
Context variables go up the stack until a function is found.
getVariableAD(double[]) - Static method in class org.jmol.script.SV
 
getVariableList() - Method in class org.jmol.viewer.GlobalSettings
 
getVariableList(Map<String, SV>, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
 
getVariableList(Lst<?>) - Static method in class org.jmol.script.SV
 
getVariableMap(Map<String, ?>) - Static method in class org.jmol.script.SV
 
getVarList(String) - Static method in class jspecview.source.JDXReader
 
getVarParameter(String, boolean) - Method in class org.jmol.script.ScriptParam
 
getVDW(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getVDW(int) - Method in interface org.jmol.api.PymolAtomReader
 
getVdwLabel() - Method in enum class org.jmol.c.VDW
 
getVdwType(String) - Static method in enum class org.jmol.c.VDW
 
getVdwType2(String) - Static method in enum class org.jmol.c.VDW
 
getVector(int) - Method in class javajs.util.Quat
 
getVector(Location) - Method in class com.sparshui.common.Location
 
getVectorScaled(int, float) - Method in class javajs.util.Quat
 
getVersion() - Method in class javajs.util.CifDataParser
 
getVersion() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
 
getVersion() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
getVersion() - Method in interface org.openscience.jmol.app.JmolPlugin
 
getVertexCount(int) - Static method in class org.jmol.util.Geodesic
 
getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
 
getVertexVector(int) - Static method in class org.jmol.util.Geodesic
 
getVertexVectors() - Static method in class org.jmol.util.Geodesic
 
getVertexVectors() - Static method in class org.jmol.util.Normix
 
getVertices() - Method in class org.jmol.util.MeshSurface
 
getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
 
getVertices(Mesh) - Method in class org.jmol.shapesurface.Isosurface
 
getVerticesFromOABC(T3[]) - Static method in class org.jmol.util.BoxInfo
 
getVib() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getVib(char) - Method in class org.jmol.modelset.Atom
 
getVibCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
also handles modulation info
getVibration(boolean) - Method in interface org.jmol.api.JmolModulationSet
 
getVibration(boolean) - Method in class org.jmol.util.ModulationSet
 
getVibration(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getVibrationPoint(Vibration, T3, float) - Method in class org.jmol.viewer.TransformManager
return
getVibrationVector() - Method in class org.jmol.modelset.Atom
 
getView() - Method in class jspecview.common.PanelData
 
getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getViewpoint() - Method in class org.jmol.export._VrmlExporter
 
getViewTitle() - Method in class jspecview.common.PanelData
 
getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
 
getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
 
getVisibleSet(boolean) - Method in class org.jmol.modelset.AtomCollection
 
getVisibleVBS() - Method in class org.jmol.shape.Mesh
 
getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
 
getVisibleVertexBitSet() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelDataAt(int) - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
getWebSite() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
getWebSite() - Method in interface org.openscience.jmol.app.JmolPlugin
 
getWidth() - Method in interface jspecview.api.JSVViewPanel
 
getWidth() - Method in class jspecview.common.JSViewer
 
getWidth() - Method in class jspecview.js2d.JsMainPanel
 
getWidth() - Method in class jspecview.js2d.JsPanel
 
getWidth() - Method in class org.jmol.awtjs.swing.Component
 
getWindow(Container) - Static method in class jspecview.java.AwtPlatform
 
getWindow(Container) - Static method in class org.jmol.awt.Platform
 
getWindowBorder(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWindowInnerDimension(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWindowName() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
getWindowName() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getWindowPosition(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWindowSize(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
getWordContents() - Method in class jspecview.popup.JSVPopupResourceBundle
 
getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
 
getWordContents() - Method in class org.jmol.popup.PopupResource
 
getWrappedStateScript() - Method in class org.jmol.viewer.Viewer
 
getWyckoffPosition(boolean) - Method in class org.jmol.modelset.Atom
 
getWyckoffPosition(Viewer, P3, String) - Method in interface org.jmol.api.SymmetryInterface
 
getWyckoffPosition(Viewer, P3, String) - Method in class org.jmol.symmetry.Symmetry
 
getX() - Method in class com.sparshui.common.Location
 
getX() - Method in class com.sparshui.common.messages.events.RotateEvent
 
getX() - Method in class com.sparshui.common.messages.events.TouchEvent
 
getX() - Method in class com.sparshui.common.messages.events.ZoomEvent
 
getX() - Method in class jspecview.common.PeakInfo
 
getX() - Method in class org.jmol.script.ScriptMathProcessor
 
getX(int) - Method in class jme.JMEmol
 
getXdirection() - Method in class com.sparshui.common.messages.events.FlickEvent
 
getXFactor() - Method in class jspecview.source.JDXDataObject
Returns the original x factor
getXMax() - Method in class jspecview.common.PeakInfo
 
getXMin() - Method in class jspecview.common.PeakInfo
 
getXML(BufferedReader) - Method in class jspecview.source.AnIMLReader
 
getXmlAttrib(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
 
getXmlData(String, String, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
 
getXmlDataLF(String, String, boolean, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
 
getXmlPoint(String, String) - Method in class org.jmol.jvxl.readers.XmlReader
 
getXOffset(int) - Static method in class org.jmol.viewer.JC
X offset in pixels.
getXPixel() - Method in class jspecview.common.PeakInfo
 
getXSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getXTok() - Method in class org.jmol.script.ScriptMathProcessor
 
getXUnits() - Method in class jspecview.source.JDXDataObject
Returns the units for x-axis when spectrum is displayed
getXVal() - Method in class jspecview.common.Coordinate
Returns the x value of the coordinate
getXVal2() - Method in class jspecview.common.Measurement
 
getXYCoords() - Method in class jspecview.common.IntegralData
 
getXYCoords() - Method in class jspecview.common.Spectrum
Returns the array of coordinates
getXYZ() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getXYZ() - Method in class org.jmol.modelset.Atom
 
getXYZ() - Method in class org.jmol.smiles.SmilesAtom
 
getXYZ() - Method in interface org.jmol.util.Node
 
getXYZ() - Method in interface org.jmol.util.SimpleNode
 
getXYZFromMatrix(M4, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getXYZFromMatrixFrac(M4, boolean, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getXYZFromRsVs(Matrix, Matrix, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getxyzTrans(T3) - Method in class org.jmol.symmetry.SymmetryOperation
 
getY() - Method in class com.sparshui.common.Location
 
getY() - Method in class com.sparshui.common.messages.events.RotateEvent
 
getY() - Method in class com.sparshui.common.messages.events.TouchEvent
 
getY() - Method in class com.sparshui.common.messages.events.ZoomEvent
 
getY(int) - Method in class jme.JMEmol
 
getY2D() - Method in class jspecview.source.JDXDataObject
 
getY2DPPM() - Method in class jspecview.source.JDXDataObject
 
getYdirection() - Method in class com.sparshui.common.messages.events.FlickEvent
 
getYellowField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
 
getYellowField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
 
getYellowValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
getYellowValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
getYFactor() - Method in class jspecview.source.JDXDataObject
Returns the original y factor
getYMax() - Method in class jspecview.common.PeakInfo
 
getYMin() - Method in class jspecview.common.PeakInfo
 
getYOffset(int) - Static method in class org.jmol.viewer.JC
Y offset in pixels; negative of this is the actual screen offset
getYRef() - Method in class jspecview.source.JDXDataObject
 
getYUnits() - Method in class jspecview.source.JDXDataObject
Returns the units for y-axis when spectrum is displayed
getYVal() - Method in class jspecview.common.Coordinate
Returns the y value of the coordinate
getYVal2() - Method in class jspecview.common.Measurement
 
getYValueAt(double) - Method in class jspecview.common.Spectrum
 
getYValueAt(Coordinate[], double) - Static method in class jspecview.common.Coordinate
 
getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
 
getZapName() - Method in class org.jmol.viewer.Viewer
 
getZCurrent(float, float, int) - Method in class org.jmol.g3d.PrecisionRenderer
 
getZipDirectory(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getZipDirectoryAndClose(BufferedInputStream, String) - Method in interface javajs.api.GenericZipTools
 
getZipDirectoryAndClose(BufferedInputStream, String) - Method in class javajs.util.ZipTools
 
getZipDirectoryAsString(String) - Method in class org.jmol.viewer.Viewer
 
getZipDirectoryAsStringAndClose(BufferedInputStream) - Method in interface javajs.api.GenericZipTools
 
getZipDirectoryAsStringAndClose(BufferedInputStream) - Method in class javajs.util.ZipTools
 
getZipFileContentsAsBytes(BufferedInputStream, String[], int) - Method in interface javajs.api.GenericZipTools
 
getZipFileContentsAsBytes(BufferedInputStream, String[], int) - Method in class javajs.util.ZipTools
 
getZipFileDirectory(BufferedInputStream, String[], int, boolean) - Method in interface javajs.api.GenericZipTools
 
getZipFileDirectory(BufferedInputStream, String[], int, boolean) - Method in class javajs.util.ZipTools
iteratively drills into zip files of zip files to extract file content or zip file directory.
getZipOutputStream(Object) - Method in interface javajs.api.GenericZipTools
 
getZipOutputStream(Object) - Method in class javajs.util.ZipTools
 
getZipRoot(String) - Static method in class javajs.util.Rdr
We define a request for zip file extraction by vertical bar: zipName|interiorFileName.
getZoomSetting() - Method in class org.jmol.viewer.TransformManager
 
GhemicalMMReader - Class in org.jmol.adapter.readers.simple
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
 
GifEncoder - Class in javajs.img
GifEncoder extensively adapted for Jmol by Bob Hanson Color quantization roughly follows the GIMP method "dither Floyd-Steinberg (normal)" but with some twists.
GifEncoder() - Constructor for class javajs.img.GifEncoder
 
GL_LINE_LOOP - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_LINE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_LINES - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_POINTS - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_TRIANGLE_FAN - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_TRIANGLE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_TRIANGLES - Static variable in class org.jmol.shapecgo.CGOMesh
 
GLOBAL_AROMATICBONDS - Static variable in class org.jmol.viewer.JC
 
GLOBAL_CONECT - Static variable in class org.jmol.viewer.JC
 
GLOBAL_DOMAINS - Static variable in class org.jmol.viewer.JC
 
GLOBAL_FRACTCOORD - Static variable in class org.jmol.viewer.JC
 
GLOBAL_ISPDB - Static variable in class org.jmol.viewer.JC
 
GLOBAL_MODULATED - Static variable in class org.jmol.viewer.JC
 
GLOBAL_SUPERCELL - Static variable in class org.jmol.viewer.JC
 
GLOBAL_SYMMETRY - Static variable in class org.jmol.viewer.JC
 
GLOBAL_UNITCELLS - Static variable in class org.jmol.viewer.JC
 
GLOBAL_VALIDATIONS - Static variable in class org.jmol.viewer.JC
 
globalBooleans - Static variable in class org.jmol.viewer.JC
 
GlobalSettings - Class in org.jmol.viewer
 
goButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
GOLD - Static variable in class org.jmol.util.C
 
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
gotocmd - Static variable in class org.jmol.script.T
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
gotoTop() - Method in class org.jmol.console.ScriptEditor
 
grabPixels(Object, int, int, int[]) - Method in class jspecview.java.AwtPlatform
 
grabPixels(Object, int, int, int[]) - Method in class jspecview.js2d.JsPlatform
 
grabPixels(Object, int, int, int[]) - Method in interface org.jmol.api.GenericPlatform
 
grabPixels(Object, int, int, int[]) - Method in class org.jmol.awt.Platform
 
grabPixels(Object, int, int, int[]) - Method in class org.jmol.awtjs2d.Platform
 
Graphics3D - Class in org.jmol.g3d
Provides high-level graphics primitives for 3D visualization for the software renderers.
Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
 
graphicsForMetrics - Variable in class org.jmol.util.GData
 
graphSets - Variable in class jspecview.common.PanelData
 
GRAY - Static variable in class org.jmol.util.C
 
GREEN - Static variable in class org.jmol.util.C
 
greyscalerendering - Static variable in class org.jmol.script.T
 
Grid - Class in org.jmol.awtjs.swing
 
GridBagConstraints - Class in org.jmol.awtjs.swing
 
GridBagConstraints(int, int, int, int, double, double, int, int, Insets, int, int) - Constructor for class org.jmol.awtjs.swing.GridBagConstraints
 
GridBagLayout - Class in org.jmol.awtjs.swing
 
GridBagLayout() - Constructor for class org.jmol.awtjs.swing.GridBagLayout
 
gridColor - Variable in class jspecview.common.PanelData
 
GRIDCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
gridheight - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
gridOn - Variable in class jspecview.common.PanelData
 
GRIDON - Enum constant in enum class jspecview.common.ScriptToken
 
gridpoints - Static variable in class org.jmol.script.T
 
gridwidth - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
gridx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
gridy - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
gRight - Variable in class org.jmol.util.GenericApplet
 
GromacsReader - Class in org.jmol.adapter.readers.more
 
GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
 
gromacsWideFormat - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
group - Variable in class org.jmol.modelset.Atom
 
group - Static variable in class org.jmol.script.T
 
group() - Method in class org.jmol.util.PatternMatcher.JSPattern
 
Group - Class in com.sparshui.server
Represents a group of touch points for the gesture server.
Group - Class in org.jmol.modelset
The essential container for every atom.
Group() - Constructor for class org.jmol.modelset.Group
 
Group(int, Lst<GestureType>, ServerToClientProtocol) - Constructor for class com.sparshui.server.Group
Construct a new group with the given gesture IDs and the given connection to the client.
GROUP - Enum constant in enum class org.jmol.c.PAL
 
group1 - Variable in class org.jmol.modelset.Group
 
group1 - Static variable in class org.jmol.script.T
 
group3 - Variable in class org.jmol.adapter.smarter.Atom
 
group3Counts - Variable in class org.jmol.modelset.ModelLoader
 
group3Lists - Variable in class org.jmol.modelset.ModelLoader
 
group3NameCount - Static variable in class org.jmol.modelsetbio.BioResolver
 
group3Names - Static variable in class org.jmol.modelset.Group
 
groupCount - Variable in class org.jmol.modelset.Chain
 
groupCount - Variable in class org.jmol.modelset.Model
 
groupid - Static variable in class org.jmol.script.T
 
groupID - Variable in class org.jmol.modelset.Group
 
GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JC
 
GROUPID_ARGININE - Static variable in class org.jmol.viewer.JC
 
GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JC
 
GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JC
 
GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_LYSINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JC
 
GROUPID_PROLINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JC
 
GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JC
 
GROUPID_WATER - Static variable in class org.jmol.viewer.JC
 
groupindex - Static variable in class org.jmol.script.T
 
groupIndex - Variable in class org.jmol.modelset.Group
 
groups - Variable in class org.jmol.modelset.Chain
Groups form the essence of what a Chain is.
groups - Variable in class org.jmol.modelset.ModelLoader
 
growArray(double[], int) - Static method in class jme.JMEUtil
 
growArray(int[][], int) - Static method in class jme.JMEUtil
 
growArray(int[], int) - Static method in class jme.JMEUtil
 
growArray(String[], int) - Static method in class jme.JMEUtil
 
growArray(T[], int) - Static method in class jme.JMEUtil
 
growAtomArrays(int) - Method in class org.jmol.modelset.ModelSet
 
GS - Static variable in class org.jmol.quantum.QS
 
GT - Class in org.jmol.i18n
The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScript
GT() - Constructor for class org.jmol.i18n.GT
 
GT(Viewer, String) - Constructor for class org.jmol.i18n.GT
 
guessMimeTypeForBytes(byte[]) - Static method in class javajs.util.Rdr
 
guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
GuiMap - Class in org.openscience.jmol.app.jmolpanel
 
GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
 
GulpReader - Class in org.jmol.adapter.readers.xtal
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
 
GWT() - Constructor for class jme.JMEUtil.GWT
 
GZIPException - Exception Class in com.jcraft.jzlib
 
GZIPException() - Constructor for exception class com.jcraft.jzlib.GZIPException
 
GZIPException(String) - Constructor for exception class com.jcraft.jzlib.GZIPException
 
GZIPHeader - Class in com.jcraft.jzlib
 
GZIPHeader() - Constructor for class com.jcraft.jzlib.GZIPHeader
 
GZIPInputStream - Class in com.jcraft.jzlib
 
GZIPInputStream() - Constructor for class com.jcraft.jzlib.GZIPInputStream
 
GZIPOutputStream - Class in com.jcraft.jzlib
 
GZIPOutputStream() - Constructor for class com.jcraft.jzlib.GZIPOutputStream
 

H

halo - Static variable in class org.jmol.script.T
 
Halos - Class in org.jmol.shape
 
Halos() - Constructor for class org.jmol.shape.Halos
 
HalosRenderer - Class in org.jmol.render
 
HalosRenderer() - Constructor for class org.jmol.render.HalosRenderer
 
halt - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
haltExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
 
haltExecution() - Method in class org.jmol.script.ScriptEval
 
haltScriptExecution() - Method in class org.jmol.api.JmolViewer
 
haltScriptExecution() - Method in class org.jmol.viewer.Viewer
 
handleAssignNew(MouseState, MouseState, MeasurementPending, int, int) - Method in class org.jmol.modelkit.ModelKit
handle a mouse-generated assignNew event
handleError(Throwable, boolean) - Method in class org.jmol.viewer.Viewer
 
handleEvent(Event) - Method in interface org.jmol.api.JmolAppletInterface
 
handleEvent(Event) - Method in class org.jmol.util.GenericApplet
 
handleEvent(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
handleOutputToFile(Map<String, Object>, boolean) - Method in class org.jmol.viewer.OutputManagerAwt
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
handleOutputToFile(Map<String, Object>, boolean) - Method in class org.jmol.viewer.OutputManagerJS
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
HAS_CLIENT - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
HAS_DRIVER - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
hasConstraint(int, boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
 
hasContent() - Method in class org.jmol.g3d.Graphics3D
 
hasCurrentMeasurements(Annotation.AType) - Method in class jspecview.common.PanelData
 
hasDatabasePrefix(String) - Static method in class org.jmol.viewer.Viewer
 
hasFileLoaded(String) - Method in class jspecview.common.PanelData
 
hasFocus() - Method in interface jspecview.api.JSVPanel
 
hasFocus() - Method in class jspecview.common.PanelData
 
hasFocus() - Method in class jspecview.js2d.JsPanel
 
hasFocus() - Method in class org.jmol.viewer.Viewer
 
hasFocus(Object) - Method in class jspecview.java.AwtPlatform
 
hasFocus(Object) - Method in class jspecview.js2d.JsPlatform
 
hasFocus(Object) - Method in interface org.jmol.api.GenericPlatform
 
hasFocus(Object) - Method in class org.jmol.awt.Platform
 
hasFocus(Object) - Method in class org.jmol.awtjs2d.Platform
 
hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
hash - Static variable in class org.jmol.script.T
 
hashCode() - Method in class javajs.util.A4
Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.BArray
 
hashCode() - Method in class javajs.util.BS
Returns a hash code value for this bit set.
hashCode() - Method in class javajs.util.M3
Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.M4
Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T3
Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T3d
Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T3i
Returns a hash number based on the data values in this object.
hashCode() - Method in class javajs.util.T4
Returns a hash number based on the data values in this object.
hashCode() - Method in class org.jmol.modelset.Atom
 
hashCode() - Method in class org.jmol.script.T
 
hasMeasure(int[]) - Method in class org.jmol.modelset.Trajectory
 
hasMoreElements() - Method in class jspecview.tree.SimpleTreeEnumeration
 
hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
normal iterator predicate
hasMoreTokens() - Method in class jspecview.common.ScriptTokenizer
 
hasNext() - Method in class jspecview.source.JDXDecompressor
 
hasNext() - Method in class jspecview.source.XMLParser
 
hasNext() - Method in class org.jmol.adapter.smarter.StructureIterator
 
hasNext() - Method in interface org.jmol.api.AtomIndexIterator
 
hasNext() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapterBondIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
hasNext() - Method in interface org.jmol.modelset.BondIterator
 
hasNext() - Method in class org.jmol.symmetry.UnitCellIterator
 
hasNext2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
hasOuputSocket() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
hasOuputSocket() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
hasPlane() - Method in class org.jmol.jvxl.data.VolumeData
 
hasPrevious() - Method in class jme.JME
 
hasRasmolHBonds - Variable in class org.jmol.modelset.Model
 
hasRingData(int) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
 
hasSelected - Variable in class org.jmol.viewer.Viewer
 
hasStructure - Variable in class org.jmol.modelsetbio.BioPolymer
 
hasStructure(String, String[], int) - Method in interface org.jmol.api.SmilesMatcherInterface
 
hasStructure(String, String[], int) - Method in class org.jmol.smiles.SmilesMatcher
Look for pattern in each smilesSet string.
hasStructure(String, String, boolean) - Method in class org.jmol.viewer.Viewer
 
hasValues() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
hasVibration() - Method in class org.jmol.modelset.Atom
 
hasWingPoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
hAtomRadius - Variable in class org.jmol.atomdata.AtomData
 
hAtoms - Variable in class org.jmol.atomdata.AtomData
 
have(byte[], byte) - Static method in class org.jmol.modelsetbio.Monomer
 
haveAccess(Viewer.ACCESS) - Method in class org.jmol.viewer.Viewer
 
haveAnisou - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
haveAtomFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
haveAtropicBonds - Variable in class org.jmol.modelset.BondCollection
 
haveBioModels - Variable in class org.jmol.modelset.ModelSet
 
haveBorder - Variable in class org.openscience.jmol.app.JmolApp
 
haveBsDisplay - Variable in class org.jmol.render.MeshRenderer
 
haveChirality - Variable in class org.jmol.modelset.AtomCollection
 
haveCommon(BS, BS) - Static method in class org.jmol.util.BSUtil
 
haveConsole - Variable in class org.openscience.jmol.app.JmolApp
 
haveContourData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
haveData - Variable in class javajs.util.CifDataParser
 
haveDisplay - Variable in class org.jmol.viewer.Viewer
 
haveDisplay - Variable in class org.openscience.jmol.app.JmolApp
 
haveDisplay - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
haveDocumentAccess - Variable in class org.jmol.util.GenericApplet
 
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
haveFileSet() - Method in class org.jmol.viewer.Viewer
 
haveHiddenBonds - Variable in class org.jmol.modelset.BondCollection
 
haveMacro - Variable in class org.jmol.script.ScriptCompiler
 
haveModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
haveModified - Variable in class org.jmol.modelset.MeasurementPending
 
haveMultiTouchInput - Variable in class org.jmol.viewer.ActionManager
 
haveNboCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveNboOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveNotifiedError - Variable in class org.jmol.util.GenericApplet
 
haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
 
haveParameters - Variable in class org.jmol.modelsetbio.BioPolymer
 
havePartialChargeFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
havePlanarContours - Variable in class org.jmol.shape.Mesh
 
havePoints - Variable in class org.jmol.quantum.MOCalculation
 
haveQuads - Variable in class org.jmol.util.MeshSurface
 
haveReference - Variable in class org.jmol.thread.JmolThread
 
haveSelectedSpectrum() - Method in class jspecview.common.PanelData
 
haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
 
haveStraightness - Variable in class org.jmol.modelset.AtomCollection
 
haveSurfaceAtoms - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
haveTarget - Variable in class org.jmol.modelset.MeasurementPending
 
haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
 
haveTranslucentObjects() - Method in class org.jmol.export.Export3D
 
haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
 
haveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
haveUnitCell - Variable in class org.jmol.adapter.writers.XtlWriter
 
haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
 
haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
 
haveUnitCells - Variable in class org.jmol.modelset.ModelSet
 
haveXyPoints - Variable in class org.jmol.shape.Mesh
 
HB - Enum Class in org.jmol.c
Enum for hydrogen bonding donor/acceptor type
hBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
hbond - Static variable in class org.jmol.script.T
 
HBond - Class in org.jmol.modelset
 
HBond(Atom, Atom, int, short, short, float) - Constructor for class org.jmol.modelset.HBond
 
hbondhxdistancemaximum - Static variable in class org.jmol.script.T
 
hbondnodistancemaximum - Static variable in class org.jmol.script.T
 
hbondsangleminimum - Static variable in class org.jmol.script.T
 
hbondsbackbone - Static variable in class org.jmol.script.T
 
hbondsrasmol - Static variable in class org.jmol.script.T
 
hbondssolid - Static variable in class org.jmol.script.T
 
HC - Static variable in class org.jmol.quantum.QS
 
hDashes - Static variable in class org.jmol.render.FontLineShapeRenderer
 
HEADER_GAMESS_OCCUPANCIES - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_GAMESS_ORIGINAL - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_GAMESS_UK_MO - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_NONE - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
headerTable - Variable in class jspecview.source.JDXHeader
 
headless - Variable in class org.jmol.viewer.Viewer
determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN , ANIMATION ON turns SPIN into just ROTATE
height - Variable in class javajs.img.ImageEncoder
 
height - Variable in class org.jmol.awtjs.swing.Component
 
height - Variable in class org.jmol.awtjs.swing.Dimension
 
height - Variable in class org.jmol.util.GData
 
height - Variable in class org.jmol.util.Rectangle
 
height - Variable in class org.jmol.viewer.TransformManager
 
helix - Static variable in class org.jmol.script.T
 
Helix - Class in org.jmol.modelsetbio
 
HELIX - Enum constant in enum class org.jmol.c.STR
 
helix310 - Static variable in class org.jmol.script.T
 
HELIX310 - Enum constant in enum class org.jmol.c.STR
 
helixalpha - Static variable in class org.jmol.script.T
 
HELIXALPHA - Enum constant in enum class org.jmol.c.STR
 
helixpi - Static variable in class org.jmol.script.T
 
HELIXPI - Enum constant in enum class org.jmol.c.STR
 
helixRockets - Variable in class org.jmol.renderbio.RocketsRenderer
 
helixstep - Static variable in class org.jmol.script.T
 
help - Static variable in class org.jmol.script.T
 
HELP - Enum constant in enum class jspecview.common.ScriptToken
 
HelpDialog - Class in org.openscience.jmol.app.jmolpanel
 
HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
 
HelpDialog(JFrame, String, boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
 
HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
If url is null, then the default help url is taken.
helper - Variable in class org.jmol.popup.GenericPopup
 
helppath - Static variable in class org.jmol.script.T
 
hermitelevel - Static variable in class org.jmol.script.T
 
HermiteRenderer - Class in org.jmol.g3d
Implementation of hermite curves for drawing smoothed curves that pass through specified points.
HermiteRenderer() - Constructor for class org.jmol.g3d.HermiteRenderer
 
hetero - Static variable in class org.jmol.script.T
 
HEX_TO_RHOMB - Static variable in class org.jmol.util.SimpleUnitCell
 
hi - Variable in class org.jmol.util.ColorEncoder
 
hidden - Variable in class org.jmol.modelset.Text
 
hidden - Static variable in class org.jmol.script.T
 
HIDDEN - Enum constant in enum class jspecview.common.ScriptToken
 
hiddenlinesdashed - Static variable in class org.jmol.script.T
 
hide - Static variable in class org.jmol.script.T
 
hidenameinpopup - Static variable in class org.jmol.script.T
 
hidenavigationpoint - Static variable in class org.jmol.script.T
 
hidenotselected - Static variable in class org.jmol.script.T
 
HIGH - Static variable in class org.jmol.util.ColorEncoder
 
highlight - Static variable in class org.jmol.script.T
 
highlight(BS) - Method in class org.jmol.viewer.Viewer
 
HIGHLIGHT - Enum constant in enum class jspecview.common.ScriptToken
 
highlightBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
from Sticks
highlightColor - Variable in class jspecview.common.PanelData
 
HIGHLIGHTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
highresolution - Static variable in class org.jmol.script.T
 
history - Static variable in class org.jmol.script.T
 
historyButton - Variable in class org.jmol.console.GenericConsole
 
historyDisabled - Variable in class org.jmol.script.ScriptEval
 
historyFile - Variable in class org.openscience.jmol.app.JmolApp
 
historyFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
HistoryFile - Class in org.openscience.jmol.app
The history file contains data from previous uses of Jmol.
HistoryFile(File, String) - Constructor for class org.openscience.jmol.app.HistoryFile
Creates a history file.
historyFind(String, int) - Method in class org.jmol.viewer.Viewer
 
historylevel - Static variable in class org.jmol.script.T
 
hkl - Static variable in class org.jmol.script.T
 
hklParameter(int, Lst<P3>, boolean) - Method in class org.jmol.script.ScriptParam
 
holdRepaint - Variable in class org.jmol.render.RepaintManager
 
homeAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
homePosition() - Method in class org.jmol.api.JmolViewer
 
homePosition() - Method in class org.jmol.viewer.Viewer
 
homePosition(boolean) - Method in class org.jmol.viewer.TransformManager
 
homo - Static variable in class org.jmol.script.T
 
HORIZONTAL_SPLIT - Static variable in class org.jmol.awtjs.swing.JSplitPane
 
HOTPINK - Static variable in class org.jmol.util.C
 
hover - Static variable in class org.jmol.script.T
 
Hover - Class in org.jmol.shape
 
Hover() - Constructor for class org.jmol.shape.Hover
 
HOVER - Enum constant in enum class org.jmol.c.CBK
 
hoverdelay - Static variable in class org.jmol.script.T
 
hoverEnabled - Variable in class org.jmol.thread.JmolThread
 
hoverlabel - Static variable in class org.jmol.script.T
 
hoverLabel - Variable in class org.jmol.shape.Mesh
 
hoverOnPt(int, int, String, String, T3) - Method in class org.jmol.viewer.Viewer
Hover over an arbitrary point.
HoverRenderer - Class in org.jmol.render
 
HoverRenderer() - Constructor for class org.jmol.render.HoverRenderer
 
hoverText - Variable in class org.jmol.shape.Hover
 
hoverWatcherThread - Variable in class org.jmol.viewer.ActionManager
 
HoverWatcherThread - Class in org.jmol.thread
 
HoverWatcherThread(ActionManager, MouseState, MouseState, Viewer) - Constructor for class org.jmol.thread.HoverWatcherThread
 
HS - Static variable in class org.jmol.quantum.QS
 
hslToRGB(P3) - Static method in class javajs.util.CU
Convert HSL (hue/saturation/luninance) values to RGB
ht3 - Variable in class org.jmol.util.GData
 
htAtomicPotentials - Variable in class org.jmol.quantum.MepCalculation
 
htBooleans - Variable in class jspecview.common.Parameters
 
htCheckbox - Variable in class org.jmol.popup.GenericPopup
 
htDialogs - Variable in class jspecview.dialog.DialogManager
 
htElementMap - Static variable in class org.jmol.util.Elements
 
htFields - Static variable in class javajs.util.CifDataParser
A global, static map that contains field information.
htGroup - Static variable in class org.jmol.modelsetbio.BioResolver
 
htGroup1 - Variable in class org.jmol.adapter.readers.cif.CifReader
 
htGroup1 - Static variable in class org.jmol.modelsetbio.NucleicPolymer
 
htHetero - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
htMenus - Variable in class org.jmol.popup.GenericPopup
 
htMessageCallbacks - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
htMin - Variable in class org.jmol.modelset.MeasurementData
 
html5Applet - Variable in class jspecview.common.JSViewer
 
html5Applet - Variable in class org.jmol.viewer.Viewer
 
HTMLElement - Interface in org.jmol.awtjs.swing
 
htmlMenuOpener(String) - Method in class org.jmol.awtjs.swing.AbstractButton
 
htmlName - Variable in class org.jmol.util.GenericApplet
 
htmlName - Variable in class org.jmol.viewer.Viewer
 
HTMLWindowEvent - Interface in org.jmol.awtjs.swing
The window.Event in HTML5 See SwingController.
htModelAtomMap - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
htObjects - Variable in class org.jmol.shape.MeshCollection
 
htParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
htParams - Variable in class org.jmol.util.GenericApplet
 
htPeaks - Variable in class org.jmol.modelset.ModelSet
 
htRegistry - Static variable in class org.jmol.util.GenericApplet
 
htSites - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
htSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
htTracker - Variable in class org.jmol.symmetry.CIPDataTracker
a table to track decision making when only one atom is selected for calculation
htUij - Variable in class org.jmol.util.ModulationSet
current value of anisotropic parameter modulation
htUserFunctions - Variable in class org.jmol.script.ScriptCompiler
 
HUGE - Static variable in class org.jmol.util.GData
 
HYDRO - Enum constant in enum class org.jmol.c.VDW
 
hydrogen - Static variable in class org.jmol.script.T
 
hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
 
hydrogenCount - Variable in class org.jmol.modelset.Model
 
hydrogensAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
hydrophobicity - Static variable in class org.jmol.script.T
 
HyperChemReader - Class in org.jmol.adapter.readers.simple
Support for .hin, HyperChem's native file format.
HyperChemReader() - Constructor for class org.jmol.adapter.readers.simple.HyperChemReader
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 

I

i - Variable in class org.jmol.util.Point3fi
index in full collection
i(int) - Static method in class org.jmol.script.T
 
i(String, int) - Static method in class org.jmol.i18n.GT
 
iA - Variable in class org.jmol.util.MeshSurface
 
iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
 
iB - Variable in class org.jmol.util.MeshSurface
 
iC - Variable in class org.jmol.util.MeshSurface
 
IC - Static variable in class org.jmol.quantum.QS
 
ich - Variable in class javajs.util.CifDataParser
pointer to current character on str
ichComment - Variable in class org.jmol.script.ScriptCompiler
 
ichCurrentCommand - Variable in class org.jmol.script.ScriptCompiler
 
ichEnd - Variable in class org.jmol.script.ScriptCompiler
 
ichToken - Variable in class org.jmol.script.ScriptCompiler
 
iCommand - Variable in class org.jmol.script.ScriptCompiler
 
iCommandError - Variable in class org.jmol.script.ScriptContext
 
iCommandError - Variable in class org.jmol.script.ScriptError
 
id - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
 
id - Variable in class jspecview.common.PanelNode
 
id - Variable in class jspecview.common.Spectrum
 
id - Variable in class org.jmol.awtjs.swing.Component
 
id - Variable in enum class org.jmol.c.PAL
 
id - Variable in class org.jmol.minimize.Minimizer
 
id - Variable in class org.jmol.modelset.TickInfo
 
id - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
 
id - Variable in class org.jmol.script.ScriptContext
 
id - Static variable in class org.jmol.script.T
 
id - Variable in class org.jmol.shapespecial.Polyhedron
 
id - Variable in class org.jmol.util.BZone
 
id - Variable in class org.jmol.util.Tensor
 
ID_ALL - Static variable in class org.jmol.modelset.Atom
 
ID_ATOMS - Static variable in class org.jmol.modelset.Atom
 
ID_CHIME - Static variable in class org.jmol.modelset.Atom
 
ID_U - Static variable in class org.jmol.modelset.Atom
 
ID_XTAL - Static variable in class org.jmol.modelset.Atom
 
ident - Variable in class jspecview.export.AMLExporter
 
ident - Variable in class jspecview.export.CMLExporter
 
identifier - Variable in class jspecview.source.AnIMLReader
 
identifier - Static variable in class org.jmol.script.T
 
identify - Static variable in class org.jmol.script.T
 
identity(int, int) - Static method in class javajs.util.Matrix
Generate identity matrix
idFontFace - Variable in class org.jmol.util.Font
 
idFontStyle - Variable in class org.jmol.util.Font
 
idSpherical - Static variable in class org.jmol.quantum.QS
 
ifcmd - Static variable in class org.jmol.script.T
 
iformat(int, int) - Static method in class jme.JMEUtil
right-justify using spaces
ignore - Static variable in class org.jmol.script.T
 
ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
 
ignoreError - Variable in class org.jmol.script.ScriptError
 
ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
ignoreStructure - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
 
iHaveCoefMaps - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
 
iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cif.CifReader
 
iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHideBackground - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
ijkToPoint3f(int, P3, int, int) - Static method in class org.jmol.util.SimpleUnitCell
Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499 for example, a 3x3x3 block of 27 cells: {444 666 1} or {1494949 1515151 1} or {1499499499 1501501501 1}
image - Variable in class org.jmol.console.ImageDialog
 
image - Variable in class org.jmol.modelset.Text
 
image - Static variable in class org.jmol.script.T
 
IMAGE - Enum constant in enum class org.jmol.c.CBK
 
IMAGE_OR_SCENE - Static variable in class org.jmol.viewer.JC
 
IMAGE_TYPES - Static variable in class org.jmol.viewer.JC
 
imageableHeight - Variable in class jspecview.common.PrintLayout
 
imageableWidth - Variable in class jspecview.common.PrintLayout
 
imageableX - Variable in class jspecview.common.PrintLayout
 
imageableY - Variable in class jspecview.common.PrintLayout
 
imageChoices - Variable in class org.jmol.dialog.Dialog
 
ImageDialog - Class in org.jmol.console
 
ImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Constructor for class org.jmol.console.ImageDialog
 
ImageEncoder - Class in javajs.img
Generic abstract image creator: (1) set parameters (2) encode the image bytes, if necessary (3) generate the image
ImageEncoder() - Constructor for class javajs.img.ImageEncoder
 
imageExtensions - Variable in class org.jmol.dialog.Dialog
 
imageFontScaling - Variable in class org.jmol.render.FontLineShapeRenderer
 
imageFontScaling - Variable in class org.jmol.render.MeshRenderer
 
imageFontScaling - Variable in class org.jmol.viewer.Viewer
 
imageScale - Variable in class org.jmol.modelset.Text
 
imagestate - Static variable in class org.jmol.script.T
 
imageType - Variable in class org.jmol.dialog.Dialog
 
imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
imesh - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
implicitStringCommand - Static variable in class org.jmol.script.T
 
in - Static variable in class org.jmol.script.T
 
inchi - Static variable in class org.jmol.script.T
 
inchi() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
InChIJNI - Class in org.jmol.inchi
 
InChIJNI() - Constructor for class org.jmol.inchi.InChIJNI
 
InChIJS - Class in org.jmol.inchi
This class adapts Richard Apodaca's 2020 molfile-to-inchi LLVM-derived Web Assembly implementation of IUPAC InChI v.
InChIJS() - Constructor for class org.jmol.inchi.InChIJS
 
inchikey - Static variable in class org.jmol.script.T
 
increasing - Variable in class jspecview.source.AnIMLReader
 
increment - Static variable in class org.jmol.script.T
 
incrementID() - Method in class org.jmol.modelsetbio.ProteinStructure
 
incrementModel(int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
inDefinedStateBlock - Variable in class org.jmol.modelset.StateScript
 
indent - Variable in class org.jmol.util.JSONWriter
 
INDENT - Static variable in class org.jmol.shapecgo.CGOMesh
 
index - Variable in class jspecview.application.AwtTreeNode
 
index - Variable in class jspecview.tree.SimpleTreeNode
 
index - Variable in class org.jmol.adapter.smarter.Atom
 
index - Variable in class org.jmol.minimize.MinBond
 
index - Variable in class org.jmol.modelset.Measurement
 
index - Variable in class org.jmol.quantum.SlaterData
 
index - Variable in class org.jmol.script.SV
 
index - Variable in class org.jmol.shape.Mesh
 
index - Variable in class org.jmol.util.BZone
 
index - Variable in class org.jmol.util.Edge
 
indexes - Variable in class org.jmol.minimize.MMConstraint
 
indexInFrame(Atom) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
indexInModel - Variable in class org.jmol.util.JmolMolecule
 
indexOf(String) - Method in class javajs.util.SB
 
indexOf2(String, int) - Method in class javajs.util.SB
 
inflate(int) - Method in class com.jcraft.jzlib.Inflater
 
inflater - Variable in class com.jcraft.jzlib.InflaterInputStream
 
Inflater - Class in com.jcraft.jzlib
 
Inflater() - Constructor for class com.jcraft.jzlib.Inflater
 
InflaterInputStream - Class in com.jcraft.jzlib
 
InflaterInputStream(InputStream, Inflater, int, boolean) - Constructor for class com.jcraft.jzlib.InflaterInputStream
 
info - Variable in class org.jmol.atomdata.RadiusData
 
info - Static variable in class org.jmol.script.T
 
info - Variable in class org.jmol.shapespecial.Ellipsoid
 
info - Variable in class org.openscience.jmol.app.JmolApp
 
info(String) - Method in class org.jmol.util.DefaultLogger
 
info(String) - Static method in class org.jmol.util.Logger
og* Writes a log at INFO level.
info(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at INFO level.
INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_IS_HEXAGONAL - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_IS_RHOMBOHEDRAL - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_SPACE_GROUP - Static variable in class org.jmol.viewer.JC
 
INFO_SPACE_GROUP_ASSIGNED - Static variable in class org.jmol.viewer.JC
 
INFO_SPACE_GROUP_INDEX - Static variable in class org.jmol.viewer.JC
 
INFO_SPACE_GROUP_INFO - Static variable in class org.jmol.viewer.JC
 
INFO_SPACE_GROUP_NAME - Static variable in class org.jmol.viewer.JC
 
INFO_SPACE_GROUP_NOTE - Static variable in class org.jmol.viewer.JC
 
INFO_SPACE_GROUP_TITLE - Static variable in class org.jmol.viewer.JC
 
INFO_UNIT_CELL - Static variable in class org.jmol.viewer.JC
 
INFO_UNIT_CELL_CONVENTIONAL - Static variable in class org.jmol.viewer.JC
 
INFO_UNIT_CELL_OFFSET - Static variable in class org.jmol.viewer.JC
 
INFO_UNIT_CELL_PARAMS - Static variable in class org.jmol.viewer.JC
 
INFO_UNIT_CELL_RANGE - Static variable in class org.jmol.viewer.JC
used to set atom symmetry 555 556 etc.
INFO_UNIT_CELLS - Static variable in class org.jmol.viewer.JC
 
infofontsize - Static variable in class org.jmol.script.T
 
INFORMATION_MESSAGE - Static variable in class jspecview.dialog.DialogManager
 
infoText - Variable in class jme.JME
 
inFront - Variable in class org.jmol.modelset.Measurement
 
inGreyscaleMode - Variable in class org.jmol.util.GData
 
INHERIT - Static variable in class org.jmol.util.ColorEncoder
 
INHERIT_ALL - Static variable in class org.jmol.util.C
 
INHERIT_COLOR - Static variable in class org.jmol.util.C
 
init() - Method in class jspecview.appletjs.JSVApplet
Initializes applet with parameters and load the JDXSource called by the browser
init() - Method in class jspecview.appletjs.JSVAppletPro
 
init() - Method in class org.jmol.symmetry.CIPData
initializer -- called also by CIPDataSmiles
init(float[]) - Method in class org.jmol.util.SimpleUnitCell
 
init(int, boolean) - Method in class com.jcraft.jzlib.Inflater
 
init(int, int, boolean) - Method in class com.jcraft.jzlib.Deflater
 
init(Object) - Method in class org.jmol.scriptext.MathExt
 
init(Object) - Method in class org.jmol.scriptext.ScriptExt
 
init(Object) - Method in class org.jmol.scriptext.SmilesExt
 
init(Object) - Method in class org.jmol.util.GenericApplet
 
init(String, Object, String, SC) - Method in interface org.jmol.api.SC
 
init(String, Object, String, SC) - Method in class org.jmol.awt.AwtSwingComponent
 
init(String, Object, String, SC) - Method in class org.jmol.awtjs.swing.AbstractButton
 
init(String, Viewer, Lst<Object>) - Method in class org.jmol.modelset.MeasurementData
 
init(URL, String) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
INIT - Static variable in class org.jmol.thread.JmolThread
 
initArrays(int) - Method in class org.jmol.quantum.NMRNoeMatrix
create an empty atom list for subsequent population with atoms
initBS() - Method in class org.jmol.renderbio.BioMeshRenderer
 
initForm(JSViewer, OC) - Method in class jspecview.export.AMLExporter
 
initForm(JSViewer, OC) - Method in class jspecview.export.CMLExporter
 
initForm(JSViewer, OC) - Method in class jspecview.export.SVGExporter
 
initialEndIndex - Variable in class jspecview.common.JSViewer
 
initialize - Static variable in class org.jmol.script.T
 
initialize() - Method in class jme.JME
 
initialize(boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.MOCalculation
 
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
 
initialize(int, P3[], BS) - Method in class org.jmol.bspt.Bspf
 
initialize(int, T3[], P4) - Method in class org.jmol.shape.Mesh
 
initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
initialize(T3, float, boolean) - Method in class org.jmol.bspt.CubeIterator
initialize to return all points within the sphere defined by center and radius
initialize(JSViewer, PopupResource, String) - Method in class jspecview.popup.JSVGenericPopup
 
initialize(AtomSetCollectionReader, int) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
initialize(AtomSetCollectionReader, int) - Method in interface org.jmol.adapter.smarter.MSInterface
 
initialize(ShapeRenderer, BioShape, int) - Method in class org.jmol.renderbio.BioMeshRenderer
 
initialize(Viewer, GenericPlatform) - Method in class org.jmol.g3d.Graphics3D
 
initialize(Viewer, GenericPlatform) - Method in class org.jmol.util.GData
 
initialize(Viewer, PopupResource, String) - Method in class org.jmol.popup.JmolGenericPopup
 
initialize0(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
 
initializeAnnotation(SV, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
initializeAnnotation(SV, int, int) - Method in class org.jmol.dssx.AnnotationParser
We create a main list of mappings, where each mapping has _atoms and _path
initializeBspf() - Method in class org.jmol.modelset.ModelSet
 
initializeBspt(int) - Method in class org.jmol.modelset.ModelSet
 
initializeExporter(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
 
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.Export3D
 
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
 
initializeHydrogenAddition() - Method in class org.jmol.modelsetbio.BioResolver
 
initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
 
initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
 
initializeOnePointQC() - Method in class org.jmol.quantum.QuantumCalculation
 
initializeOrientation(M3) - Method in interface org.jmol.api.SymmetryInterface
 
initializeOrientation(M3) - Method in class org.jmol.symmetry.Symmetry
 
initializeOutput(Viewer, double, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
 
initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.export.Export3D
 
initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
 
initializeReader() - Method in class org.jmol.adapter.readers.cif.CifReader
 
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
 
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
initializeReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.AmsReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.JSONReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.OrcaReader
 
initializeReader() - Method in class org.jmol.adapter.readers.spartan.OdysseyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
 
initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CmdfReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
not sure how to work with symmetry here...
initializeReader() - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeShape(Viewer, ModelSet, int) - Method in class org.jmol.shape.Shape
 
initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeSymmetryOptions() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeTrajectoryFile() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initialStartIndex - Variable in class jspecview.common.JSViewer
 
initMany(Lst<Spectrum>, int, int) - Method in class jspecview.common.PanelData
 
initModelSet() - Method in class org.jmol.shape.AtomShape
 
initModelSet() - Method in class org.jmol.shape.Measures
 
initModelSet() - Method in class org.jmol.shape.Shape
 
initModelSet() - Method in class org.jmol.shape.TextShape
 
initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
 
initModelSet() - Method in class org.jmol.shapespecial.Vectors
 
initOne(Spectrum) - Method in class jspecview.common.PanelData
 
initOptions() - Method in class org.jmol.util.GenericApplet
 
initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
 
initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._PovrayExporter
 
initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._TachyonExporter
 
initParams(String) - Method in class jspecview.app.JSVApp
starts or restarts applet display from scratch or from a JSVApplet.script() JavaScript command Involves a two-pass sequence through parsing the parameters, because order is not important in this sort of call.
initRenderer() - Method in class org.jmol.render.AxesRenderer
 
initRenderer() - Method in class org.jmol.render.BbcageRenderer
 
initRenderer() - Method in class org.jmol.render.MeasuresRenderer
 
initRenderer() - Method in class org.jmol.render.ShapeRenderer
 
initRenderer() - Method in class org.jmol.render.UccageRenderer
 
initRenderer() - Method in class org.jmol.renderspecial.DotsRenderer
 
initShape() - Method in class org.jmol.shape.AtomShape
 
initShape() - Method in class org.jmol.shape.Axes
 
initShape() - Method in class org.jmol.shape.Bbcage
 
initShape() - Method in class org.jmol.shape.Echo
 
initShape() - Method in class org.jmol.shape.FontLineShape
 
initShape() - Method in class org.jmol.shape.Frank
 
initShape() - Method in class org.jmol.shape.Hover
 
initShape() - Method in class org.jmol.shape.Labels
 
initShape() - Method in class org.jmol.shape.Measures
 
initShape() - Method in class org.jmol.shape.MeshCollection
 
initShape() - Method in class org.jmol.shape.Shape
 
initShape() - Method in class org.jmol.shape.Sticks
 
initShape() - Method in class org.jmol.shape.Uccage
 
initShape() - Method in class org.jmol.shapebio.Backbone
 
initShape() - Method in class org.jmol.shapebio.BioShapeCollection
 
initShape() - Method in class org.jmol.shapebio.Cartoon
 
initShape() - Method in class org.jmol.shapebio.MeshRibbon
 
initShape() - Method in class org.jmol.shapebio.Rockets
 
initShape() - Method in class org.jmol.shapebio.Trace
 
initShape() - Method in class org.jmol.shapespecial.Dipoles
 
initShape() - Method in class org.jmol.shapespecial.Dots
 
initShape() - Method in class org.jmol.shapespecial.Draw
 
initShape() - Method in class org.jmol.shapespecial.Ellipsoids
 
initShape() - Method in class org.jmol.shapespecial.GeoSurface
 
initShape() - Method in class org.jmol.shapesurface.Contact
 
initShape() - Method in class org.jmol.shapesurface.Isosurface
 
initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
 
initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
 
initShape() - Method in class org.jmol.shapesurface.NBO
 
initShape() - Method in class org.jmol.shapesurface.Plot3D
 
initShape() - Method in class org.jmol.shapesurface.Pmesh
 
initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
initSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
 
initSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
initSwing(String, PopupResource, Object, boolean, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
 
initVars() - Method in class org.jmol.export._PovrayExporter
 
initVars() - Method in class org.jmol.export._TachyonExporter
 
initViewer() - Method in class jspecview.appletjs.JSVApplet
 
inline - Static variable in class org.jmol.script.T
 
inp - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
input - Variable in class org.jmol.console.GenericConsole
 
INPUT_DEVICE - Static variable in class com.sparshui.common.ConnectionType
 
InputDeviceConnection - Class in com.sparshui.server
Represents a connection to the input device.
InputDeviceConnection(GestureServer, Socket) - Constructor for class com.sparshui.server.InputDeviceConnection
Create a new input device connection with the given gesture server and socket.
inputFileName - Variable in class org.jmol.dialog.Dialog
 
InputReader - Class in org.jmol.adapter.readers.simple
 
InputReader() - Constructor for class org.jmol.adapter.readers.simple.InputReader
 
InputScannerThread - Class in org.openscience.jmol.app
 
inRange(int, int, int) - Method in class org.jmol.viewer.MouseState
 
inscode - Static variable in class org.jmol.script.T
 
insert(int, String) - Method in class javajs.util.SB
 
insert(SC, int) - Method in interface org.jmol.api.SC
 
insert(SC, int) - Method in class org.jmol.awt.AwtSwingComponent
 
insert(SC, int) - Method in class org.jmol.awtjs.swing.AbstractButton
 
insertComponent(Component, int) - Method in class org.jmol.awtjs.swing.Container
 
insertion - Static variable in class org.jmol.script.T
 
INSERTION - Enum constant in enum class org.jmol.c.PAL
 
insertionCode - Variable in class org.jmol.adapter.smarter.Atom
 
insertNodeInto(JSVTreeNode, JSVTreeNode, int) - Method in class jspecview.tree.SimpleTreeModel
 
insertString(int, String, Object) - Method in interface org.jmol.awtjs.swing.Document
 
insertString(int, String, Object) - Method in class org.jmol.awtjs.swing.JTextPane
 
Insets - Class in org.jmol.awtjs.swing
 
Insets(int, int, int, int) - Constructor for class org.jmol.awtjs.swing.Insets
 
insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
insideout - Static variable in class org.jmol.script.T
 
insideOut - Variable in class org.jmol.jvxl.data.JvxlData
 
insideOut - Variable in class org.jmol.shape.Mesh
 
INSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
Int2IntHash - Class in org.jmol.util
 
Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
 
integer - Static variable in class org.jmol.script.T
 
integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptError
 
Integral - Class in jspecview.common
 
Integral() - Constructor for class jspecview.common.Integral
 
IntegralData - Class in jspecview.common
from IntegralGraph a data structure for integration settings
IntegralData(double, double, double, Spectrum) - Constructor for class jspecview.common.IntegralData
 
IntegralData(Spectrum, Parameters) - Constructor for class jspecview.common.IntegralData
 
IntegralData.IntMode - Enum Class in jspecview.common
 
integralDrawAll - Variable in class jspecview.common.Parameters
 
integralMinY - Variable in class jspecview.common.Parameters
 
integralOffset - Variable in class jspecview.common.Parameters
 
INTEGRALOFFSET - Enum constant in enum class jspecview.common.ScriptToken
 
integralPlotColor - Variable in class jspecview.common.PanelData
 
INTEGRALPLOTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
integralRange - Variable in class jspecview.common.Parameters
 
INTEGRALRANGE - Enum constant in enum class jspecview.common.ScriptToken
 
integralShiftMode - Variable in class jspecview.common.PanelData
 
INTEGRATE - Enum constant in enum class jspecview.common.ScriptToken
 
integrateAll(ColorParameters) - Method in class jspecview.common.PanelData
 
integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
integration - Variable in class org.jmol.jvxl.data.JvxlData
 
integration - Variable in class org.jmol.quantum.QuantumCalculation
 
Integration - Enum constant in enum class jspecview.common.Annotation.AType
 
INTEGRATION - Enum constant in enum class jspecview.common.ScriptToken
 
IntegrationDialog - Class in jspecview.dialog
Dialog for managing the integral listing for a Spectrum within a GraphSet
IntegrationDialog() - Constructor for class jspecview.dialog.IntegrationDialog
 
INTEGRATIONRATIOS - Enum constant in enum class jspecview.common.ScriptToken
 
Interface - Class in javajs.api
 
Interface - Class in org.jmol.api
 
Interface() - Constructor for class javajs.api.Interface
 
Interface() - Constructor for class org.jmol.api.Interface
 
INTERFACE - Enum constant in enum class jspecview.common.ScriptToken
 
interfaceOverlaid - Variable in class jspecview.common.JSViewer
 
interior - Static variable in class org.jmol.script.T
 
intermolecular - Static variable in class org.jmol.script.T
 
internal - Static variable in class org.jmol.script.T
 
internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
internalSlab - Variable in class org.jmol.viewer.TransformManager
 
internalTranslation - Variable in class org.jmol.viewer.TransformManager
 
interrupt() - Method in interface org.jmol.api.JmolNavigatorInterface
 
interrupt() - Method in class org.jmol.thread.AnimationThread
 
interrupt() - Method in class org.jmol.thread.JmolThread
 
interrupt() - Method in class org.jmol.thread.MoveToThread
 
intersection - Variable in class org.jmol.jvxl.readers.Parameters
 
intersection - Static variable in class org.jmol.script.T
 
intersection(int[], int[]) - Static method in class jme.JMEUtil
 
intersectLine(P3[], int, P3, V3) - Method in class org.jmol.util.Triangulator
 
intersectPlane(P4, T3[], int) - Method in class org.jmol.util.Triangulator
a generic cell - plane intersector -- used for finding the plane through a not static so as to allow JavaScript to not load it as core.
intersects(BS) - Method in class javajs.util.BS
Returns true if the specified BitSet has any bits set to true that are also set to true in this BitSet.
intparam - Static variable in class org.jmol.script.T
 
intParameter(int) - Method in class org.jmol.script.ScriptParam
 
intParameter(int) - Method in class org.jmol.scriptext.ScriptExt
 
intParameterRange(int, int, int) - Method in class org.jmol.script.ScriptParam
 
intproperty - Static variable in class org.jmol.script.T
 
intramolecular - Variable in class org.jmol.modelset.MeasurementData
 
intramolecular - Static variable in class org.jmol.script.T
 
intToByteArray(byte[], int, int) - Static method in class com.sparshui.common.utils.Converter
 
intToByteArray(int) - Static method in class com.sparshui.common.utils.Converter
Converts an integer intBits into a byte array.
intToFloat(int) - Static method in class javajs.util.BC
 
intToSignedInt(int) - Static method in class javajs.util.BC
 
intValue - Variable in class org.jmol.script.T
 
inv() - Method in class javajs.util.Quat
 
INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
invalidatePolygons() - Method in class org.jmol.util.MeshSurface
 
invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
 
invalidateVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
 
invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
 
InvalidSmilesException - Exception Class in org.jmol.smiles
Exception thrown for invalid SMILES String
InvalidSmilesException(String) - Constructor for exception class org.jmol.smiles.InvalidSmilesException
Constructs a InvalidSmilesException with a detail message.
invArg() - Method in class org.jmol.script.ScriptError
 
invArg() - Method in class org.jmol.scriptext.ScriptExt
 
invArgStr(String) - Method in class org.jmol.script.ScriptError
 
inverse() - Method in class javajs.util.Matrix
Matrix inverse or pseudoinverse
invert() - Method in class javajs.util.M3
Sets the value of this matrix to its inverse.
invert() - Method in class javajs.util.M4
Sets the value of this matrix to its inverse.
invertAtomCoord(P3, P4, BS, int, boolean) - Method in class org.jmol.viewer.Viewer
 
invertInPlace(BS, int) - Static method in class org.jmol.util.BSUtil
inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
invertM(M3) - Method in class javajs.util.M3
Sets the value of this matrix to the matrix inverse of the passed matrix m1.
invertSelected - Static variable in class org.jmol.script.T
 
invertSelected(P3, P4, int, BS) - Method in class org.jmol.modelset.ModelSet
Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.
invertSelected(P3, P4, int, BS) - Method in class org.jmol.viewer.Viewer
 
INVERTY - Enum constant in enum class jspecview.common.ScriptToken
 
invertYAxis() - Method in class jspecview.source.JDXDataObject
 
invPO() - Method in class org.jmol.scriptext.ScriptExt
 
ipadx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
ipady - Variable in class org.jmol.awtjs.swing.GridBagConstraints
 
IRMODE - Enum constant in enum class jspecview.common.ScriptToken
 
iRowColSelected - Variable in class jspecview.dialog.JSVDialog
 
is(int) - Method in class org.jmol.modelset.Bond
 
is(MouseState) - Method in class org.jmol.viewer.MouseState
 
IS - Static variable in class org.jmol.quantum.QS
 
IS_APPEND - Static variable in interface org.jmol.api.JmolScriptManager
 
IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
 
is1D() - Method in class jspecview.source.JDXDataObject
 
is2D - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
is2DPoint(T3) - Static method in class org.jmol.shapespecial.Draw
 
isAB(Object) - Static method in class javajs.util.AU
 
isAB(Object) - Static method in class jspecview.common.JSVFileManager
 
isAbsorbance() - Method in class jspecview.source.JDXDataObject
 
isActive - Variable in class org.jmol.shape.AtomShape
 
isActive() - Method in class org.jmol.shapespecial.Ellipsoids
 
isActiveLevel(int) - Static method in class org.jmol.util.Logger
Tells if a logging level is active.
isAD(Object) - Static method in class javajs.util.AU
 
isADD(Object) - Static method in class javajs.util.AU
 
isADDD(Object) - Static method in class javajs.util.AU
 
isAdded(int) - Method in class org.jmol.modelset.Group
 
isADF - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
isAF(Object) - Static method in class javajs.util.AU
 
isAFF(Object) - Static method in class javajs.util.AU
 
isAFFF(Object) - Static method in class javajs.util.AU
 
isAFloat(Object) - Static method in class javajs.util.AU
 
isAI(Object) - Static method in class javajs.util.AU
 
isAII(Object) - Static method in class javajs.util.AU
 
isAll - Variable in class org.jmol.modelset.MeasurementData
 
isAmide - Variable in class org.jmol.minimize.MinBond
 
isAngstroms - Variable in class org.jmol.jvxl.readers.JvxlReader
 
isAngstroms - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
isAngstroms - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
isAnisotropic - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isAntialiased() - Method in interface org.jmol.api.JmolGraphicsInterface
 
isAntialiased() - Method in class org.jmol.export.Export3D
is full scene / oversampling antialiasing in effect
isAntialiased() - Method in class org.jmol.util.GData
is full scene / oversampling antialiasing in effect
isAP(Object) - Static method in class javajs.util.AU
 
isAppendSelected() - Method in class org.jmol.dialog.FilePreview
 
isApplet - Variable in class jspecview.common.JSViewer
 
isApplet - Variable in class org.jmol.popup.GenericPopup
 
isApplet - Variable in class org.jmol.viewer.Viewer
 
isApplet() - Method in class jspecview.common.JSVFileManager
 
isApprox(V3d, V3d, double) - Static method in class org.jmol.minimize.Util
 
isaromatic - Static variable in class org.jmol.script.T
 
isAromatic - Variable in class org.jmol.minimize.MinBond
 
isArrayParameter(int) - Method in class org.jmol.script.ScriptParam
 
isAS(Object) - Static method in class javajs.util.AU
 
isASS(Object) - Static method in class javajs.util.AU
 
isAtomExpression(int) - Method in class org.jmol.script.ScriptEval
 
isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
 
isAtomPDB(int) - Method in class org.jmol.modelset.ModelSet
 
isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
 
isAtropism(int) - Static method in class org.jmol.util.Edge
 
isAutoOverlayFromJmolClick() - Method in class jspecview.source.JDXDataObject
 
isAV(Object) - Static method in class org.jmol.util.Escape
 
isBarb - Variable in class org.jmol.shapespecial.DrawMesh
 
isBase64() - Method in class javajs.util.OC
 
isBase64(SB) - Static method in class javajs.util.Rdr
 
isBiColor() - Method in enum class org.jmol.c.STER
 
isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
 
isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
 
isBicolorMap - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
isBigEndian - Variable in class javajs.util.BinaryDocument
 
isBigEndian() - Method in interface javajs.api.GenericOutputChannel
 
isBigEndian() - Method in class javajs.util.OC
 
isBinary - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isBinary(BufferedInputStream, int) - Static method in class javajs.util.Rdr
Just looking for non-printable characters.
isBinaryUrl(String) - Method in interface javajs.api.js.J2SObjectInterface
 
isBio - Variable in class org.jmol.symmetry.Symmetry
 
isBio() - Method in interface org.jmol.api.SymmetryInterface
 
isBio() - Method in class org.jmol.symmetry.Symmetry
 
isBioModel - Variable in class org.jmol.modelset.Model
 
isBiomolecule - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
isBioShape - Variable in class org.jmol.shape.Shape
 
isBondable(float, float, float, float, float) - Method in class org.jmol.modelset.ModelSet
 
isBonded(Atom) - Method in class org.jmol.modelset.Atom
 
isBondSet - Variable in class org.jmol.script.ScriptParam
 
isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
 
isBound(int, int) - Method in class org.jmol.viewer.Viewer
 
isBZip2B(byte[]) - Static method in class javajs.util.Rdr
 
isBZip2S(InputStream) - Static method in class javajs.util.Rdr
 
isCA2(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isCarbohydrate - Variable in class org.jmol.renderbio.BackboneRenderer
 
isCarbohydrate - Variable in class org.jmol.renderbio.CartoonRenderer
 
isCarbohydrate - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
isCarbohydrate - Variable in class org.jmol.renderbio.RibbonsRenderer
 
isCarbohydrate - Variable in class org.jmol.renderbio.RocketsRenderer
 
isCarbohydrate - Variable in class org.jmol.renderbio.StrandsRenderer
 
isCarbohydrate - Variable in class org.jmol.renderbio.TraceRenderer
 
isCarbohydrate() - Method in class org.jmol.modelset.Group
 
isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
 
isCartoonsSelected() - Method in class org.jmol.dialog.FilePreview
 
isCDX - Variable in class org.jmol.adapter.readers.xml.XmlCdxReader
true when this reader is being used after CDX conversion
isCellEditable(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
isCenterParameter(int) - Method in class org.jmol.script.ScriptParam
 
isChain - Variable in class org.jmol.smiles.SmilesBond
 
isChanged() - Method in class com.sparshui.server.TouchPoint
Get the value of the changed flag.
isClaimed() - Method in class com.sparshui.server.TouchPoint
The GestureServer needs to know whether an incoming touchPoint is bound to a client or not so that it can tell the input device whether or not to consume the event.
isClearAll() - Method in class jspecview.common.PeakInfo
 
isClickable() - Method in class org.jmol.modelset.Atom
 
isClipped(int, int) - Method in class org.jmol.export.Export3D
 
isClipped(int, int) - Method in class org.jmol.util.GData
 
isClipped(int, int, int) - Method in class org.jmol.export.Export3D
 
isClipped3(int, int, int) - Method in class org.jmol.util.GData
 
isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
 
isClippedXY(int, int, int) - Method in class org.jmol.util.GData
 
isClippedZ(int) - Method in class org.jmol.util.GData
 
isColixColorInherited(short) - Static method in class org.jmol.util.C
 
isColixLastAvailable(short) - Static method in class org.jmol.util.C
 
isColixTranslucent(short) - Static method in class org.jmol.util.C
 
isColorParam(int) - Method in class org.jmol.script.ScriptParam
 
isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
 
isColorSolid - Variable in class org.jmol.util.MeshSurface
 
isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptCompiler
 
isCommensurate - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
isComplete - Variable in class org.jmol.script.ScriptContext
 
isCompoundDocumentB(byte[]) - Static method in class javajs.util.Rdr
 
isCompoundDocumentS(InputStream) - Static method in class javajs.util.Rdr
 
isCompoundSource - Variable in class jspecview.source.JDXSource
 
isConcatenated - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isConnect() - Method in class org.jmol.modelset.StateScript
 
isConnected(Atom[], int) - Method in class org.jmol.modelset.Measurement
 
isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
 
isContainedIn(BS) - Method in class org.jmol.modelset.Model
 
isContinuous() - Method in class jspecview.source.JDXDataObject
Returns true if spectrum is continuous
isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isContoured - Variable in class org.jmol.jvxl.data.JvxlData
 
isContoured - Variable in class org.jmol.jvxl.readers.Parameters
 
isCore - Variable in class org.jmol.quantum.SlaterData
 
isCourseGrained - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isCovalent() - Method in class org.jmol.modelset.Bond
 
isCovalent() - Method in class org.jmol.smiles.SmilesBond
 
isCovalent() - Method in class org.jmol.util.Edge
 
isCovalent() - Method in interface org.jmol.util.SimpleEdge
 
isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
 
isCovalentNotPartial0() - Method in class org.jmol.modelset.Bond
 
iscroll - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
isCrossLinked(Group) - Method in class org.jmol.modelset.Group
 
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
 
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isCrossLinked(Node) - Method in class org.jmol.modelset.Atom
 
isCrossLinked(Node) - Method in class org.jmol.smiles.SmilesAtom
 
isCrossLinked(Node) - Method in interface org.jmol.util.Node
 
iScrPt - Variable in class org.jmol.viewer.TransformManager
 
isCurrentGraphSet(GraphSet) - Method in class jspecview.common.PanelData
 
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.data.JvxlData
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
 
isCyclic() - Method in class org.jmol.modelsetbio.BioPolymer
 
isDatabaseCode(char) - Static method in class org.jmol.viewer.Viewer
 
isDataFlavorSupported(DataFlavor) - Method in class jspecview.java.AwtClipboard
 
isDataFlavorSupported(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
 
isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
 
isDefault - Variable in class jspecview.common.ColorParameters
 
isDefined() - Method in class org.jmol.smiles.SmilesAtom
 
isDeleted() - Method in class org.jmol.modelset.Atom
 
isDeleted() - Method in class org.jmol.smiles.SmilesAtom
 
isDeleted() - Method in interface org.jmol.util.Node
 
isDeleted(Atom) - Static method in class org.jmol.modelset.AtomCollection
 
isDialog() - Method in interface jspecview.api.AnnotationData
 
isDialog() - Method in class jspecview.common.MeasurementData
 
isDialog() - Method in class jspecview.dialog.JSVDialog
 
isDigit(char) - Static method in class javajs.util.PT
 
isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
 
isDirectory() - Method in interface org.jmol.api.GenericFileInterface
 
isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
 
isDna() - Method in class org.jmol.modelset.Group
group ID-based definition
isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isDnaByID() - Method in class org.jmol.modelset.Group
group ID-based definition
isDoublePrecision - Static variable in class org.jmol.viewer.Viewer
 
isDrawPolygon - Variable in class org.jmol.util.MeshSurface
 
isDSSP1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isDssrSet - Variable in class org.jmol.modelsetbio.NucleicPolymer
 
isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isEcho - Variable in class org.jmol.modelset.Text
 
isEditor - Variable in class org.jmol.script.ScriptContext
 
isEditorScript - Variable in class org.jmol.script.ScriptContext
 
iSelected - Variable in class jspecview.dialog.JSVDialog
 
isElement(int, int) - Static method in class org.jmol.util.Elements
 
isEmbeddable(String) - Static method in class org.jmol.viewer.FileManager
Check to see if it is possible that this file has been embedded by Jmol using JC.EMBEDDED_SCRIPT_TAG.
isEmbeddedExpression - Variable in class org.jmol.script.ScriptCompiler
 
isEmpty() - Method in class javajs.util.BS
Returns true if this BitSet contains no bits that are set to true.
isEmpty() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
isEnabled() - Method in interface jspecview.api.JSVViewPanel
 
isEnabled() - Method in class jspecview.js2d.JsMainPanel
 
isEnabled() - Method in class jspecview.js2d.JsPanel
 
isEnabled() - Method in interface org.jmol.api.JmolModulationSet
 
isEnabled() - Method in interface org.jmol.api.SC
 
isEnabled() - Method in class org.jmol.awt.AwtSwingComponent
 
isEnabled() - Method in class org.jmol.awtjs.swing.Component
 
isEnabled() - Method in class org.jmol.util.ModulationSet
 
isEquiv(Tensor) - Method in class org.jmol.util.Tensor
 
iSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
isExecuting() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isExecuting() - Method in class org.jmol.script.ScriptEval
 
isExport - Variable in class org.jmol.render.ShapeRenderer
 
isExportMode(String) - Static method in enum class jspecview.common.ExportType
 
isExportXAxisLeftToRight() - Method in class jspecview.common.Spectrum
 
isFieldValid() - Method in class org.jmol.adapter.readers.cif.BCIFReader
 
isFieldValid() - Method in class org.jmol.adapter.readers.cif.CifReader
 
isFinalized - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isFinite(double) - Static method in class org.jmol.minimize.Util
 
isFixed - Variable in class org.jmol.shape.MeshCollection
 
isFloatInfo(String) - Static method in class org.jmol.util.Tensor
 
isFloatParameter(int) - Method in class org.jmol.script.ScriptParam
 
isFloatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
 
isFocusable() - Method in interface jspecview.api.JSVViewPanel
 
isFocusable() - Method in class jspecview.js2d.JsMainPanel
 
isFocusable() - Method in class jspecview.js2d.JsPanel
 
isForcedSubset() - Method in class jspecview.common.Spectrum
 
isFullyLit() - Method in class org.jmol.jvxl.readers.Parameters
 
isFunction(String) - Method in class org.jmol.script.ScriptEval
 
isFunction(String) - Method in class org.jmol.viewer.Viewer
 
isGC() - Method in class jspecview.source.JDXDataObject
 
isGhostPass - Variable in class org.jmol.render.MeshRenderer
 
isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isGzipB(byte[]) - Static method in class javajs.util.Rdr
 
isGzipS(InputStream) - Static method in class javajs.util.Rdr
 
isHeadless() - Method in class jspecview.java.AwtPlatform
 
isHeadless() - Method in class jspecview.js2d.JsPlatform
 
isHeadless() - Method in interface org.jmol.api.GenericPlatform
 
isHeadless() - Method in class org.jmol.awt.Platform
 
isHeadless() - Method in class org.jmol.awtjs2d.Platform
 
isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isHelix() - Method in class org.jmol.modelsetbio.Monomer
 
isHetero - Variable in class org.jmol.adapter.smarter.Atom
 
isHetero() - Method in class org.jmol.modelset.Atom
 
isHetero(String) - Method in class org.jmol.modelsetbio.BioResolver
MMCif, Gromacs, MdTop, Mol2 readers only
isHexagonal(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
isHexagonalSG(int, float[]) - Static method in class org.jmol.symmetry.UnitCell
 
isHidden - Variable in class org.jmol.modelset.Measurement
 
isHidden() - Method in class org.jmol.modelkit.ModelKit
 
isHighDPI() - Static method in class jme.JMEUtil
Check if the applet is showing in highDPI or not.
isHighPrecision - Variable in class org.jmol.adapter.writers.XtlWriter
in SwingJS this is always true
isHighPrecision - Static variable in class org.jmol.viewer.Viewer
adjustable
isHNMR() - Method in class jspecview.source.JDXDataObject
Determines if a spectrum is an HNMR spectrum
isHoverable() - Method in class org.jmol.viewer.ActionManager
 
iShowSolid - Variable in class org.jmol.renderspecial.DotsRenderer
 
isHydrogen() - Method in class org.jmol.modelset.Bond
 
isHydrogen() - Method in class org.jmol.smiles.SmilesBond
 
isHydrogen() - Method in class org.jmol.util.Edge
 
isHZtoPPM() - Method in class jspecview.source.JDXDataObject
Determines if the spectrum should be displayed with abscissa unit of Part Per Million (PPM) instead of Hertz (HZ)
isIDcmd(int) - Static method in class org.jmol.script.T
commands that allow implicit ID as first parameter
isImaginary() - Method in class jspecview.source.JDXDataObject
 
isInchiOpposite(int, int, int, int) - Method in class org.jmol.inchi.InChIJNI
 
isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
 
isInDisplayRange(int, int) - Method in class org.jmol.util.GData
 
isInitializedIndex(int) - Method in class org.jmol.bspt.Bspf
 
isInPosition(V3, float) - Method in class org.jmol.viewer.TransformManager
 
isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
 
isInRange(Atom, Atom, float, float, boolean, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
Consider the min/max option for CONNECT
isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
 
isInsideOut() - Method in class org.jmol.jvxl.readers.Parameters
 
isIntegralDrag - Variable in class jspecview.common.PanelData
 
isInTetrahedron(P3, P3, P3, P3, P3, P4, V3, V3, boolean) - Static method in class javajs.util.Measure
 
isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
 
isInTriangle(P3, P3, P3, P3, V3, V3, V3) - Static method in class javajs.util.Measure
 
isInverted() - Method in class jspecview.source.JDXDataObject
 
isIsotropic - Variable in class org.jmol.util.Tensor
 
isJmolDataFrame - Variable in class org.jmol.modelset.Model
 
isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
 
isJmolDataFrameForModel(int) - Method in class org.jmol.modelset.ModelSet
 
isJmolType(String) - Static method in class org.jmol.viewer.FileManager
Check to see if this is a Jmol WRITE file type that might be or have attached a ZIP collection .
isJNLP - Variable in class org.jmol.viewer.Viewer
 
isJS - Static variable in class jspecview.common.JSViewer
 
isJS - Variable in class org.jmol.popup.GenericPopup
 
isJS - Variable in class org.jmol.script.ScriptEval
 
isJS - Variable in class org.jmol.thread.JmolThread
 
isJS - Static variable in class org.jmol.util.GenericApplet
 
isJS - Static variable in class org.jmol.viewer.Viewer
 
isJSNoAWT - Variable in class org.jmol.viewer.Viewer
 
isJSThread - Variable in class org.jmol.script.ScriptContext
 
isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
 
iskiosk - Static variable in class org.jmol.script.T
 
isKiosk - Variable in class org.openscience.jmol.app.JmolApp
 
isKnownPDBGroup(String, int) - Method in class org.jmol.modelsetbio.BioResolver
 
isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
after reading a model, Q: Is this the last model?
isLeadAtom() - Method in class org.jmol.modelset.Atom
 
isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
 
isLeadAtom() - Method in interface org.jmol.util.Node
 
isLeadAtom(int) - Method in class org.jmol.modelset.Group
 
isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
 
isLeaf() - Method in interface jspecview.api.JSVTreeNode
 
isLeaf() - Method in class jspecview.tree.SimpleTreeNode
 
isLetter(char) - Static method in class javajs.util.PT
 
isLetterOrDigit(char) - Static method in class javajs.util.PT
 
isLigand - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isLike(String, String) - Static method in class javajs.util.PT
a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
isLike(SV, SV) - Static method in class org.jmol.script.SV
a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
isLinked - Variable in class jspecview.common.PanelData
 
isLocal(String) - Static method in class javajs.util.OC
 
isLocal(String) - Static method in class jspecview.common.JSVFileManager
 
isLoggable(int[], int) - Method in class org.jmol.minimize.Minimizer
 
isLoop - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isLoopKey() - Method in class org.jmol.adapter.readers.cif.CifReader
 
isLowerCase(char) - Static method in class javajs.util.PT
 
isM3D - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
 
isMagCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isMapped - Variable in class org.jmol.jvxl.readers.Parameters
 
isMatch(String, String) - Static method in class jspecview.common.Parameters
 
isMatch(String, String, boolean, boolean) - Static method in class javajs.util.PT
A general non-regex (for performance) text matcher that utilizes ? and *.
isMathExpressionCommand - Variable in class org.jmol.script.ScriptCompiler
 
isMeasure - Variable in class org.jmol.modelset.Text
 
isMenuItem(Object) - Method in class org.jmol.console.GenericConsole
 
isMenuItem(Object) - Method in class org.jmol.console.JmolConsole
 
isMenuItem(Object) - Method in class org.jmol.consolejs.AppletConsole
 
isMerged - Variable in class org.jmol.util.MeshSurface
 
isMessagePackB(byte[]) - Static method in class javajs.util.Rdr
 
isMessagePackS(InputStream) - Static method in class javajs.util.Rdr
 
isMin(Map<String, Integer>) - Method in class org.jmol.modelset.Measurement
 
isMMCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isModelConnected - Variable in class org.jmol.jvxl.data.JvxlData
 
isModelConnected - Variable in class org.jmol.jvxl.readers.Parameters
 
isModelConnected - Variable in class org.jmol.shape.Mesh
 
isModelKit - Variable in class org.jmol.modelset.Model
 
isModelKitOption(char, String) - Method in class org.jmol.viewer.Viewer
Check for an option type 'M' 'S' 'U' 'B'.
isModelkitPickingRotateBond() - Method in class org.jmol.viewer.Viewer
 
isModelPDB(int) - Method in class org.jmol.viewer.Viewer
 
isModulated - Variable in class org.jmol.util.Tensor
 
isModulated(int) - Method in class org.jmol.modelset.AtomCollection
 
isMolecular - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isMonoclinicSG(int) - Static method in class org.jmol.symmetry.UnitCell
 
isMouseDown - Variable in class jspecview.app.GenericMouse
 
isMouseUp() - Method in class jspecview.common.PanelData
 
isMovie - Variable in class org.jmol.viewer.AnimationManager
 
isMS() - Method in class jspecview.source.JDXDataObject
 
isMTClient() - Method in class org.jmol.viewer.ActionManager
 
isMTServer() - Method in class org.jmol.viewer.ActionManager
 
isMultiTouch - Variable in class org.jmol.viewer.ActionManager
 
isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
 
isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
 
isNaN() - Method in class org.jmol.script.SV
 
isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
 
isNavigating() - Method in class org.jmol.viewer.TransformManager
 
isNear(double, double) - Static method in class org.jmol.minimize.Util
 
isNear(TouchPoint) - Method in class com.sparshui.server.TouchPoint
 
isNear3(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
 
isNearZero(double) - Static method in class org.jmol.minimize.Util
 
isNearZero2(double, double) - Static method in class org.jmol.minimize.Util
 
isNegDisorder - Variable in class org.jmol.adapter.smarter.Atom
 
isNegligible(double, double) - Static method in class org.jmol.minimize.Util
 
isNegligible3(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNewSet - Variable in class org.jmol.script.ScriptCompiler
 
isNext(String) - Method in class org.jmol.jvxl.readers.XmlReader
 
isNMR() - Method in class jspecview.source.JDXDataObject
 
isNonStringPrimitive(Object) - Static method in class javajs.util.PT
 
isNonzero() - Method in class org.jmol.util.ModulationSet
 
isNonzero() - Method in class org.jmol.util.Vibration
 
isNucleic - Variable in class org.jmol.renderbio.BackboneRenderer
 
isNucleic - Variable in class org.jmol.renderbio.CartoonRenderer
 
isNucleic - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
isNucleic - Variable in class org.jmol.renderbio.RibbonsRenderer
 
isNucleic - Variable in class org.jmol.renderbio.RocketsRenderer
 
isNucleic - Variable in class org.jmol.renderbio.StrandsRenderer
 
isNucleic - Variable in class org.jmol.renderbio.TraceRenderer
 
isNucleic() - Method in class org.jmol.modelset.Group
group ID-based definition
isNucleic() - Method in class org.jmol.modelsetbio.BioPolymer
 
isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isNucleic() - Method in class org.jmol.smiles.SmilesAtom
 
isNucleicMonomer() - Method in class org.jmol.modelset.Group
 
isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isNull(String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
isNumericAndNonZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
isOccupied() - Method in class org.jmol.modelset.Atom
 
IsoExt - Class in org.jmol.scriptext
 
IsoExt() - Constructor for class org.jmol.scriptext.IsoExt
 
isOffsetAbsolute(int) - Static method in class org.jmol.viewer.JC
 
isomeshes - Variable in class org.jmol.shapesurface.Isosurface
 
isOneOf(String, String) - Static method in class javajs.util.PT
 
isOpen(Lst<PanelNode>, String) - Static method in class jspecview.common.PanelNode
 
isOpenShell() - Method in class org.jmol.adapter.readers.quantum.NBOParser
 
isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isOrderH(int) - Static method in class org.jmol.util.Edge
 
isOrderly - Variable in class org.jmol.modelset.Model
a flag that, when false, indicates that the model has atoms in different regions of the Atom[] array
isosurface - Static variable in class org.jmol.script.T
 
Isosurface - Class in org.jmol.shapesurface
 
Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
 
isosurfacekey - Static variable in class org.jmol.script.T
 
IsosurfaceMesh - Class in org.jmol.shapesurface
 
isosurfacepropertysmoothing - Static variable in class org.jmol.script.T
 
isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.T
 
IsosurfaceRenderer - Class in org.jmol.rendersurface
 
IsosurfaceRenderer() - Constructor for class org.jmol.rendersurface.IsosurfaceRenderer
 
ISOTOPE_MASS_OFFSET - Static variable in class org.jmol.util.Elements
 
ISOTOPE_NUMBER_MASK - Static variable in class org.jmol.util.Elements
 
isotopeMass - Static variable in class org.jmol.util.Elements
 
isotropy() - Method in class org.jmol.util.Tensor
isotropy = average of eigenvalues
isPaletteVariable(byte) - Static method in enum class org.jmol.c.PAL
 
isParallel() - Method in class org.jmol.viewer.Viewer
 
isPartial() - Method in class org.jmol.modelset.Bond
 
isPartial() - Method in class org.jmol.smiles.SmilesBond
 
isPartial() - Method in class org.jmol.util.Edge
 
isPass2 - Variable in class org.jmol.util.GData
 
isPaused - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
isPaused() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isPaused() - Method in class org.jmol.script.ScriptEval
 
isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
 
isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
 
isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
 
isPeriodic - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isPhosphorusOnly - Variable in class org.jmol.renderbio.BackboneRenderer
 
isPhosphorusOnly - Variable in class org.jmol.renderbio.CartoonRenderer
 
isPhosphorusOnly - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
isPhosphorusOnly - Variable in class org.jmol.renderbio.RibbonsRenderer
 
isPhosphorusOnly - Variable in class org.jmol.renderbio.RocketsRenderer
 
isPhosphorusOnly - Variable in class org.jmol.renderbio.StrandsRenderer
 
isPhosphorusOnly - Variable in class org.jmol.renderbio.TraceRenderer
 
isPickAtomAssignCharge() - Method in class org.jmol.modelkit.ModelKit
 
isPickleB(byte[]) - Static method in class javajs.util.Rdr
 
isPickleS(InputStream) - Static method in class javajs.util.Rdr
 
isPixels - Variable in class jspecview.common.Annotation
 
isPlugin - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
isPlugin() - Method in class org.openscience.jmol.app.janocchio.Nmr
 
isPngZipB(byte[]) - Static method in class javajs.util.Rdr
 
isPngZipStream(InputStream) - Static method in class javajs.util.Rdr
 
isPoint3f(int) - Method in class org.jmol.script.ScriptParam
 
isPolarSG(int) - Static method in class org.jmol.symmetry.UnitCell
 
isPolygonDisplayable(int) - Method in class org.jmol.render.MeshRenderer
 
isPolygonDisplayable(int) - Method in class org.jmol.renderspecial.DrawRenderer
 
isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
 
isPolymer - Variable in class org.jmol.render.AxesRenderer
 
isPolymer - Variable in class org.jmol.render.BbcageRenderer
 
isPolymer - Variable in class org.jmol.render.UccageRenderer
 
isPolymer() - Method in interface org.jmol.api.SymmetryInterface
 
isPolymer() - Method in class org.jmol.symmetry.Symmetry
 
isPolymer() - Method in class org.jmol.util.SimpleUnitCell
 
isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
 
isPossibleHBond(HB, HB) - Static method in enum class org.jmol.c.HB
 
isPreviewOnly - Variable in class org.jmol.viewer.Viewer
 
isPrimitive - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isPrinting - Variable in class jspecview.common.PanelData
 
isPrintOnly - Variable in class org.jmol.viewer.Viewer
 
isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
 
isPro() - Method in interface jspecview.api.JSVAppletInterface
 
isPro() - Method in class jspecview.app.JSVApp
 
isPro() - Method in class jspecview.app.JSVAppPro
 
isPro() - Method in class jspecview.appletjs.JSVApplet
 
isPro() - Method in class jspecview.appletjs.JSVAppletPro
 
isPro() - Method in class jspecview.application.MainFrame
 
isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isProtein() - Method in class org.jmol.modelset.Group
group ID-based definition
isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isPurine() - Method in class org.jmol.modelset.Atom
 
isPurine() - Method in class org.jmol.modelset.Group
group ID-based definition
isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPurine() - Method in class org.jmol.smiles.SmilesAtom
 
isPurine() - Method in interface org.jmol.util.Node
 
isPurineByID() - Method in class org.jmol.modelset.Group
group ID-based definition
isPyrimidine() - Method in class org.jmol.modelset.Atom
 
isPyrimidine() - Method in class org.jmol.modelset.Group
group ID-based definition
isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
 
isPyrimidine() - Method in interface org.jmol.util.Node
 
isPyrimidineByID() - Method in class org.jmol.modelset.Group
 
isQuantumBasisSupported(char) - Static method in class org.jmol.quantum.QS
 
isQueueProcessing() - Method in interface org.jmol.api.JmolScriptManager
 
isQueueProcessing() - Method in class org.jmol.script.ScriptManager
 
isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isQuote(char) - Method in class javajs.util.CifDataParser
CIF 1.0 only; we handle various quote types here
isQuote(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
Includes all possible operator tokens
isRadio - Variable in class org.jmol.awtjs.swing.JRadioButtonMenuItem
 
isRandom - Variable in class javajs.util.BinaryDocument
 
isRemote(String) - Static method in class javajs.util.OC
 
isRenderScalable() - Method in class org.jmol.shapespecial.DrawMesh
 
isRepaintPending() - Method in interface org.jmol.api.JmolRepaintManager
 
isRepaintPending() - Method in class org.jmol.render.RepaintManager
 
isRepaintPending() - Method in class org.jmol.viewer.Viewer
 
isReset - Variable in class org.jmol.thread.JmolThread
 
isReversed - Variable in class org.jmol.util.ColorEncoder
 
isRhombohedral(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
isRna() - Method in class org.jmol.modelset.Group
group ID-based definition
isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isRnaByID() - Method in class org.jmol.modelset.Group
group ID-based definition
isRotation() - Method in class javajs.util.M3
 
isScalable() - Method in class jspecview.source.JDXDataObject
 
isScalar(SV) - Static method in class org.jmol.script.SV
 
isScaleSet - Variable in class org.jmol.shapespecial.DrawMesh
 
isScript() - Static method in class jme.JMEUtil.GWT
 
isScriptExecuting() - Method in class org.jmol.api.JmolViewer
 
isScriptExecuting() - Method in class org.jmol.viewer.Viewer
 
isScriptQueued() - Method in interface org.jmol.api.JmolScriptManager
 
isScriptQueued() - Method in class org.jmol.script.ScriptManager
 
isScriptType(String) - Static method in class org.jmol.viewer.FileManager
 
isSelected - Variable in class jspecview.common.PanelNode
 
isSelected() - Method in interface org.jmol.api.JmolAbstractButton
 
isSelected() - Method in interface org.jmol.api.SC
 
isSelected() - Method in class org.jmol.awt.AwtSwingComponent
 
isSelected() - Method in class org.jmol.awtjs.swing.AbstractButton
 
isSelected() - Method in class org.jmol.console.JmolLabel
 
isSelected(int) - Method in class org.jmol.viewer.SelectionManager
 
isSelected(Object) - Method in interface jspecview.api.PlatformDialog
 
isSelected(Object) - Method in class jspecview.java.AwtDialog
 
isSelected(Object) - Method in class jspecview.js2d.JsDialog
 
isSelected(BS) - Method in class org.jmol.modelset.Group
 
isSelected(BS, int) - Method in class org.jmol.util.Tensor
 
isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
isServer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
isSet - Variable in class org.jmol.shape.AtomShape
 
isSetBrace - Variable in class org.jmol.script.ScriptCompiler
 
isSetOrDefine - Variable in class org.jmol.script.ScriptCompiler
 
isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isSheet() - Method in class org.jmol.modelsetbio.Monomer
 
isShell - Variable in class org.jmol.render.MeshRenderer
 
isShell - Variable in class org.jmol.shape.Mesh
 
isShowAllStacked() - Method in class jspecview.common.PanelData
 
isSigned - Variable in class jspecview.common.JSViewer
 
isSigned - Variable in class org.jmol.popup.GenericPopup
 
isSigned - Variable in class org.jmol.util.GenericApplet
 
isSigned() - Method in interface jspecview.api.JSVAppletInterface
 
isSigned() - Method in interface jspecview.api.ScriptInterface
 
isSigned() - Method in class jspecview.app.JSVApp
 
isSigned() - Method in class jspecview.app.JSVAppPro
 
isSigned() - Method in class jspecview.appletjs.JSVApplet
 
isSigned() - Method in class jspecview.application.JSpecView
 
isSigned() - Method in class jspecview.application.MainFrame
 
isSignedApplet - Variable in class org.jmol.viewer.Viewer
 
isSilent - Variable in class org.jmol.jvxl.readers.Parameters
 
isSilent - Variable in class org.openscience.jmol.app.JmolApp
 
isSimple() - Method in interface org.jmol.api.SymmetryInterface
 
isSimple() - Method in class org.jmol.symmetry.Symmetry
 
isSimulation - Variable in class jspecview.common.PanelNode
 
isSimulation - Variable in class jspecview.source.JDXDataObject
 
isSingleThreaded - Variable in class jspecview.common.JSViewer
 
isSingleThreaded - Variable in class org.jmol.viewer.Viewer
 
isSingleThreaded() - Method in class jspecview.java.AwtPlatform
 
isSingleThreaded() - Method in class jspecview.js2d.JsPlatform
 
isSingleThreaded() - Method in interface org.jmol.api.GenericPlatform
 
isSingleThreaded() - Method in class org.jmol.awt.Platform
 
isSingleThreaded() - Method in class org.jmol.awtjs2d.Platform
 
isSlab - Variable in class org.jmol.render.AxesRenderer
 
isSlab - Variable in class org.jmol.render.BbcageRenderer
 
isSlab - Variable in class org.jmol.render.UccageRenderer
 
isSlab() - Method in interface org.jmol.api.SymmetryInterface
 
isSlab() - Method in class org.jmol.symmetry.Symmetry
 
isSlab() - Method in class org.jmol.util.SimpleUnitCell
 
isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
 
isSlabEnabled - Variable in class org.jmol.export._PovrayExporter
 
isSlabEnabled - Variable in class org.jmol.export._TachyonExporter
 
isSmilesCanonical(String) - Static method in class org.jmol.viewer.JC
 
isSorting() - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
isSpaceGroupInfoKey(String) - Static method in class org.jmol.viewer.JC
When UNITCELL NONE is given, clear out all space group and unit cell keys from model info.
isSpinFixed - Variable in class org.jmol.viewer.TransformManager
 
isSpinInternal - Variable in class org.jmol.viewer.TransformManager
 
isSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isSquared - Variable in class org.jmol.jvxl.readers.Parameters
 
isSquaredLinear - Variable in class org.jmol.jvxl.readers.Parameters
 
isSSG - Variable in class org.jmol.symmetry.SpaceGroup
 
isStackable() - Method in class jspecview.source.JDXDataObject
 
isStarted() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
isStarted() - Method in interface org.openscience.jmol.app.JmolPlugin
 
isStateScript - Variable in class org.jmol.script.ScriptEval
 
isStateScript - Variable in class org.jmol.script.ScriptCompiler
 
isStateScript() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isStateScript() - Method in class org.jmol.script.ScriptEval
 
isStepping() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isStepping() - Method in class org.jmol.script.ScriptEval
 
isStereoOpposite(int, int, int) - Method in class org.jmol.smiles.SmilesAtom
 
isStereoSlave - Variable in class org.jmol.util.GenericApplet
 
isStopped() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isStopped() - Method in class org.jmol.script.ScriptEval
 
isStringArray(String) - Static method in class org.jmol.util.Escape
 
isSubstructure(String, String) - Method in class org.jmol.viewer.Viewer
 
isSupercell() - Method in interface org.jmol.api.SymmetryInterface
 
isSupercell() - Method in class org.jmol.symmetry.Symmetry
 
isSupercell() - Method in class org.jmol.util.SimpleUnitCell
 
isSUPERCELL - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
actual SUPERCELL keyword, not just "cell="
isSurface - Variable in class org.jmol.shapespecial.Dots
 
isSwingJS - Static variable in class jspecview.common.JSViewer
 
isSwingJS - Static variable in class org.jmol.viewer.Viewer
 
isSymmetryCell(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
isSymmetryCell(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
isSyntaxAndFileCheck - Variable in class org.jmol.viewer.Viewer
 
isSyntaxCheck - Variable in class org.jmol.viewer.Viewer
 
isTainted - Variable in class org.jmol.popup.GenericPopup
 
isTainted() - Method in class org.jmol.modelset.Measurement
 
isTar(BufferedInputStream) - Static method in class javajs.util.Rdr
 
isTerminator(char) - Method in class javajs.util.CifDataParser
The token terminator is space or tab in CIF 1.0, but it can be quoted strings in CIF 2.0.
isTetragonalSG(int) - Static method in class org.jmol.symmetry.UnitCell
 
isTracker() - Method in class org.jmol.symmetry.CIPData
Subclass identifier
isTracker() - Method in class org.jmol.symmetry.CIPDataTracker
 
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isTrajectory - Variable in class org.jmol.modelset.Measurement
 
isTrajectory - Variable in class org.jmol.modelset.ModelLoader
 
isTrajectory(int) - Method in class org.jmol.modelset.ModelSet
could be the base model or one of the subframes
isTrajectoryMeasurement(int[]) - Method in class org.jmol.modelset.ModelSet
 
isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelSet
 
isTranslucent - Variable in class org.jmol.render.MeshRenderer
 
isTranslucent - Variable in class org.jmol.util.ColorEncoder
 
isTranslucentInherit - Variable in class org.jmol.render.MeshRenderer
 
isTransmittance() - Method in class jspecview.source.JDXDataObject
 
isTrue(String) - Static method in class jspecview.common.Parameters
 
isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
 
isTwoSided - Variable in class org.jmol.shape.Mesh
 
isUnits(String) - Static method in class org.jmol.modelset.Measurement
 
isUnmodulated - Variable in class org.jmol.util.Tensor
 
isUpperCase(char) - Static method in class javajs.util.PT
 
isURL(String) - Static method in class jspecview.common.JSVFileManager
 
isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
 
isUserFunction(String) - Method in class org.jmol.script.ScriptCompiler
 
isValid - Variable in class org.jmol.bspt.Bspf
 
isValid - Variable in class org.jmol.jvxl.data.JvxlData
 
isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
isValid - Variable in class org.jmol.modelset.Measurement
 
isValid - Variable in class org.jmol.shape.Mesh
 
isValid - Variable in class org.jmol.shapespecial.Ellipsoid
 
isValid - Variable in class org.jmol.shapespecial.Polyhedron
 
isValid() - Method in class jspecview.common.SubSpecChangeEvent
 
isValid() - Method in class org.jmol.modelset.Measurement
 
isValid() - Method in class org.jmol.modelset.StateScript
 
isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.readers.xtal.ShelxReader
 
isValidFontName(String) - Method in class jspecview.common.ColorParameters
 
isValidFontName(String) - Method in class jspecview.java.AwtParameters
 
isValidFontName(String) - Method in class jspecview.js2d.JsParameters
 
isValidSym1(char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidSym2(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidSymNoCase(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isVariableType(Object) - Static method in class org.jmol.script.SV
Must be updated if getVariable is updated!
isVector - Variable in class org.jmol.shapespecial.DrawMesh
 
isView - Variable in class jspecview.common.PanelNode
 
isView - Variable in class jspecview.source.JDXSource
 
isVisible - Variable in class org.jmol.modelset.Measurement
 
isVisible - Variable in class org.jmol.shape.Bbcage
 
isVisible() - Method in interface jspecview.api.AnnotationData
 
isVisible() - Method in interface jspecview.api.JSVViewPanel
 
isVisible() - Method in interface jspecview.api.PlatformDialog
 
isVisible() - Method in class jspecview.common.MeasurementData
 
isVisible() - Method in class jspecview.dialog.JSVDialog
 
isVisible() - Method in class jspecview.js2d.JsMainPanel
 
isVisible() - Method in class jspecview.js2d.JsPanel
 
isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
isVisible() - Method in class org.jmol.awtjs.swing.Component
 
isVisible(int) - Method in class org.jmol.modelset.Atom
 
isVisibleForMe(Atom) - Method in class org.jmol.render.ShapeRenderer
 
isVisibleNormix(short) - Method in class org.jmol.render.MeshRenderer
 
isWebGL - Variable in class org.jmol.popup.GenericPopup
 
isWebGL - Variable in class org.jmol.viewer.Viewer
 
isWebGL() - Method in interface org.jmol.api.JmolRendererInterface
 
isWebGL() - Method in class org.jmol.export.Export3D
 
isWebGL() - Method in class org.jmol.g3d.Graphics3D
 
isWhitespace(char) - Static method in class javajs.util.PT
 
isWhiteSpace(String, int) - Static method in class javajs.util.PT
 
isWild(String) - Static method in class javajs.util.PT
 
isWindowCentered() - Method in class org.jmol.viewer.TransformManager
 
isWithin(int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
isWithin(P3) - Method in class org.jmol.util.BoxInfo
 
isWithinCell(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
isWithinStructure(STR) - Method in class org.jmol.modelset.Group
 
isWithinStructure(STR) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isWithinUnitCell(P3, float, float, float) - Method in interface org.jmol.api.SymmetryInterface
 
isWithinUnitCell(P3, float, float, float) - Method in class org.jmol.symmetry.Symmetry
 
isXIncreasing() - Method in class jspecview.source.JDXDataObject
Returns true if the spectrum is increasing; used by SVGExporter only
isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
isXtalState() - Method in class org.jmol.modelkit.ModelKit
 
isXYZ - Variable in class org.jmol.modelset.ModelSet
 
isYInRange(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
Determines if the y values of a spectrum are in a certain range
isZipB(byte[]) - Static method in class javajs.util.Rdr
 
isZipFile(InputStream) - Static method in class jspecview.common.JSVFileManager
 
isZipS(InputStream) - Static method in class javajs.util.Rdr
Check for a ZIP input stream - starting with "PKinvalid input: '<'03>invalid input: '<'04>"
isZipStream(Object) - Method in interface javajs.api.GenericZipTools
 
isZipStream(Object) - Method in class javajs.util.ZipTools
 
isZipStream(Object) - Method in class org.jmol.viewer.FileManager
 
itemKeys - Variable in class org.jmol.console.KeyJMenu
 
itemStateChanged(ItemEvent) - Method in class org.jmol.awt.AwtPopupHelper
 
itemStateChanged(ItemEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
itemStateChanged(ItemEvent) - Method in class org.jmol.dialog.Dialog.ExportChoiceListener
 
iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelsetbio.BioResolver
Pull in all spans of helix, etc.
iToken - Variable in class org.jmol.script.ScriptParam
 
itokenInfix - Variable in class org.jmol.script.ScriptCompiler
 
iType - Variable in class com.sparshui.GestureType
 
iType - Variable in class org.jmol.util.Tensor
 
iValue(T) - Static method in class org.jmol.script.SV
 
ivspoints - Variable in class jspecview.source.AnIMLReader
 

J

J2SIgnoreImport - Annotation Interface in javajs
 
J2SObjectInterface - Interface in javajs.api.js
methods in j2s JavaScript accessed in Jmol
J2SRequireImport - Annotation Interface in javajs
 
JaguarReader - Class in org.jmol.adapter.readers.quantum
Jaguar reader tested for the two samples files in CVS.
JaguarReader() - Constructor for class org.jmol.adapter.readers.quantum.JaguarReader
 
JanaReader - Class in org.jmol.adapter.readers.xtal
A reader for Jana M50+M40 file pairs.
JanaReader() - Constructor for class org.jmol.adapter.readers.xtal.JanaReader
 
javajs - package javajs
 
javajs.api - package javajs.api
 
javajs.api.js - package javajs.api.js
 
javajs.export - package javajs.export
 
javajs.img - package javajs.img
 
javajs.util - package javajs.util
 
javascript - Static variable in class org.jmol.script.T
 
JButton - Class in org.jmol.awtjs.swing
 
JButton() - Constructor for class org.jmol.awtjs.swing.JButton
 
jc - Variable in class org.jmol.awt.AwtSwingComponent
 
JC - Class in org.jmol.viewer
 
JC() - Constructor for class org.jmol.viewer.JC
 
jcampdx - Variable in class jspecview.source.JDXHeader
 
JcampdxReader - Class in org.jmol.adapter.readers.more
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ...
JcampdxReader() - Constructor for class org.jmol.adapter.readers.more.JcampdxReader
 
jcd - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
JCH3_AYDIN_GUETHER - Static variable in class org.jmol.quantum.NMRCalculation
 
JCH3_NONE - Static variable in class org.jmol.quantum.NMRCalculation
 
JCH3_TVAROSKA_TARAVEL - Static variable in class org.jmol.quantum.NMRCalculation
 
JCH3_WASYLISHEN_SCHAEFER - Static variable in class org.jmol.quantum.NMRCalculation
 
JCheckBox - Class in org.jmol.awtjs.swing
 
JCheckBox() - Constructor for class org.jmol.awtjs.swing.JCheckBox
 
JCheckBoxMenuItem - Class in org.jmol.awtjs.swing
 
JCheckBoxMenuItem() - Constructor for class org.jmol.awtjs.swing.JCheckBoxMenuItem
 
JComboBox<T> - Class in org.jmol.awtjs.swing
 
JComboBox(String[]) - Constructor for class org.jmol.awtjs.swing.JComboBox
 
JComponent - Class in org.jmol.awtjs.swing
 
JComponent(String) - Constructor for class org.jmol.awtjs.swing.JComponent
 
JContentPane - Class in org.jmol.awtjs.swing
 
JContentPane() - Constructor for class org.jmol.awtjs.swing.JContentPane
 
JDialog - Class in org.jmol.awtjs.swing
There is really no need here for awt.Dialog.
JDialog() - Constructor for class org.jmol.awtjs.swing.JDialog
 
JDXDataObject - Class in jspecview.source
spectrum data AS READ FROM FILE
JDXDataObject() - Constructor for class jspecview.source.JDXDataObject
 
JDXDecompressor - Class in jspecview.source
JDXDecompressor contains static methods to decompress the data part of JCAMP-DX spectra that have been compressed using DIF, FIX, SQZ or PAC formats.
JDXDecompressor(String, int) - Constructor for class jspecview.source.JDXDecompressor
 
JDXDecompressor(JDXSourceStreamTokenizer, double, double, double, double, int) - Constructor for class jspecview.source.JDXDecompressor
Initialises the JDXDecompressor from the compressed data, the x factor, the y factor and the deltaX value
JDXDecompressorTest - Class in jspecview.source
 
JDXDecompressorTest() - Constructor for class jspecview.source.JDXDecompressorTest
 
JDXExporter - Class in jspecview.export
class JDXExporter contains methods for exporting a JCAMP-DX Spectrum in one of the compression formats DIF, FIX, PAC, SQZ or as x, y values.
JDXExporter() - Constructor for class jspecview.export.JDXExporter
 
JDXHeader - Class in jspecview.source
could be a spectrum or a source
JDXHeader() - Constructor for class jspecview.source.JDXHeader
 
JDXMOLParser - Class in org.jmol.jsv
Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
JDXMOLParser() - Constructor for class org.jmol.jsv.JDXMOLParser
 
JDXReader - Class in jspecview.source
JDXFileReader reads JDX data, including complex BLOCK files that contain NTUPLE blocks or nested BLOCK data.
JDXSource - Class in jspecview.source
JDXSource is representation of all the data in the JCAMP-DX file or source.
JDXSource(int, String) - Constructor for class jspecview.source.JDXSource
 
JDXSourceStreamTokenizer - Class in jspecview.source
 
JEditorPane - Class in org.jmol.awtjs.swing
A simple implementation of a Swing JTextPane.
JEditorPane() - Constructor for class org.jmol.awtjs.swing.JEditorPane
 
JLabel - Class in org.jmol.awtjs.swing
 
JLabel(String) - Constructor for class org.jmol.awtjs.swing.JLabel
 
jme - package jme
 
JME - Class in jme
 
JME() - Constructor for class jme.JME
 
JME(JFrame, boolean) - Constructor for class jme.JME
 
jmeFile() - Method in class jme.JME
 
jmeh - Variable in class jme.JME
 
JMEmol - Class in jme
 
JMEmol(JME, JmolAdapterAtomIterator, JmolAdapterBondIterator) - Constructor for class jme.JMEmol
 
JMenu - Class in org.jmol.awtjs.swing
 
JMenu() - Constructor for class org.jmol.awtjs.swing.JMenu
 
JMenuItem - Class in org.jmol.awtjs.swing
 
JMenuItem(String) - Constructor for class org.jmol.awtjs.swing.JMenuItem
 
JMenuItem(String, int) - Constructor for class org.jmol.awtjs.swing.JMenuItem
 
JmeReader - Class in org.jmol.adapter.readers.simple
 
JmeReader() - Constructor for class org.jmol.adapter.readers.simple.JmeReader
 
jmeToMolecule(String) - Static method in class org.jmol.smiles.SmilesMatcher
 
JMEUtil - Class in jme
 
JMEUtil() - Constructor for class jme.JMEUtil
 
JMEUtil.GWT - Class in jme
Do nothing , support for JSME code splitting.
JMEUtil.JSME_RunAsyncCallback - Class in jme
 
JMEUtil.RunAsyncCallback - Interface in jme
A callback meant to be used by
JMEUtil.RunWhenDataReadyCallback - Interface in jme
 
jmol - Variable in class jspecview.application.JSpecView
 
jmol - Static variable in class org.jmol.script.T
 
Jmol - Class in org.jmol.appletjs
Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
Jmol - Class in org.openscience.jmol.app
 
Jmol(Map<String, Object>) - Constructor for class org.jmol.appletjs.Jmol
 
Jmol(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.Jmol
 
Jmol() - Static method in class org.jmol.awtjs2d.Platform
 
JMOL - Enum constant in enum class jspecview.common.ScriptToken
 
JMOL - Enum constant in enum class org.jmol.c.PAL
 
JMOL - Enum constant in enum class org.jmol.c.VDW
 
JMOL - Static variable in class org.jmol.util.ColorEncoder
 
JMOL_DIAMETER - Static variable in class org.jmol.shapecgo.CGOMesh
 
JMOL_MODEL_KIT - Static variable in class org.jmol.viewer.JC
 
JMOL_PS - Static variable in class org.jmol.shapecgo.CGOMesh
 
JMOL_SCREEN - Static variable in class org.jmol.shapecgo.CGOMesh
 
JMOL_UVMAP - Static variable in class org.jmol.shapecgo.CGOMesh
 
JmolAbstractButton - Interface in org.jmol.api
 
JmolAdapter - Class in org.jmol.api
The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
JmolAdapter() - Constructor for class org.jmol.api.JmolAdapter
 
JmolAdapterAtomIterator - Interface in org.jmol.api
 
JmolAdapterBondIterator - Class in org.jmol.api
 
JmolAdapterBondIterator() - Constructor for class org.jmol.api.JmolAdapterBondIterator
 
JmolAdapterStructureIterator - Class in org.jmol.api
 
JmolAdapterStructureIterator() - Constructor for class org.jmol.api.JmolAdapterStructureIterator
 
JmolAnnotationParser - Interface in org.jmol.api
 
jmolApp - Variable in class org.openscience.jmol.app.JmolData
 
jmolApp - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
JmolApp - Class in org.openscience.jmol.app
 
JmolApp() - Constructor for class org.openscience.jmol.app.JmolApp
 
JmolApp(String[]) - Constructor for class org.openscience.jmol.app.JmolApp
standard Jmol application entry point
JmolAppAPI - Interface in org.jmol.api
 
JmolAppConsoleInterface - Interface in org.jmol.api
 
JmolAppletInterface - Interface in org.jmol.api
This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
JmolAsyncException - Exception Class in org.jmol.viewer
 
JmolAsyncException(String) - Constructor for exception class org.jmol.viewer.JmolAsyncException
 
JmolAudio - Class in org.jmol.util
 
JmolAudio() - Constructor for class org.jmol.util.JmolAudio
 
JmolAudioPlayer - Interface in org.jmol.api
 
JmolBinding - Class in org.jmol.viewer.binding
 
JmolBinding() - Constructor for class org.jmol.viewer.binding.JmolBinding
 
JmolButton - Class in org.jmol.console
 
JmolButton(String) - Constructor for class org.jmol.console.JmolButton
 
JmolButton(ImageIcon) - Constructor for class org.jmol.console.JmolButton
 
JmolCallbackListener - Interface in org.jmol.api
 
JmolChimeMessenger - Interface in org.jmol.viewer
 
JmolConsole - Class in org.jmol.console
 
JmolConsole() - Constructor for class org.jmol.console.JmolConsole
 
JmolData - Class in org.openscience.jmol.app
 
JmolDataManager - Interface in org.jmol.api
 
JmolDataReader - Class in org.jmol.adapter.readers.pdb
JmolData file reader, for a modified PDB format
JmolDataReader() - Constructor for class org.jmol.adapter.readers.pdb.JmolDataReader
 
JmolDialogInterface - Interface in org.jmol.api
 
JmolDropEditor - Interface in org.jmol.api
 
JmolEnvCalc - Interface in org.jmol.api
 
JmolFilesReaderInterface - Interface in org.jmol.api
 
JmolFrame - Interface in jspecview.java
 
JmolFrame - Interface in org.jmol.awt
 
JmolGenericPopup - Class in org.jmol.popup
An abstract popup class that is instantiated for a given platform and context as one of:
JmolGenericPopup() - Constructor for class org.jmol.popup.JmolGenericPopup
 
JmolGestureServerInterface - Interface in org.jmol.api
 
JmolGraphicsInterface - Interface in org.jmol.api
 
JmolInChI - Interface in org.jmol.api
 
jmolinjspecview - Static variable in class org.jmol.script.T
 
JmolJDXMOLParser - Interface in org.jmol.api
 
JmolJDXMOLReader - Interface in org.jmol.api
 
jmolJME - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
JmolJME - Class in org.openscience.jmol.app.jmolpanel
 
JmolJME() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolJME
 
JmolJniClientAdapter - Class in org.jmol.multitouch.jni
 
JmolJniClientAdapter() - Constructor for class org.jmol.multitouch.jni.JmolJniClientAdapter
 
JmolJSpecView - Interface in org.jmol.api
 
JmolLabel - Class in org.jmol.console
 
JmolLabel(String, int) - Constructor for class org.jmol.console.JmolLabel
 
JmolMeasurementClient - Interface in org.jmol.api
 
JmolModulationSet - Interface in org.jmol.api
 
JmolMolecule - Class in org.jmol.util
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
JmolMolecule() - Constructor for class org.jmol.util.JmolMolecule
 
JmolMovieCreatorInterface - Interface in org.jmol.api
 
JmolMultiTouchAdapter - Interface in org.jmol.multitouch
 
JmolMultiTouchClient - Interface in org.jmol.multitouch
 
JmolMultiTouchClientAdapter - Class in org.jmol.multitouch
 
JmolMultiTouchClientAdapter() - Constructor for class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
JmolNavigatorInterface - Interface in org.jmol.api
 
JmolNMRInterface - Interface in org.jmol.api
 
jmolObject - Static variable in class jspecview.common.JSViewer
 
jmolObject - Static variable in class org.jmol.viewer.Viewer
 
jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
JmolPanel - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel(JmolApp, Splash, JFrame, JmolPanel, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel
 
JmolPanel.AboutAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ActionChangedListener - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.AnimButton - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.AppCloser - Class in org.openscience.jmol.app.jmolpanel
To shutdown when run as an application.
JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CloseAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ConsoleAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CopyImageAction - Class in org.openscience.jmol.app.jmolpanel
An Action to copy the current image into the clipboard.
JmolPanel.CopyScriptAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CreditsAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExecuteScriptAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExitAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExportAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.GaussianAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.NewAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.NewwinAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenMolAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenPdbAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenUrlAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PasteClipboardAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PovrayAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PrintAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.RecentFilesAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ResizeAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ScriptEditorAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ScriptWindowAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.SurfaceToolAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ToWebAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.TwoDEditorAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.UguideAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ViewMeasurementTableAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.WhatsNewAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.WriteAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolParallelProcessor - Interface in org.jmol.api
 
JmolPdfCreatorInterface - Interface in org.jmol.api
 
JmolPlugin - Interface in org.openscience.jmol.app
 
JmolPopup - Class in org.jmol.popup
An abstract popup class that is instantiated for a given platform and context as one of:
JmolPopup() - Constructor for class org.jmol.popup.JmolPopup
 
jmolPosition - Variable in class org.openscience.jmol.app.JmolApp
 
JmolPropertyManager - Interface in org.jmol.api
 
JmolRendererInterface - Interface in org.jmol.api
 
JmolRepaintManager - Interface in org.jmol.api
 
JmolResourceHandler - Class in org.openscience.jmol.app.jmolpanel
Provides access to resources (for example, strings and images).
JmolSceneGenerator - Interface in org.jmol.api
 
JmolScriptEditorInterface - Interface in org.jmol.api
 
JmolScriptEvaluator - Interface in org.jmol.api
 
JmolScriptFunction - Interface in org.jmol.api
 
JmolScriptManager - Interface in org.jmol.api
 
JmolSelectionListener - Interface in org.jmol.api
listen to atom selections in a Jmol Viewer
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS - Search tag in package org.jmol.smiles
Section
Jmol SMILES and Jmol SMARTS Definition of "aromatic" - Search tag in package org.jmol.smiles
Section
JmolSparshClientAdapter - Class in org.jmol.multitouch.sparshui
 
JmolSparshClientAdapter() - Constructor for class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
JmolStateCreator - Class in org.jmol.viewer
 
JmolStateCreator() - Constructor for class org.jmol.viewer.JmolStateCreator
 
JmolStatusListener - Interface in org.jmol.api
 
JmolSyncInterface - Interface in org.jmol.api
 
JmolThread - Class in org.jmol.thread
 
JmolThread() - Constructor for class org.jmol.thread.JmolThread
 
JmolToggleButton - Class in org.jmol.console
 
JmolToggleButton(ImageIcon) - Constructor for class org.jmol.console.JmolToggleButton
 
JmolToJSmolInterface - Interface in org.jmol.api.js
methods in JSmol JavaScript accessed in Jmol
JmolTouchSimulator - Class in com.sparshui.inputdevice
allows Jmol to implement multitouch testing using the mouse press CTRL-LEFT and drag twice for a two-stroke multitouch gesture that will be sent to the server in an interlaced fashion.
JmolTouchSimulator() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator
 
JmolTouchSimulator.TouchData - Class in com.sparshui.inputdevice
 
JmolTouchSimulator.TouchDataComparator - Class in com.sparshui.inputdevice
 
JmolTouchSimulatorInterface - Interface in org.jmol.api
 
JmolUtil - Class in org.jmol.io
 
JmolUtil() - Constructor for class org.jmol.io.JmolUtil
 
JmolViewer - Class in org.jmol.api
JmolViewer is the main API for the Viewer class.
JmolViewer() - Constructor for class org.jmol.api.JmolViewer
 
JmolWriter - Interface in org.jmol.api
 
JmolZipUtilities - Interface in org.jmol.api
 
join - Static variable in class org.jmol.script.T
 
join(String[], char, int) - Static method in class javajs.util.PT
 
JPanel - Class in org.jmol.awtjs.swing
 
JPanel(LayoutManager) - Constructor for class org.jmol.awtjs.swing.JPanel
 
JPEG_CONTINUE_STRING - Static variable in class org.jmol.viewer.FileManager
 
JPEG_EXTENSIONS - Static variable in class org.jmol.viewer.JC
 
JPG - Enum constant in enum class jspecview.common.ExportType
 
Jpg64Encoder - Class in javajs.img
 
Jpg64Encoder() - Constructor for class javajs.img.Jpg64Encoder
 
JpgEncoder - Class in javajs.img
JpegEncoder - The JPEG main program which performs a jpeg compression of an image.
JpgEncoder() - Constructor for class javajs.img.JpgEncoder
 
jpiDispose() - Method in class jspecview.popup.JSVGenericPopup
 
jpiDispose() - Method in interface org.jmol.api.GenericMenuInterface
 
jpiDispose() - Method in class org.jmol.popup.GenericPopup
 
jpiDispose() - Method in class org.jmol.popup.JmolGenericPopup
 
jpiDispose() - Method in class org.jmol.popup.JmolPopup
 
jpiGetMenuAsObject() - Method in class jspecview.popup.JSVGenericPopup
 
jpiGetMenuAsObject() - Method in interface org.jmol.api.GenericMenuInterface
 
jpiGetMenuAsObject() - Method in class org.jmol.popup.JmolGenericPopup
 
jpiGetMenuAsString(String) - Method in interface org.jmol.api.GenericMenuInterface
 
jpiGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
 
jpiInitialize(PlatformViewer, String) - Method in class jspecview.java.AwtPopup
 
jpiInitialize(PlatformViewer, String) - Method in class jspecview.js2d.JsPopup
 
jpiInitialize(PlatformViewer, String) - Method in interface org.jmol.api.GenericMenuInterface
 
jpiInitialize(PlatformViewer, String) - Method in class org.jmol.popup.JmolGenericPopup
 
jpiShow(int, int) - Method in class jspecview.popup.JSVGenericPopup
 
jpiShow(int, int) - Method in interface org.jmol.api.GenericMenuInterface
 
jpiShow(int, int) - Method in class org.jmol.modelkit.ModelKitPopup
 
jpiShow(int, int) - Method in class org.jmol.popup.JmolGenericPopup
 
jpiUpdateComputedMenus() - Method in class jspecview.popup.JSVGenericPopup
 
jpiUpdateComputedMenus() - Method in interface org.jmol.api.GenericMenuInterface
 
jpiUpdateComputedMenus() - Method in class org.jmol.modelkit.ModelKitPopup
 
jpiUpdateComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
JPopupMenu - Class in org.jmol.awtjs.swing
 
JPopupMenu(String) - Constructor for class org.jmol.awtjs.swing.JPopupMenu
 
JRadioButtonMenuItem - Class in org.jmol.awtjs.swing
 
JRadioButtonMenuItem() - Constructor for class org.jmol.awtjs.swing.JRadioButtonMenuItem
 
JSAppletObject - Interface in javajs.api.js
 
JSConsole - Interface in org.jmol.api.js
 
JScrollPane - Class in org.jmol.awtjs.swing
 
JScrollPane(JComponent) - Constructor for class org.jmol.awtjs.swing.JScrollPane
 
JsDialog - Class in jspecview.js2d
just a class I made to separate the construction of the AnnotationDialogs from their use
JsDialog(DialogManager, JSVDialog, String) - Constructor for class jspecview.js2d.JsDialog
 
JsDialogManager - Class in jspecview.js2d
A DialogManager for JavaScript.
JsDialogManager() - Constructor for class jspecview.js2d.JsDialogManager
 
jsDocumentBase - Static variable in class jspecview.common.JSVFileManager
 
jsDocumentBase - Static variable in class org.jmol.viewer.Viewer
 
jsEval(String) - Method in class org.jmol.viewer.Viewer
 
jsEvalSV(String) - Method in class org.jmol.viewer.Viewer
 
JSExporter - Class in org.jmol.export
A class to output WebGL graphics.
JSExporter() - Constructor for class org.jmol.export.JSExporter
 
JsFileHelper - Class in jspecview.js2d
 
JsFileHelper() - Constructor for class jspecview.js2d.JsFileHelper
 
JSFunction - Interface in javajs.api
A flag that this object is really a JavaScript function that, for example, might be called from setTimeout().
JsG2D - Class in jspecview.js2d
generic 2D drawing methods for JSpecView -- JavaScript version
JsG2D - Class in org.jmol.awtjs2d
generic 2D drawing methods -- JavaScript version
JsG2D() - Constructor for class jspecview.js2d.JsG2D
 
JsG2D() - Constructor for class org.jmol.awtjs2d.JsG2D
 
JSInterface - Interface in javajs.api
called by JSmol JavaScript methods using this._applet.xxxx()
JSJmolPopup - Class in org.jmol.awtjs2d
 
JSJmolPopup() - Constructor for class org.jmol.awtjs2d.JSJmolPopup
The main popup window for the applet -- as JavaScript
JSJSONParser - Class in javajs.util
a very simple JSON parser for JSON objects that are compatible with JavaScript A gross simplification of https://github.com/douglascrockford/JSON-java A SUBSET of JSON with similarly to window.JSON.parse(): In JavaScript returns "null" for a null value, not null -- requires quoted strings for keys and values -- does not allow /xxx/ objects
JSJSONParser() - Constructor for class javajs.util.JSJSONParser
 
JsMainPanel - Class in jspecview.js2d
 
JsMainPanel() - Constructor for class jspecview.js2d.JsMainPanel
 
JSME_RunAsyncCallback() - Constructor for class jme.JMEUtil.JSME_RunAsyncCallback
 
JSModelKitPopup - Class in org.jmol.awtjs2d
 
JSModelKitPopup() - Constructor for class org.jmol.awtjs2d.JSModelKitPopup
 
JSmolAppletObject - Interface in org.jmol.api.js
 
json - Static variable in class org.jmol.script.T
 
JSONEncodable - Interface in javajs.api
 
JSONException - Exception Class in javajs.util
 
JSONException(String) - Constructor for exception class javajs.util.JSONException
 
JsonNioClient - Interface in org.openscience.jmol.app.jsonkiosk
a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
JsonNioClient.TouchHandler - Class in org.openscience.jmol.app.jsonkiosk
 
JsonNioClientThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
 
JsonNioServer - Interface in org.openscience.jmol.app.jsonkiosk
 
JsonNioServerThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
 
JsonNioService - Class in org.openscience.jmol.app.jsonkiosk
A class for interacting with Jmol over local sockets.
JsonNioService() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
JsonNioService.JsonNioClientThread - Class in org.openscience.jmol.app.jsonkiosk
 
JsonNioService.JsonNioServerThread - Class in org.openscience.jmol.app.jsonkiosk
 
JSONReader - Class in org.jmol.adapter.readers.simple
 
JSONReader() - Constructor for class org.jmol.adapter.readers.simple.JSONReader
 
JSONWriter - Class in org.jmol.util
 
JSONWriter() - Constructor for class org.jmol.util.JSONWriter
 
JsPanel - Class in jspecview.js2d
JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
JsParameters - Class in jspecview.js2d
 
JsParameters() - Constructor for class jspecview.js2d.JsParameters
 
JSPattern(String, boolean) - Constructor for class org.jmol.util.PatternMatcher.JSPattern
 
JSpecView - Class in jspecview.application
The Main Class or Entry point of the JSpecView Application.
JSpecView - Class in org.jmol.jsv
 
JSpecView() - Constructor for class org.jmol.jsv.JSpecView
 
JSpecView(boolean, JSVInterface) - Constructor for class jspecview.application.JSpecView
 
jspecview.api - package jspecview.api
 
jspecview.api.js - package jspecview.api.js
 
jspecview.app - package jspecview.app
 
jspecview.appletjs - package jspecview.appletjs
 
jspecview.application - package jspecview.application
 
jspecview.common - package jspecview.common
 
jspecview.dialog - package jspecview.dialog
 
jspecview.exception - package jspecview.exception
 
jspecview.export - package jspecview.export
 
jspecview.java - package jspecview.java
 
jspecview.js2d - package jspecview.js2d
 
jspecview.popup - package jspecview.popup
 
jspecview.source - package jspecview.source
 
jspecview.tree - package jspecview.tree
 
JsPlatform - Class in jspecview.js2d
JavaScript 2D canvas version requires Ajax-based URL stream processing.
JsPlatform() - Constructor for class jspecview.js2d.JsPlatform
 
JSplitPane - Class in org.jmol.awtjs.swing
 
JSplitPane(int) - Constructor for class org.jmol.awtjs.swing.JSplitPane
 
JsPopup - Class in jspecview.js2d
 
JsPopup() - Constructor for class jspecview.js2d.JsPopup
 
JSPopupHelper - Class in org.jmol.awtjs2d
For menus, popup-related awt/swing class references are in this file.
JSPopupHelper(GenericPopup) - Constructor for class org.jmol.awtjs2d.JSPopupHelper
 
jsSurface(Object, T3[], T3[], int[][], int, int, int, BS, int, int, int[], int[]) - Method in class org.jmol.export.JSExporter
 
JSV - Enum constant in enum class jspecview.common.ScriptToken
 
JSV_CLOSE - Static variable in class org.jmol.viewer.JC
 
JSV_NOT - Static variable in class org.jmol.viewer.JC
 
JSV_SELECT - Static variable in class org.jmol.viewer.JC
 
JSV_SEND_C13SIMULATE - Static variable in class org.jmol.viewer.JC
 
JSV_SEND_H1SIMULATE - Static variable in class org.jmol.viewer.JC
 
JSV_SEND_JDXMOL - Static variable in class org.jmol.viewer.JC
 
JSV_SETPEAKS - Static variable in class org.jmol.viewer.JC
 
JSV_STRUCTURE - Static variable in class org.jmol.viewer.JC
 
JSVApp - Class in jspecview.app
JSpecView Applet class.
JSVApp(AppletFrame, boolean) - Constructor for class jspecview.app.JSVApp
 
JSVAppInterface - Interface in jspecview.api
 
JSVApplet - Class in jspecview.appletjs
Entry point for the web.
JSVApplet(Map<String, Object>) - Constructor for class jspecview.appletjs.JSVApplet
 
JSVAppletInterface - Interface in jspecview.api
 
JSVAppletObject - Interface in jspecview.api.js
 
JSVAppletPro - Class in jspecview.appletjs
A signed applet that has an Advanced...
JSVAppletPro(Map<String, Object>) - Constructor for class jspecview.appletjs.JSVAppletPro
 
JSVAppPro - Class in jspecview.app
 
JSVAppPro(AppletFrame, boolean) - Constructor for class jspecview.app.JSVAppPro
 
JSVDialog - Class in jspecview.dialog
 
JSVDialog() - Constructor for class jspecview.dialog.JSVDialog
 
JSVersion - Class in jspecview.common
 
JSVersion() - Constructor for class jspecview.common.JSVersion
 
JSVException - Exception Class in jspecview.exception
JSVException is the base class from which all exceptions in JSpecView is inherited.
JSVException(String) - Constructor for exception class jspecview.exception.JSVException
Constructor that takes a string specifying exception details
JSVExporter - Interface in jspecview.api
 
JSVFileDropper - Interface in jspecview.api
 
JSVFileHelper - Interface in jspecview.api
 
JSVFileManager - Class in jspecview.common
 
JSVFileManager() - Constructor for class jspecview.common.JSVFileManager
 
JSVGenericPopup - Class in jspecview.popup
 
JSVGenericPopup() - Constructor for class jspecview.popup.JSVGenericPopup
 
JSViewer - Class in jspecview.common
This class encapsulates all general functionality of applet and app.
JSViewer(ScriptInterface, boolean, boolean) - Constructor for class jspecview.common.JSViewer
 
JSVInterface - Interface in org.jmol.api
and interface for JSpecView for the Jmol application
JSVMainPanel - Interface in jspecview.api
 
jsvp - Variable in class jspecview.app.GenericMouse
 
jsvp - Variable in class jspecview.common.PanelData
 
jsvp - Variable in class jspecview.common.PanelNode
 
jsvp - Variable in class jspecview.dialog.JSVDialog
 
JSVPanel - Interface in jspecview.api
 
JSVPdfWriter - Interface in jspecview.api
 
JSVPopupResourceBundle - Class in jspecview.popup
 
JSVPopupResourceBundle() - Constructor for class jspecview.popup.JSVPopupResourceBundle
 
jsvpPopupMenu - Variable in class jspecview.common.JSViewer
 
JSVPrintDialog - Interface in jspecview.api
 
JSVToJSmolInterface - Interface in jspecview.api.js
 
JSVTree - Interface in jspecview.api
 
JSVTreeNode - Interface in jspecview.api
 
JSVTreePath - Interface in jspecview.api
 
JSVViewPanel - Interface in jspecview.api
 
JSVZipFileSequentialReader - Class in jspecview.common
Reads the entire contents of a ZIP file as though it were one straight file Skips and entry that contains '\0' Allows for a moderate amount of buffered reading via mark()
JSVZipFileSequentialReader() - Constructor for class jspecview.common.JSVZipFileSequentialReader
 
JSVZipInterface - Interface in jspecview.api
 
JSVZipReader - Interface in jspecview.api
 
JSVZipUtil - Class in jspecview.common
 
JSVZipUtil() - Constructor for class jspecview.common.JSVZipUtil
 
JTable - Class in org.jmol.awtjs.swing
 
JTable(AbstractTableModel) - Constructor for class org.jmol.awtjs.swing.JTable
 
JTextField - Class in org.jmol.awtjs.swing
 
JTextField(String) - Constructor for class org.jmol.awtjs.swing.JTextField
 
JTextPane - Class in org.jmol.awtjs.swing
A simple implementation of a Swing JTextPane.
JTextPane() - Constructor for class org.jmol.awtjs.swing.JTextPane
 
jumpBestFrame() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
JumpBestFrameAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
 
jumpToSpectrum(Spectrum) - Method in class jspecview.common.PanelData
 
jumpToSpectrumIndex(int, boolean) - Method in class jspecview.common.PanelData
 
justifymeasurements - Static variable in class org.jmol.script.T
 
Jvxl - Class in org.openscience.jvxl
 
Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
 
JVXL_VERSION - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
JVXL_VERSION_XML - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
JVXL_VERSION1 - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
jvxlAppendEncodedNumber(SB, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
JvxlCoder - Class in org.jmol.jvxl.data
 
JvxlCoder() - Constructor for class org.jmol.jvxl.data.JvxlCoder
 
jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlCompressString(String, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCreateHeader(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
Creates a two-line header for the XJVXL file.
jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlCutoffRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlData - Variable in class org.jmol.shape.MeshCollection
 
jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
JvxlData - Class in org.jmol.jvxl.data
 
JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDecodeBitSet(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlDecodeBitSetRange(String, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlDecodeContourData(JvxlData, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlDecodeVertexData(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
decode vertex data found within element as created by jvxlEncodeVertexData (see above)
jvxlDecompressString(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlEncodeBitSet(BS) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeBitSet0(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeBitSetBuffer(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeColorData(float[], float, float, int, int, boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlExcluded - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileSource - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileTitle - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFractionAsCharacter(float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionAsCharacterRange(float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetData(VoxelDataCreator, Parameters, VolumeData, String[], Lst<P3>, float[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
jvxlGetFile(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetFile(VolumeData, JvxlData, String[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetInfo(JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetInfoData(JvxlData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlParseEncodedInt(String, int, int, int[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
 
JvxlReader - Class in org.jmol.jvxl.readers
 
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
jvxlReadSurfaceInfo() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSetColorRanges(float, float, float, float, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlUpdateInfo(String[], long) - Method in class org.jmol.jvxl.data.JvxlData
 
jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlVolumeDataXml - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlVoxelBitSet - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
JvxlWrite - Class in org.openscience.jvxl.simplewriter
 
JvxlWrite() - Constructor for class org.openscience.jvxl.simplewriter.JvxlWrite
 
JvxlXmlReader - Class in org.jmol.jvxl.readers
 
JZlib - Class in com.jcraft.jzlib
 
JZlib() - Constructor for class com.jcraft.jzlib.JZlib
 
jzSetDOS(OutputStream, Deflater, int, boolean) - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
jzt - Variable in class javajs.util.CompoundDocument
 

K

ka - Variable in class org.jmol.minimize.MinAngle
 
keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
keepHydrogens - Variable in class jme.JME
 
key - Variable in class org.jmol.minimize.MinObject
 
KEY_MAX - Static variable in class javajs.util.CifDataParser
The maximum number of columns (data keys) passed to the parser or found in the file for a given loop_ or category.subkey listing.
keybuf - Variable in class org.jmol.viewer.MouseState
 
keyDown(KeyEvent, int) - Method in class jme.JME
 
KeyJCheckBox - Class in org.jmol.console
 
KeyJCheckBox(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBox
 
KeyJCheckBoxMenuItem - Class in org.jmol.console
 
KeyJCheckBoxMenuItem(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBoxMenuItem
 
KeyJMenu - Class in org.jmol.console
 
KeyJMenu(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenu
 
KeyJMenuItem - Class in org.jmol.console
 
KeyJMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenuItem
 
KeyJRadioButtonMenuItem - Class in org.jmol.console
 
KeyJRadioButtonMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJRadioButtonMenuItem
 
keyPressed(int) - Method in class jspecview.application.CommandHistory
 
keyPressed(int, int) - Method in class jspecview.common.PanelData
 
keyPressed(int, int) - Method in interface org.jmol.api.EventManager
 
keyPressed(int, int) - Method in class org.jmol.viewer.ActionManager
called by MouseManager.keyPressed
keyPressed(KeyEvent) - Method in class jme.JME
 
keyPressed(KeyEvent) - Method in class jspecview.app.GenericMouse
 
keyPressed(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
 
keyPressedEvent(int, char) - Method in class jspecview.application.MainFrame
 
keyReleased(int) - Method in class jspecview.common.PanelData
 
keyReleased(int) - Method in interface org.jmol.api.EventManager
 
keyReleased(int) - Method in class org.jmol.viewer.ActionManager
 
keyReleased(KeyEvent) - Method in class jme.JME
 
keyReleased(KeyEvent) - Method in class jspecview.app.GenericMouse
 
keyReleased(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
 
keys - Static variable in class org.jmol.script.T
 
keyTyped(int, int) - Method in class jspecview.common.PanelData
 
keyTyped(int, int) - Method in interface org.jmol.api.EventManager
 
keyTyped(int, int) - Method in class org.jmol.viewer.ActionManager
 
keyTyped(KeyEvent) - Method in class jme.JME
 
keyTyped(KeyEvent) - Method in class jspecview.app.GenericMouse
 
keyTyped(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
 
keyXy - Variable in class org.jmol.shapesurface.Isosurface
 
kioskFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
KioskFrame - Class in org.openscience.jmol.app.jsonkiosk
A borderless rectangle, like the applet, that contains the application for use in kiosk-style displays, as for example projected on the wall as in http://molecularPlayground.org
KioskFrame(int, int, int, int, JPanel) - Constructor for class org.openscience.jmol.app.jsonkiosk.KioskFrame
 
knownGroupID(String) - Static method in class org.jmol.modelsetbio.BioResolver
 

L

label - Static variable in class org.jmol.script.T
 
label - Variable in class org.jmol.shapespecial.Ellipsoid
 
LABEL - Enum constant in enum class jspecview.common.ScriptToken
 
LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
LABEL_DEFAULT_OFFSET - Static variable in class org.jmol.viewer.JC
 
LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JC
 
LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JC
 
LABEL_EXPLICIT - Static variable in class org.jmol.viewer.JC
 
LABEL_FLAGS - Static variable in class org.jmol.viewer.JC
 
LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
LABEL_OFFSET_MAX - Static variable in class org.jmol.viewer.JC
 
LABEL_POINTER_BACKGROUND - Static variable in class org.jmol.viewer.JC
 
LABEL_POINTER_NONE - Static variable in class org.jmol.viewer.JC
 
LABEL_POINTER_ON - Static variable in class org.jmol.viewer.JC
 
LABEL_ZPOS_FRONT - Static variable in class org.jmol.viewer.JC
 
LABEL_ZPOS_GROUP - Static variable in class org.jmol.viewer.JC
 
label1 - Variable in class org.jmol.console.GenericConsole
 
labelColix - Variable in class org.jmol.modelset.Measurement
 
labelColix - Variable in class org.jmol.render.LabelsRenderer
 
labelFormat - Variable in class org.jmol.shape.Hover
 
LabelNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
 
labelpointerwidth - Static variable in class org.jmol.script.T
 
labelPointerWidth - Variable in class org.jmol.viewer.GlobalSettings
 
labels - Static variable in class org.jmol.console.GenericConsole
 
labels - Variable in class org.jmol.shape.Axes
 
labels - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
 
Labels - Class in org.jmol.shape
 
Labels() - Constructor for class org.jmol.shape.Labels
 
labelSetter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
LabelSetter - Class in org.openscience.jmol.app.janocchio
 
LabelSetter(NMR_Viewer, NoeTable, CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.LabelSetter
 
LabelsRenderer - Class in org.jmol.render
 
LabelsRenderer() - Constructor for class org.jmol.render.LabelsRenderer
 
LabelToken - Class in org.jmol.modelset
 
LabelToken() - Constructor for class org.jmol.modelset.LabelToken
 
labelX - Variable in class jme.AtomDisplayLabel
 
labelY - Variable in class jme.AtomDisplayLabel
 
labToXyz(P3, P3) - Method in class javajs.img.GifEncoder
 
language - Variable in class org.jmol.i18n.Language
 
language - Static variable in class org.jmol.script.T
 
language - Variable in class org.jmol.util.GenericApplet
 
Language - Class in org.jmol.i18n
 
languagetranslation - Static variable in class org.jmol.script.T
 
last - Static variable in class org.jmol.script.T
 
LAST_AVAILABLE_COLIX - Static variable in class org.jmol.util.C
 
lastAtomIndex - Variable in class org.jmol.modelset.Group
 
lastDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
 
lastElement() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
lastFlowCommand - Variable in class org.jmol.script.ScriptCompiler
 
lastFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
 
lastIndexOf(String) - Method in class javajs.util.SB
 
lastMoData - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
lastModelIndex - Variable in class org.jmol.atomdata.AtomData
 
lastModelSet - Variable in class org.jmol.modelkit.ModelKit
 
lastMotionEventNumber - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
lastNorm - Variable in class jspecview.dialog.JSVDialog
 
lastPressTime - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
lastRepaintTime - Variable in class org.jmol.thread.JmolThread
 
lastToken - Variable in class org.jmol.script.ScriptCompiler
 
lastX - Variable in class jspecview.export.AMLExporter
 
lastX - Variable in class jspecview.export.CMLExporter
 
lastX - Variable in class jspecview.source.AnIMLReader
 
latestMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
lattice - Static variable in class org.jmol.script.T
 
lattice - Variable in class org.jmol.shape.Mesh
 
LATTICE_VECTOR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
latticeOffset - Variable in class org.jmol.render.MeshRenderer
 
latticeScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
latticeType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
launchMainFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
launchMainFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
layout - Variable in class jspecview.common.PrintLayout
The paper orientation ("portrait" or "landscape")
layoutDialog() - Method in class jspecview.dialog.JSVDialog
 
LayoutManager - Class in org.jmol.awtjs.swing
 
LayoutManager() - Constructor for class org.jmol.awtjs.swing.LayoutManager
 
layoutWindow(String) - Method in class org.jmol.console.AppletConsole
 
layoutWindow(String) - Method in class org.jmol.console.GenericConsole
 
layoutWindow(String) - Method in class org.jmol.consolejs.AppletConsole
 
layoutWindow(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
lcaocartoon - Static variable in class org.jmol.script.T
 
LcaoCartoon - Class in org.jmol.shapesurface
 
LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
 
LcaoCartoonRenderer - Class in org.jmol.rendersurface
 
LcaoCartoonRenderer() - Constructor for class org.jmol.rendersurface.LcaoCartoonRenderer
 
leadatom - Static variable in class org.jmol.script.T
 
leadAtomIndex - Variable in class org.jmol.modelset.Group
 
leadAtomIndices - Variable in class org.jmol.modelsetbio.BioPolymer
 
leadAtomIndices - Variable in class org.jmol.renderbio.BackboneRenderer
 
leadAtomIndices - Variable in class org.jmol.renderbio.CartoonRenderer
 
leadAtomIndices - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
leadAtomIndices - Variable in class org.jmol.renderbio.RibbonsRenderer
 
leadAtomIndices - Variable in class org.jmol.renderbio.RocketsRenderer
 
leadAtomIndices - Variable in class org.jmol.renderbio.StrandsRenderer
 
leadAtomIndices - Variable in class org.jmol.renderbio.TraceRenderer
 
leadMidpoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
leadPoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
left - Variable in class jspecview.common.PanelData
 
left - Static variable in class org.jmol.script.T
 
LEFT - Static variable in class org.jmol.awtjs.swing.SwingConstants
 
LEFT - Static variable in class org.jmol.viewer.binding.Binding
 
leftAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
leftbrace - Static variable in class org.jmol.script.T
 
leftDifference(Quat) - Method in class javajs.util.Quat
 
leftdivide - Static variable in class org.jmol.script.T
 
leftJustify(SB, String, String) - Static method in class javajs.util.PT
 
leftMargin - Static variable in class jspecview.common.PanelData
 
leftPanel - Variable in class jspecview.java.AwtDialog
 
leftPanel - Variable in class jspecview.js2d.JsDialog
 
leftparen - Static variable in class org.jmol.script.T
 
leftsquare - Static variable in class org.jmol.script.T
 
legacyautobonding - Static variable in class org.jmol.script.T
 
legacyhaddition - Static variable in class org.jmol.script.T
 
legacyjavafloat - Static variable in class org.jmol.script.T
 
legacyJavaFloat - Variable in class org.jmol.viewer.GlobalSettings
 
legend - Variable in class jspecview.common.PanelNode
 
len - Variable in class com.jcraft.jzlib.InflaterInputStream
 
length - Static variable in class org.jmol.script.T
 
length() - Method in class javajs.util.BS
Returns the "logical size" of this BitSet: the index of the highest set bit in the BitSet plus one.
length() - Method in class javajs.util.SB
 
length() - Method in class javajs.util.T3
Returns the length of this vector.
length() - Method in class javajs.util.V3d
Returns the length of this vector.
length() - Method in interface org.jmol.api.GenericFileInterface
 
lengthSquared() - Method in class javajs.util.T3
Returns the squared length of this vector.
lengthSquared() - Method in class javajs.util.V3d
Returns the squared length of this vector.
LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
 
LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
 
LEVEL_ERROR - Static variable in class org.jmol.util.Logger
 
LEVEL_FATAL - Static variable in class org.jmol.util.Logger
 
LEVEL_INFO - Static variable in class org.jmol.util.Logger
 
LEVEL_MAX - Static variable in class org.jmol.util.Logger
 
LEVEL_WARN - Static variable in class org.jmol.util.Logger
 
LEXICAL_COMPARATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
 
LIGHT_GRAY - Static variable in class jspecview.common.ColorParameters
 
lighting - Static variable in class org.jmol.script.T
 
lighting - Variable in class org.jmol.shape.Mesh
 
lightSource - Variable in class org.jmol.export.___Exporter
 
LIME - Static variable in class org.jmol.util.C
 
LimitedLineReader - Class in javajs.util
A simple class to read a designated number of bytes from a file and then return them line by line, skipping lines that start with #, and including the \n or \r characters at line ends.
LimitedLineReader(BufferedReader, int) - Constructor for class javajs.util.LimitedLineReader
 
line - Variable in class javajs.util.CifDataParser
from buffered reader
line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
line - Variable in class org.jmol.jvxl.readers.JvxlReader
 
line - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
line - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
line - Static variable in class org.jmol.script.T
 
LINE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
LINE_SEGMENT - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
lineCurrent - Variable in class org.jmol.script.ScriptCompiler
 
linedata - Static variable in class org.jmol.script.T
 
lineData - Variable in class org.jmol.shape.Mesh
 
lineHeight - Variable in class org.jmol.modelset.Text
 
lineIndices - Variable in class org.jmol.script.ScriptContext
 
lines - Variable in class org.jmol.modelset.Text
 
lines - Static variable in class org.jmol.script.T
 
lineto(int, int) - Method in class javajs.export.PDFCreator
 
lineTo(Object, int, int) - Method in class jspecview.common.PDFWriter
 
lineTo(Object, int, int) - Method in class jspecview.java.AwtG2D
 
lineTo(Object, int, int) - Method in class jspecview.js2d.JsG2D
 
lineTo(Object, int, int) - Method in interface org.jmol.api.GenericGraphics
 
lineTo(Object, int, int) - Method in class org.jmol.awt.AwtG2D
 
lineTo(Object, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
LINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
 
lineWidthMad - Variable in class org.jmol.export.___Exporter
 
link - Static variable in class org.jmol.script.T
 
LINK - Enum constant in enum class jspecview.common.ScriptToken
 
LINK_TYPE_AROM - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_BITS - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_DELO - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_DOUBLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_GENERIC_LINK - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
types set by filter TOPOSE_TYPES in the format of one or more of {v, vw, hb} separated by "+"; default is v+hb
LINK_TYPE_HBOND - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_OCTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_OTHER - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_PI - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_POLY - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_QUADRUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_QUINTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_SEPTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_SEXTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_SINGLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_TRIPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
LINK_TYPE_VDW - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
Opens a web page in an external browser
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
Follows the reference in an link.
linkedMesh - Variable in class org.jmol.shape.Mesh
 
linkedMesh - Variable in class org.jmol.shape.MeshCollection
 
linkSpectra(PanelData.LinkMode) - Method in class jspecview.common.PanelData
 
linkTypes - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
 
list - Variable in class org.jmol.awtjs.swing.Container
 
list - Static variable in class org.jmol.script.T
 
list(SB) - Method in class org.jmol.shapespecial.Polyhedron
 
LIST - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
listBS(BS) - Method in class org.jmol.script.ScriptEval
 
listCommands - Variable in class org.jmol.viewer.Viewer
 
ListDataReader - Class in javajs.util
VectorDataReader subclasses BufferedReader and overrides its read, readLine, mark, and reset methods so that JmolAdapter works with Vector arrays without any further adaptation.
ListDataReader() - Constructor for class javajs.util.ListDataReader
 
listf - Static variable in class org.jmol.script.T
 
listParameter(int, int, int) - Method in class org.jmol.script.ScriptParam
 
listParameter4(int, int, int, boolean) - Method in class org.jmol.script.ScriptParam
 
listSavedStates() - Method in class org.jmol.viewer.StateManager
 
ListSelectionModel - Interface in org.jmol.awtjs.swing
 
lo - Variable in class org.jmol.util.ColorEncoder
 
load - Static variable in class org.jmol.script.T
 
load(BufferedReader) - Method in class jspecview.application.DisplaySchemesProcessor
Loads the display schemes into memory and stores them in a Vector
load(InputStream) - Method in class jspecview.application.DisplaySchemesProcessor
 
load(String) - Method in class jspecview.application.DisplaySchemesProcessor
Loads the display schemes into memory and stores them in a Vector
LOAD - Enum constant in enum class jspecview.common.ScriptToken
 
LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JC
 
loadAndRun(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
loadatomdatatolerance - Static variable in class org.jmol.script.T
 
loadButton - Variable in class org.jmol.console.GenericConsole
 
loadContent(String) - Method in interface org.jmol.api.JmolDropEditor
Deprecated.
loadContent(String) - Method in class org.jmol.console.ScriptEditor
 
loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
loadData() - Method in class jspecview.dialog.JSVDialog
 
loadDefault() - Method in class jspecview.application.DisplaySchemesProcessor
Load a default DisplayScheme if xml file not found
loadDefaultShapes(ModelSet) - Method in class org.jmol.viewer.ShapeManager
 
loadDOMNode(Object) - Method in interface org.jmol.api.JmolAppletInterface
 
loadDOMNode(Object) - Method in class org.jmol.util.GenericApplet
 
loadFile(String) - Method in interface org.jmol.api.JmolDropEditor
 
loadFile(String) - Method in class org.jmol.console.ScriptEditor
 
loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
When dropped, if the data are 2D, then read directly into JME.
loadFileAsync(String, String, int, boolean) - Method in class org.jmol.script.ScriptEval
Allows asynchronous file loading from the LOAD or SCRIPT command.
loadFileAsynchronously(Object, JSAppletObject, String, Object) - Method in interface javajs.api.js.J2SObjectInterface
 
LOADFILECALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
 
loadFileResourceAsync(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
loadFileResourceAsync(String) - Method in class org.jmol.script.ScriptEval
load a static file asynchronously
loadformat - Static variable in class org.jmol.script.T
 
loadGeometries - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
loadImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
Load an image
loadImage(GenericPlatform, String, String, byte[], Object) - Method in interface org.jmol.api.js.JmolToJSmolInterface
 
loadImageData(Object, String, String, Object) - Method in class org.jmol.viewer.Viewer
NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage
loadImaginary - Variable in class jspecview.common.JSViewer
 
LOADIMAGINARY - Enum constant in enum class jspecview.common.ScriptToken
 
loadInline(String) - Method in interface jspecview.api.JSVAppletInterface
Loads in-line JCAMP-DX data into the existing applet window
loadInline(String) - Method in class jspecview.app.JSVApp
Loads in-line JCAMP-DX data into the existing applet window
loadInline(String) - Method in class jspecview.appletjs.JSVApplet
 
loadInline(String) - Method in class jspecview.application.MainFrame
 
loadInline(String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String) - Method in class org.jmol.api.JmolViewer
 
loadInline(String) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(String) - Method in class org.jmol.viewer.Viewer
from Applet and external applications only
loadInline(String[]) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String[]) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[]) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(String[]) - Method in class org.jmol.viewer.Viewer
external apps only
loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
external apps and applet only
loadInline(String[], String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String[], String) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(String, char) - Method in class org.jmol.api.JmolViewer
 
loadInline(String, char) - Method in class org.jmol.viewer.Viewer
external apps only
loadInline(String, String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String, String) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(List<Object>, boolean) - Method in class org.jmol.api.JmolViewer
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
loadInline(List<Object>, boolean) - Method in class org.jmol.viewer.Viewer
External applications only; does not preserve state -- intentionally!
loadInlineAppend(String, boolean) - Method in class org.jmol.api.JmolViewer
 
loadInlineAppend(String, boolean) - Method in class org.jmol.viewer.Viewer
used by applet and console
loadInlineArray(String[], String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
loadInlineArray(String[], String, boolean) - Method in class org.jmol.util.GenericApplet
 
loadInlineString(String, String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
loadInlineString(String, String, boolean) - Method in class org.jmol.util.GenericApplet
 
loadligandformat - Static variable in class org.jmol.script.T
 
LoadMeasureThread - Class in org.openscience.jmol.app.janocchio
 
LoadMeasureThread() - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
LoadMeasureThread(NMR_JmolPanel, String) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
LoadMeasureThreadJSON - Class in org.openscience.jmol.app.janocchio
 
LoadMeasureThreadJSON(NMR_JmolPanel, Map<String, Object>) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
loadModelFromFile(String, String, String[], Object, boolean, Map<String, Object>, SB, SB, int, String) - Method in class org.jmol.viewer.Viewer
Used by the ScriptEvaluator LOAD command to open one or more files.
loadScript - Variable in class org.jmol.modelset.Model
 
loadShape(int) - Method in class org.jmol.viewer.ShapeManager
 
loadState - Variable in class org.jmol.modelset.Model
 
LOADSTRUCT - Enum constant in enum class org.jmol.c.CBK
 
loadVibrations - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
lobe - Static variable in class org.jmol.script.T
 
Location - Class in com.sparshui.common
Represents a 2D location with float values.
Location() - Constructor for class com.sparshui.common.Location
Cosntruct a default location.
Location(float, float) - Constructor for class com.sparshui.common.Location
Construct a specific location.
LocContact - Variable in class jspecview.source.AnIMLReader
 
LOCCRC - Static variable in class javajs.api.GenericZipInputStream
 
LOCEXT - Static variable in class javajs.api.GenericZipInputStream
 
LOCFLG - Static variable in class javajs.api.GenericZipInputStream
 
LOCHDR - Static variable in class javajs.api.GenericZipInputStream
 
LOCHOW - Static variable in class javajs.api.GenericZipInputStream
 
LOCLEN - Static variable in class javajs.api.GenericZipInputStream
 
LOCNAM - Static variable in class javajs.api.GenericZipInputStream
 
LocName - Variable in class jspecview.source.AnIMLReader
 
LOCSIG - Static variable in class javajs.api.GenericZipInputStream
 
LOCSIZ - Static variable in class javajs.api.GenericZipInputStream
 
LOCTIM - Static variable in class javajs.api.GenericZipInputStream
 
LOCVER - Static variable in class javajs.api.GenericZipInputStream
 
log - Static variable in class org.jmol.script.T
 
log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
Method to output a log.
log(String) - Static method in class jme.JMEUtil.GWT
 
log(String) - Method in interface org.jmol.atomdata.AtomDataServer
 
log(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
log(String) - Method in class org.jmol.viewer.Viewer
 
logcommands - Static variable in class org.jmol.script.T
 
logCommands - Variable in class org.jmol.viewer.GlobalSettings
 
logfile - Static variable in class org.jmol.script.T
 
Logger - Class in org.jmol.util
Logger mechanism.
LoggerInterface - Interface in org.jmol.util
Interface used for the logging mechanism.
loggestures - Static variable in class org.jmol.script.T
 
logGestures - Variable in class org.jmol.viewer.GlobalSettings
 
logging - Variable in class javajs.img.ImageEncoder
 
logInfo(String) - Method in class org.jmol.symmetry.CIPChirality
 
loglevel - Static variable in class org.jmol.script.T
 
logLevel() - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
logMessages - Variable in class org.jmol.script.ScriptCompiler
 
lonepair - Static variable in class org.jmol.script.T
 
longdate - Variable in class jspecview.export.AMLExporter
 
longdate - Variable in class jspecview.export.CMLExporter
 
longDate - Variable in class jspecview.source.JDXHeader
 
LongDate - Variable in class jspecview.source.AnIMLReader
 
longToByteArray(byte[], int, long) - Static method in class com.sparshui.common.utils.Converter
 
lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptEval
 
lookupInterpolatedVoxelValue(T3, boolean) - Method in class org.jmol.jvxl.data.VolumeData
 
lookupSpecialAtomID(String) - Method in class org.jmol.modelsetbio.BioResolver
 
loop - Static variable in class org.jmol.script.T
 
LoopedStreams - Class in org.openscience.jmol.app.jmolpanel
 
LoopedStreams() - Constructor for class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
LOW - Static variable in class org.jmol.util.ColorEncoder
 
lowPrecision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
lp - Static variable in class org.jmol.script.T
 
Lst<V> - Class in javajs.util
created to remove ambiguities in add and remove
Lst() - Constructor for class javajs.util.Lst
 
lstDipoles - Variable in class org.jmol.shapespecial.Dipole
 
lstNCS - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
lumo - Static variable in class org.jmol.script.T
 

M

m - Variable in class javajs.util.Matrix
 
m - Variable in class org.jmol.util.MeshSlicer
 
m00 - Variable in class javajs.util.M34
The first element of the first row
m01 - Variable in class javajs.util.M34
The second element of the first row.
m02 - Variable in class javajs.util.M34
third element of the first row.
m03 - Variable in class javajs.util.M4
The fourth element of the first row.
m10 - Variable in class javajs.util.M34
The first element of the second row.
m11 - Variable in class javajs.util.M34
The second element of the second row.
m12 - Variable in class javajs.util.M34
The third element of the second row.
m13 - Variable in class javajs.util.M4
The fourth element of the second row.
m20 - Variable in class javajs.util.M34
The first element of the third row.
m21 - Variable in class javajs.util.M34
The second element of the third row.
m22 - Variable in class javajs.util.M34
The third element of the third row.
m23 - Variable in class javajs.util.M4
The fourth element of the third row.
M3 - Class in javajs.util
A single precision floating point 3 by 3 matrix.
M3() - Constructor for class javajs.util.M3
Constructs and initializes a Matrix3f to all zeros.
m30 - Variable in class javajs.util.M4
The first element of the fourth row.
m31 - Variable in class javajs.util.M4
The second element of the fourth row.
m32 - Variable in class javajs.util.M4
The third element of the fourth row.
m33 - Variable in class javajs.util.M4
The fourth element of the fourth row.
M34 - Class in javajs.util
A base class for both M3 and M4 to conserve code size.
M34() - Constructor for class javajs.util.M34
 
M4 - Class in javajs.util
A single precision floating point 4 by 4 matrix.
M4() - Constructor for class javajs.util.M4
all zeros
MAC_COMMAND - Static variable in class org.jmol.awtjs.Event
 
MAC_COMMAND - Static variable in class org.jmol.viewer.binding.Binding
 
macro - Static variable in class org.jmol.script.T
 
macrodirectory - Static variable in class org.jmol.script.T
 
mad - Variable in class org.jmol.modelset.Bond
 
mad - Variable in class org.jmol.modelset.Measurement
 
mad - Variable in class org.jmol.modelset.MeasurementData
 
mad - Variable in class org.jmol.render.ShapeRenderer
 
mad - Variable in class org.jmol.shape.AtomShape
 
mad - Variable in class org.jmol.shapespecial.Dipole
 
MAD_GLOBAL - Static variable in class org.jmol.modelset.Atom
 
madAtom - Variable in class org.jmol.modelset.Atom
 
madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JC
 
mads - Variable in class org.jmol.renderbio.BackboneRenderer
 
mads - Variable in class org.jmol.renderbio.CartoonRenderer
 
mads - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
mads - Variable in class org.jmol.renderbio.RibbonsRenderer
 
mads - Variable in class org.jmol.renderbio.RocketsRenderer
 
mads - Variable in class org.jmol.renderbio.StrandsRenderer
 
mads - Variable in class org.jmol.renderbio.TraceRenderer
 
mads - Variable in class org.jmol.shape.AtomShape
 
MAGENTA - Static variable in class org.jmol.util.C
 
magneticshielding - Static variable in class org.jmol.script.T
 
MagresReader - Class in org.jmol.adapter.readers.xtal
 
MagresReader() - Constructor for class org.jmol.adapter.readers.xtal.MagresReader
 
main(String[]) - Static method in class jme.JME
 
main(String[]) - Static method in class jspecview.application.JSpecView
 
main(String[]) - Static method in class jspecview.application.MainFrame
 
main(String[]) - Static method in class jspecview.source.JDXDecompressorTest
 
main(String[]) - Static method in class org.jmol.adapter.writers.CDXMLWriter
 
main(String[]) - Static method in class org.jmol.quantum.NMRNoeMatrix
 
main(String[]) - Static method in class org.jmol.symmetry.SpaceGroupFinder
 
main(String[]) - Static method in class org.molecularplayground.MPJmolApp
 
main(String[]) - Static method in class org.openscience.jmol.app.janocchio.Nmr
 
main(String[]) - Static method in class org.openscience.jmol.app.Jmol
 
main(String[]) - Static method in class org.openscience.jmol.app.JmolData
 
main(String[]) - Static method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
main(String[]) - Static method in class org.openscience.jvxl.Jvxl
 
main(String[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
MAIN - Static variable in class org.jmol.thread.JmolThread
 
mainFrame - Variable in class jspecview.application.ApplicationMenu
 
mainFrame - Variable in class jspecview.application.AppToolBar
 
MainFrame - Class in jspecview.application
The Main Class or Entry point of the JSpecView Application.
MainFrame(JSpecView, Component, JSVInterface) - Constructor for class jspecview.application.MainFrame
Constructor
mainPanel - Variable in class jspecview.common.JSViewer
 
MainPopupResourceBundle - Class in org.jmol.popup
 
MainPopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.MainPopupResourceBundle
 
mainSplitPane - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
majorVersion - Static variable in class jspecview.common.JSVersion
 
majorVersion - Static variable in class org.jmol.viewer.JC
 
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.viewer.Viewer
 
makeConnections2(float, float, int, int, BS, BS, BS, boolean, boolean, float, SB) - Method in class org.jmol.modelset.ModelSet
 
manager - Variable in class jspecview.dialog.JSVDialog
 
manager - Variable in class jspecview.java.AwtDialog
 
manager - Variable in class jspecview.js2d.JsDialog
 
manifest - Static variable in class org.jmol.script.T
 
map(Object, String, String, Map<String, Object>) - Static method in class org.jmol.console.GenericConsole
 
mapAddKey(String) - Method in class org.jmol.util.JSONWriter
 
mapAddKeyValue(String, Object, String) - Method in class org.jmol.util.JSONWriter
 
mapAddKeyValueRaw(String, Object, String) - Method in class org.jmol.util.JSONWriter
Add a key:value pair where value is already quoted
mapAddMapAllExcept(String, Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
 
mapClose() - Method in class org.jmol.util.JSONWriter
 
mapGet(String) - Method in class org.jmol.script.SV
 
mapLattice - Variable in class org.jmol.jvxl.data.JvxlData
 
mapLattice - Variable in class org.jmol.jvxl.readers.Parameters
 
mapOpen() - Method in class org.jmol.util.JSONWriter
 
mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
 
mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
 
mappingPlane - Variable in class org.jmol.jvxl.data.VolumeData
 
mapPolyhedra(int, int, boolean, M4) - Method in class org.jmol.scriptext.SmilesExt
 
mapproperty - Static variable in class org.jmol.script.T
 
mapPut(String, SV) - Method in class org.jmol.script.SV
 
mapString - Variable in class jme.AtomDisplayLabel
 
mapUnique - Variable in class org.jmol.smiles.SmilesSearch
 
marchingCubes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MarchingCubes - Class in org.jmol.jvxl.calc
 
MarchingCubes() - Constructor for class org.jmol.jvxl.calc.MarchingCubes
 
MarchingCubes(VertexDataServer, VolumeData, Parameters, BS) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
 
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MarchingSquares - Class in org.jmol.jvxl.calc
 
MarchingSquares(VertexDataServer, VolumeData, P4, float[], int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
 
mark() - Method in class jme.JMEmol
 
mark(int) - Method in class com.jcraft.jzlib.InflaterInputStream
 
mark(int) - Method in class jspecview.common.JSVZipFileSequentialReader
 
mark(long) - Method in class javajs.util.ArrayDataReader
 
mark(long) - Method in class javajs.util.ListDataReader
 
MARK - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
markLines(String, char) - Static method in class org.jmol.util.Parser
 
markSupported() - Method in class com.jcraft.jzlib.InflaterInputStream
 
markUsed - Variable in class jme.JME
 
MAROON - Static variable in class org.jmol.util.C
 
mass - Static variable in class org.jmol.script.T
 
mat4 - Variable in class org.jmol.modelset.Model
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
mat4 - Variable in class org.jmol.util.MeshSurface
 
match(String) - Method in class org.jmol.symmetry.CIPData
Return a bit set corresponding to a SMARTS
match(String) - Method in class org.jmol.symmetry.CIPDataSmiles
 
matcher(String) - Method in class org.jmol.util.PatternMatcher.JSPattern
 
matchesFilePath(String) - Method in class jspecview.source.JDXSource
 
matchesPeakTypeModel(String, String) - Method in class jspecview.common.Spectrum
Find a matching spectrum by type (IR, 1HNMR,...) and model name
mathExpressionCommand - Static variable in class org.jmol.script.T
 
MathExt - Class in org.jmol.scriptext
 
MathExt() - Constructor for class org.jmol.scriptext.MathExt
 
mathfunc - Static variable in class org.jmol.script.T
 
mathop - Static variable in class org.jmol.script.T
 
mathproperty - Static variable in class org.jmol.script.T
 
matrix - Static variable in class org.jmol.script.T
 
Matrix - Class in javajs.util
streamlined and refined for Jmol by Bob Hanson from http://math.nist.gov/javanumerics/jama/ Jama = Java Matrix class.
Matrix(double[][], int, int) - Constructor for class javajs.util.Matrix
Construct a matrix quickly without checking arguments.
matrix3f - Static variable in class org.jmol.script.T
 
matrix4f - Static variable in class org.jmol.script.T
 
matrixCartesianToFractional - Variable in class org.jmol.util.SimpleUnitCell
 
matrixCtoFNoOffset - Variable in class org.jmol.util.SimpleUnitCell
 
matrixFractionalToCartesian - Variable in class org.jmol.util.SimpleUnitCell
 
matrixFtoCNoOffset - Variable in class org.jmol.util.SimpleUnitCell
 
matrixRotate - Variable in class org.jmol.viewer.TransformManager
 
matrixStereo - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
 
matrixTest - Variable in class org.jmol.viewer.TransformManager
 
matrixToScript(Object) - Static method in class org.jmol.util.Escape
 
matrixTransform - Variable in class org.jmol.viewer.TransformManager
 
matrixTransformInv - Variable in class org.jmol.viewer.TransformManager
 
matUnitCellOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
max - Static variable in class org.jmol.script.T
 
MAX_ALPHA_SIZE - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_CODE_LEN - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
MAX_LEVEL - Static variable in class org.jmol.shapespecial.Dots
 
MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_SELECTORS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
MAX_TYPE_SUPPORTED - Static variable in class org.jmol.quantum.QS
 
MAX_WBITS - Static variable in class com.jcraft.jzlib.JZlib
 
MAXABS - Static variable in class jspecview.common.Spectrum
 
maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
 
maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
maxGrid - Variable in class org.jmol.jvxl.data.VolumeData
 
MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JC
 
MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
 
maxSerial - Variable in class org.jmol.adapter.readers.cif.CifReader
 
maxset - Static variable in class org.jmol.script.T
 
maxSphereCache - Static variable in class org.jmol.util.Shader
 
maxXOnScale - Variable in class jspecview.common.ScaleData
the maximim X value on the scale, usually maxX
maxYOnScale - Variable in class jspecview.common.ScaleData
 
maybeGetBaseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
mayScript - Variable in class org.jmol.util.GenericApplet
 
mc - Variable in class org.jmol.modelset.ModelSet
model count
MdCrdReader - Class in org.jmol.adapter.readers.more
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
MdCrdReader() - Constructor for class org.jmol.adapter.readers.more.MdCrdReader
 
MdTopReader - Class in org.jmol.adapter.readers.more
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
MdTopReader() - Constructor for class org.jmol.adapter.readers.more.MdTopReader
 
measure - Static variable in class org.jmol.script.T
 
Measure - Class in javajs.util
 
Measure - Class in org.openscience.jmol.app.janocchio
 
Measure() - Constructor for class javajs.util.Measure
 
MEASURE - Enum constant in enum class org.jmol.c.CBK
 
MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
measureallmodels - Static variable in class org.jmol.script.T
 
MeasureCouple - Class in org.openscience.jmol.app.janocchio
 
MeasureCouple(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureCouple
 
MeasureDist - Class in org.openscience.jmol.app.janocchio
Calculates the difference between calculated and experimental values for coloring table
MeasureDist(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureDist
 
measureDistanceUnits - Variable in class org.jmol.viewer.GlobalSettings
 
Measurement - Class in jspecview.common
The Measurement class stores an annotation that is a measurement
Measurement - Class in org.jmol.modelset
 
Measurement() - Constructor for class jspecview.common.Measurement
 
Measurement() - Constructor for class org.jmol.modelset.Measurement
 
measurementCount - Variable in class org.jmol.shape.Measures
 
MeasurementData - Class in jspecview.common
 
MeasurementData - Class in org.jmol.modelset
 
MeasurementData() - Constructor for class org.jmol.modelset.MeasurementData
 
measurementlabels - Static variable in class org.jmol.script.T
 
measurementnumbers - Static variable in class org.jmol.script.T
 
MeasurementPending - Class in org.jmol.modelset
 
MeasurementPending() - Constructor for class org.jmol.modelset.MeasurementPending
 
measurements - Static variable in class org.jmol.script.T
 
measurements - Variable in class org.jmol.shape.Measures
 
Measurements - Enum constant in enum class jspecview.common.Annotation.AType
 
measurementsAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
MeasurementsDialog - Class in jspecview.dialog
Dialog for managing the measurement list for a Spectrum within a GraphSet
MeasurementsDialog() - Constructor for class jspecview.dialog.MeasurementsDialog
 
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
MeasurementTable - Class in org.openscience.jmol.app.jmolpanel
 
MeasurementTable(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable
Constructor
measurementunits - Static variable in class org.jmol.script.T
 
MeasureNoe - Class in org.openscience.jmol.app.janocchio
 
MeasureNoe(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureNoe
 
Measures - Class in org.jmol.shape
 
Measures() - Constructor for class org.jmol.shape.Measures
 
MeasuresRenderer - Class in org.jmol.render
 
MeasuresRenderer() - Constructor for class org.jmol.render.MeasuresRenderer
 
menu - Static variable in class org.jmol.script.T
 
menuAddButtonGroup(SC) - Method in class org.jmol.awt.AwtPopupHelper
 
menuAddButtonGroup(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
menuAddButtonGroup(SC) - Method in interface org.jmol.popup.PopupHelper
 
menuAddSeparator(SC) - Method in class org.jmol.popup.GenericPopup
 
menuAddSubMenu(SC, SC) - Method in class org.jmol.popup.GenericPopup
 
menuCheckBoxCallback(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
menuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
 
menuClearListeners(SC) - Method in class org.jmol.awt.AwtPopupHelper
 
menuClearListeners(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
menuClearListeners(SC) - Method in interface org.jmol.popup.PopupHelper
 
menuClickCallback(SC, String) - Method in class org.jmol.modelkit.ModelKitPopup
 
menuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
 
menuCreateCheckboxItem(SC, String, String, String, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
 
menuCreateItem(SC, String, String, String) - Method in class org.jmol.popup.GenericPopup
 
menuCreatePopup(String, Object) - Method in class org.jmol.awt.AwtPopupHelper
 
menuCreatePopup(String, Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
menuCreatePopup(String, Object) - Method in interface org.jmol.popup.PopupHelper
 
menuEnable(SC, boolean) - Method in class org.jmol.popup.GenericPopup
 
menuEnabled() - Method in class org.jmol.viewer.Viewer
 
menuFocusCallback(String, String, boolean) - Method in class jspecview.java.AwtPopup
 
menuFocusCallback(String, String, boolean) - Method in class jspecview.js2d.JsPopup
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.popup.GenericPopup
 
menuGetId(SC) - Method in class org.jmol.popup.GenericPopup
 
menuGetListPosition(SC) - Method in class org.jmol.popup.GenericPopup
 
menuHidePopup(SC) - Method in class org.jmol.awt.AwtModelKitPopup
 
menuHidePopup(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
menuHidePopup(SC) - Method in class org.jmol.modelkit.ModelKitPopup
 
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awt.AwtPopupHelper
 
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
menuInsertSubMenu(SC, SC, int) - Method in interface org.jmol.popup.PopupHelper
 
menuItems - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
menuMap - Variable in class org.jmol.console.GenericConsole
 
menuName - Variable in class org.jmol.popup.GenericPopup
 
menuNewSubMenu(String, String) - Method in class org.jmol.popup.GenericPopup
 
MENUON - Enum constant in enum class jspecview.common.ScriptToken
 
menuRemoveAll(SC, int) - Method in class org.jmol.popup.GenericPopup
 
menuSetAutoscrolls(SC) - Method in class org.jmol.popup.GenericPopup
 
menuSetLabel(SC, String) - Method in class org.jmol.popup.GenericPopup
 
menuShowPopup(SC, int, int) - Method in class jspecview.java.AwtPopup
 
menuShowPopup(SC, int, int) - Method in class jspecview.js2d.JsPopup
could be frank menu or regular context menu
menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtJmolPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtModelKitPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSJmolPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.popup.GenericPopup
 
menuStructure - Variable in class org.jmol.api.JmolViewer
 
menuText - Variable in class org.jmol.popup.JmolGenericPopup
 
mep - Static variable in class org.jmol.script.T
 
mep_calcType - Variable in class org.jmol.jvxl.readers.Parameters
 
MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
MepCalculation - Class in org.jmol.quantum
 
MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
 
merge(MeshData) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
merge(MeshCollection) - Method in class org.jmol.shape.MeshCollection
called by ParallelProcessor at completion
merge(MeshCollection) - Method in class org.jmol.shapesurface.LcaoCartoon
 
merge(MeshCollection) - Method in class org.jmol.shapesurface.MolecularOrbital
 
mergeAtomArrays(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
 
mergeBufferPixel(int, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
mergeModelArrays(ModelSet) - Method in class org.jmol.modelset.ModelSet
initial transfer of model data from old to new model set.
mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
 
mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
 
merging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
mesh - Variable in class org.jmol.render.MeshRenderer
 
mesh - Static variable in class org.jmol.script.T
 
Mesh - Class in org.jmol.shape
 
Mesh() - Constructor for class org.jmol.shape.Mesh
always use Mesh().mesh1(thisID, colix, index)
mesh1(Viewer, String, short, int) - Method in class org.jmol.shape.Mesh
 
MeshCapper - Class in org.jmol.util
A class to properly cap a convoluted, closed slice of an isosurface inspired by: Computational Geometry: Algorithms and Applications Mark de Berg, Marc van Kreveld, Mark Overmars, and Otfried Schwarzkopf Springer-Verlag, Berlin Heidelberg 1997 Chapter 3.
MeshCapper() - Constructor for class org.jmol.util.MeshCapper
 
MeshCapper.MeshCapperSorter - Class in org.jmol.util
 
MeshCapperSorter() - Constructor for class org.jmol.util.MeshCapper.MeshCapperSorter
 
meshColix - Variable in class org.jmol.shape.Mesh
 
MeshCollection - Class in org.jmol.shape
 
MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
 
meshColor - Variable in class org.jmol.jvxl.data.JvxlData
 
meshCount - Variable in class org.jmol.shape.MeshCollection
 
meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MeshData - Class in org.jmol.jvxl.data
 
MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
 
MeshData.SortSet - Class in org.jmol.jvxl.data
 
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MeshDataServer - Interface in org.jmol.jvxl.api
 
meshes - Variable in class org.jmol.shape.MeshCollection
 
meshes - Variable in class org.jmol.shapebio.BioShape
 
meshReady - Variable in class org.jmol.shapebio.BioShape
 
MeshRenderer - Class in org.jmol.render
an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
MeshRenderer() - Constructor for class org.jmol.render.MeshRenderer
 
meshRibbon - Static variable in class org.jmol.script.T
 
MeshRibbon - Class in org.jmol.shapebio
 
MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
 
MeshRibbonRenderer - Class in org.jmol.renderbio
 
MeshRibbonRenderer() - Constructor for class org.jmol.renderbio.MeshRibbonRenderer
 
meshscale - Static variable in class org.jmol.script.T
 
meshSlabValue - Variable in class org.jmol.render.MeshRenderer
 
MeshSlicer - Class in org.jmol.util
 
MeshSlicer() - Constructor for class org.jmol.util.MeshSlicer
 
MeshSurface - Class in org.jmol.util
 
MeshSurface() - Constructor for class org.jmol.util.MeshSurface
 
meshType - Variable in class org.jmol.util.MeshSurface
 
message - Static variable in class org.jmol.script.T
 
MESSAGE - Enum constant in enum class org.jmol.c.CBK
 
MessagePackReader - Class in javajs.util
A simple MessagePack reader.
MessagePackReader() - Constructor for class javajs.util.MessagePackReader
 
MessagePackReader(GenericBinaryDocumentReader, boolean) - Constructor for class javajs.util.MessagePackReader
 
messageQueue - Variable in class org.jmol.viewer.StatusManager
 
messagestylechime - Static variable in class org.jmol.script.T
 
MessageType() - Constructor for class com.sparshui.common.ClientProtocol.MessageType
 
META_MASK - Static variable in class org.jmol.awtjs.Event
 
mf - Variable in class org.jmol.util.JmolMolecule
 
mi - Variable in class org.jmol.util.Point3fi
model index -- may be to a trajectory
middle - Static variable in class org.jmol.script.T
 
MIDDLE - Static variable in class org.jmol.viewer.binding.Binding
 
min - Static variable in class org.jmol.script.T
 
MIN - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
MIN_ADDH - Static variable in class org.jmol.viewer.Viewer
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
MIN_GROUP_SELECT - Static variable in class org.jmol.viewer.Viewer
 
MIN_HAVE_FIXED - Static variable in class org.jmol.viewer.Viewer
 
MIN_MODELKIT - Static variable in class org.jmol.viewer.Viewer
 
MIN_QUICK - Static variable in class org.jmol.viewer.Viewer
 
MIN_SELECT_ONLY - Static variable in class org.jmol.viewer.Viewer
 
MIN_SELECTED - Static variable in class org.jmol.viewer.Viewer
 
MIN_SILENT - Static variable in class org.jmol.viewer.Viewer
 
MIN_XX - Static variable in class org.jmol.viewer.Viewer
 
MinAngle - Class in org.jmol.minimize
 
minAngles - Variable in class org.jmol.minimize.Minimizer
 
MinAtom - Class in org.jmol.minimize
 
minAtoms - Variable in class org.jmol.minimize.Minimizer
 
MinBond - Class in org.jmol.minimize
 
minbonddistance - Static variable in class org.jmol.script.T
 
minBonds - Variable in class org.jmol.minimize.Minimizer
 
minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
minGrid - Variable in class org.jmol.jvxl.data.VolumeData
 
minHeight - Variable in class org.jmol.awtjs.swing.Component
 
MINIMIZATION - Enum constant in enum class org.jmol.c.CBK
 
minimizationcriterion - Static variable in class org.jmol.script.T
 
minimizationmaxatoms - Static variable in class org.jmol.script.T
 
minimizationOn() - Method in class org.jmol.minimize.Minimizer
 
minimizationrefresh - Static variable in class org.jmol.script.T
 
minimizationreportsteps - Static variable in class org.jmol.script.T
 
minimizationsilent - Static variable in class org.jmol.script.T
 
minimizationsteps - Static variable in class org.jmol.script.T
 
MinimizationThread - Class in org.jmol.minimize
 
MinimizationThread() - Constructor for class org.jmol.minimize.MinimizationThread
 
minimize - Static variable in class org.jmol.script.T
 
minimize(int, double, BS, BS, BS, int, String) - Method in class org.jmol.minimize.Minimizer
 
minimize(JmolScriptEvaluator, int, float, BS, BS, BS, float, int) - Method in class org.jmol.viewer.Viewer
From the MINIMIZE command and other sources.
MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JC
 
minimizeEnd(BS, boolean) - Method in class org.jmol.modelkit.ModelKit
 
Minimizer - Class in org.jmol.minimize
 
Minimizer() - Constructor for class org.jmol.minimize.Minimizer
 
MININUM_GESTURE_DELAY_MILLISECONDS - Static variable in class org.jmol.viewer.ActionManager
 
minList - Variable in class org.jmol.minimize.MMConstraint
 
minMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
minmaxmask - Static variable in class org.jmol.script.T
 
MinObject - Class in org.jmol.minimize
 
MinObject() - Constructor for class org.jmol.minimize.MinObject
 
minpixelselradius - Static variable in class org.jmol.script.T
 
MinPosition - Class in org.jmol.minimize
not implemented -- would be a force toward a given position in space
minScreenDimension - Variable in class org.jmol.export._PovrayExporter
 
minScreenDimension - Variable in class org.jmol.export._TachyonExporter
 
minset - Static variable in class org.jmol.script.T
 
MinTorsion - Class in org.jmol.minimize
 
minTorsions - Variable in class org.jmol.minimize.Minimizer
 
minus - Static variable in class org.jmol.script.T
 
minusMinus - Static variable in class org.jmol.script.T
 
minWidth - Variable in class org.jmol.awtjs.swing.Component
 
minXOnScale - Variable in class jspecview.common.ScaleData
the minimum X value on the scale, usually minX
minYOnScale - Variable in class jspecview.common.ScaleData
 
misc - Static variable in class org.jmol.script.T
 
mlp - Static variable in class org.jmol.script.T
 
MlpCalculation - Class in org.jmol.quantum
 
MlpCalculation() - Constructor for class org.jmol.quantum.MlpCalculation
 
mm - Variable in class org.jmol.viewer.Viewer
 
MMCifReader - Class in org.jmol.adapter.readers.cif
mmCIF files are recognized prior to class creation.
MMCifReader() - Constructor for class org.jmol.adapter.readers.cif.MMCifReader
 
MMCifValidationParser - Class in org.jmol.adapter.readers.cif
 
MMCifValidationParser() - Constructor for class org.jmol.adapter.readers.cif.MMCifValidationParser
 
MMConstraint - Class in org.jmol.minimize
 
MMConstraint(int[], double) - Constructor for class org.jmol.minimize.MMConstraint
 
MMTFReader - Class in org.jmol.adapter.readers.cif
JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md Note added 2024.01.19 Jose Duarte 2:03 PM (email) to MMTF-Users From July 2024 the PDB file archive will not be offered in the compressed MMTF format anymore.
MMTFReader() - Constructor for class org.jmol.adapter.readers.cif.MMTFReader
 
mo - Static variable in class org.jmol.script.T
 
MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
MOCalculation - Class in org.jmol.quantum
 
MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
 
moData - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
moData - Variable in class org.jmol.jvxl.readers.Parameters
 
modAverage - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modAxes - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modDim - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modDim - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
modDim - Variable in class org.jmol.util.Vibration
modDim will be > 0 for modulation
mode - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
mode - Variable in class org.jmol.render.LabelsRenderer
 
mode - Static variable in class org.jmol.script.T
 
mode - Variable in class org.jmol.viewer.TransformManager
 
MODE_CALC_2JHH - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CALC_3JCH - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CALC_3JHH - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CALC_ALL - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CALC_INVALID - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CALC_J - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CALC_JHH - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CALC_NOE - Static variable in class org.jmol.quantum.NMRCalculation
 
MODE_CUBE - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MODEL - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MOLECULES - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MULTIMODEL - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_RADII - Static variable in class org.jmol.atomdata.AtomData
 
MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_JVXL - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
MODE_NAVIGATION - Static variable in class org.jmol.viewer.TransformManager
 
MODE_P_ALLOW_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
 
MODE_P_CONVERT_TO_CARTESIAN - Static variable in class org.jmol.script.ScriptParam
 
MODE_P_IMPLICIT_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
 
MODE_P_INT_ONLY - Static variable in class org.jmol.script.ScriptParam
 
MODE_P_NULL_ON_ERROR - Static variable in class org.jmol.script.ScriptParam
 
MODE_P3 - Static variable in class org.jmol.script.ScriptParam
 
MODE_P34 - Static variable in class org.jmol.script.ScriptParam
 
MODE_P4 - Static variable in class org.jmol.script.ScriptParam
 
MODE_PERSPECTIVE_PYMOL - Static variable in class org.jmol.viewer.TransformManager
 
MODE_PLANES - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_PUT_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_STANDARD - Static variable in class org.jmol.viewer.TransformManager
 
model - Variable in class jspecview.export.AMLExporter
 
model - Variable in class jspecview.export.CMLExporter
 
model - Variable in class org.jmol.modelset.Chain
 
model - Variable in class org.jmol.modelsetbio.BioPolymer
 
model - Static variable in class org.jmol.script.T
 
model(int, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
Model - Class in org.jmol.modelset
 
Model() - Constructor for class org.jmol.modelset.Model
 
modelAdapter - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
modelAtomCount - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
 
modelbased - Static variable in class org.jmol.script.T
 
modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
 
modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelSet
 
modelFileNumbers - Variable in class org.jmol.modelset.ModelSet
 
modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
 
modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
 
modelindex - Static variable in class org.jmol.script.T
 
modelIndex - Variable in class org.jmol.atomdata.AtomData
 
modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
modelIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
modelIndex - Variable in class org.jmol.modelset.Model
 
modelIndex - Variable in class org.jmol.modelset.Text
 
modelIndex - Variable in class org.jmol.popup.JmolPopup
 
modelIndex - Variable in class org.jmol.shape.Mesh
 
modelIndex - Variable in class org.jmol.shape.MeshCollection
 
modelIndex - Variable in class org.jmol.shapebio.BioShape
 
modelIndex - Variable in class org.jmol.shapespecial.Polyhedron
 
modelIndex - Variable in class org.jmol.util.JmolMolecule
 
modelIndex - Variable in class org.jmol.util.Tensor
 
modelIndex(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
modelInfo - Variable in class org.jmol.popup.JmolPopup
 
modelInvRotation - Variable in class org.jmol.jvxl.readers.Parameters
 
modelIsRawPDB() - Method in class org.jmol.modelset.Atom
 
modelIsRawPDB() - Method in class org.jmol.smiles.SmilesAtom
 
modelIsRawPDB() - Method in interface org.jmol.util.Node
 
ModelKit - Class in org.jmol.modelkit
An abstract popup class that is instantiated for a given platform and context as one of:
ModelKit() - Constructor for class org.jmol.modelkit.ModelKit
 
MODELKIT - Enum constant in enum class org.jmol.c.CBK
 
MODELKIT_ADDCONSTRAINT - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ADDHYDROGEN - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ADDHYDROGENS - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ALLOPERATORS - Static variable in class org.jmol.viewer.JC
 
MODELKIT_APPLYFULL - Static variable in class org.jmol.viewer.JC
 
MODELKIT_APPLYLOCAL - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ASSIGN_BOND - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ATOMPICKINGMODE - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ATOMTYPE - Static variable in class org.jmol.viewer.JC
 
MODELKIT_AUTOBOND - Static variable in class org.jmol.viewer.JC
 
MODELKIT_BONDINDEX - Static variable in class org.jmol.viewer.JC
 
MODELKIT_BONDPICKINGMODE - Static variable in class org.jmol.viewer.JC
 
MODELKIT_BONDTYPE - Static variable in class org.jmol.viewer.JC
 
MODELKIT_BRANCH_ATOM_DRAGGED - Static variable in class org.jmol.viewer.JC
 
MODELKIT_BRANCH_ATOM_PICKED - Static variable in class org.jmol.viewer.JC
 
MODELKIT_CENTER - Static variable in class org.jmol.viewer.JC
 
MODELKIT_CLICKTOSETELEMENT - Static variable in class org.jmol.viewer.JC
 
MODELKIT_CONSTRAINT - Static variable in class org.jmol.viewer.JC
 
MODELKIT_DATA - Static variable in class org.jmol.viewer.JC
 
MODELKIT_DELETE_BOND - Static variable in class org.jmol.viewer.JC
 
MODELKIT_DISTANCE - Static variable in class org.jmol.viewer.JC
 
MODELKIT_DRAGATOM - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ELEMENT_KEY - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ELEMENT_KEY_ID - Static variable in class org.jmol.viewer.JC
 
MODELKIT_EXISTS - Static variable in class org.jmol.viewer.JC
 
MODELKIT_FRAME_RESIZED - Static variable in class org.jmol.viewer.JC
 
MODELKIT_HIDDEN - Static variable in class org.jmol.viewer.JC
 
MODELKIT_HIDEMENU - Static variable in class org.jmol.viewer.JC
 
MODELKIT_HIGHLIGHT - Static variable in class org.jmol.viewer.JC
 
MODELKIT_HOVERLABEL - Static variable in class org.jmol.viewer.JC
 
MODELKIT_INITIALIZE_MODEL - Static variable in class org.jmol.viewer.JC
 
MODELKIT_INVARIANT - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ISMOLECULAR - Static variable in class org.jmol.viewer.JC
 
MODELKIT_KEY - Static variable in class org.jmol.viewer.JC
 
MODELKIT_MINIMIZING - Static variable in class org.jmol.viewer.JC
 
MODELKIT_MODE - Static variable in class org.jmol.viewer.JC
 
MODELKIT_NEW_MODEL_ATOM_KEYS - Static variable in class org.jmol.viewer.JC
 
MODELKIT_OFFSET - Static variable in class org.jmol.viewer.JC
 
MODELKIT_REMOVEALLCONSTRAINTS - Static variable in class org.jmol.viewer.JC
 
MODELKIT_REMOVECONSTRAINT - Static variable in class org.jmol.viewer.JC
 
MODELKIT_RESET - Static variable in class org.jmol.viewer.JC
 
MODELKIT_RETAINLOCAL - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ROTATE_BOND_ATOM_INDEX - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ROTATEBONDINDEX - Static variable in class org.jmol.viewer.JC
 
MODELKIT_SCREENXY - Static variable in class org.jmol.viewer.JC
 
MODELKIT_SET_ELEMENT_KEY - Static variable in class org.jmol.viewer.JC
 
MODELKIT_SHOWSYMOPINFO - Static variable in class org.jmol.viewer.JC
 
MODELKIT_SYMMETRY - Static variable in class org.jmol.viewer.JC
 
MODELKIT_SYMOP - Static variable in class org.jmol.viewer.JC
 
MODELKIT_UDPATE_KEY_STATE - Static variable in class org.jmol.viewer.JC
 
MODELKIT_UNITCELL - Static variable in class org.jmol.viewer.JC
 
MODELKIT_UPDATE_ATOM_KEYS - Static variable in class org.jmol.viewer.JC
 
MODELKIT_UPDATE_MODEL_KEYS - Static variable in class org.jmol.viewer.JC
 
MODELKIT_VIBRATION - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JC
 
modelkitmode - Static variable in class org.jmol.script.T
 
ModelKitPopup - Class in org.jmol.modelkit
An abstract popup class that is instantiated for a given platform and context as one of:
ModelKitPopup() - Constructor for class org.jmol.modelkit.ModelKitPopup
 
ModelKitPopupResourceBundle - Class in org.jmol.modelkit
 
ModelKitPopupResourceBundle(String, Properties) - Constructor for class org.jmol.modelkit.ModelKitPopupResourceBundle
 
ModelLoader - Class in org.jmol.modelset
 
ModelLoader(Viewer, String, SB, Object, ModelSet, BS) - Constructor for class org.jmol.modelset.ModelLoader
 
modelMap - Variable in class org.jmol.adapter.readers.cif.CifReader
 
modelName - Variable in class org.jmol.atomdata.AtomData
 
modelNames - Variable in class org.jmol.modelset.ModelSet
 
modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
modelNumberParameter(int) - Method in class org.jmol.script.ScriptParam
 
modelNumbers - Variable in class org.jmol.modelset.ModelSet
 
modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelSet
 
modelRadius - Variable in class org.jmol.viewer.TransformManager
 
modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
 
ModelSet - Class in org.jmol.modelset
 
ModelSet(Viewer, String) - Constructor for class org.jmol.modelset.ModelSet
 
modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
 
modelSetName - Variable in class org.jmol.modelset.ModelSet
 
modelSetProperties - Variable in class org.jmol.modelset.ModelSet
 
modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
 
modelStartEnd - Variable in class org.jmol.adapter.smarter.Structure
 
modelType - Variable in class jspecview.source.AnIMLReader
 
modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
 
modeMultipleBond - Variable in class org.jmol.viewer.GlobalSettings
 
modifiersWhenPressed10 - Variable in class jspecview.app.GenericMouse
 
modify - Static variable in class org.jmol.script.T
 
MODIFY_ASSIGN_ATOM - Static variable in class org.jmol.viewer.Viewer
 
MODIFY_ASSIGN_BOND - Static variable in class org.jmol.viewer.Viewer
 
MODIFY_DELETE_ATOM - Static variable in class org.jmol.viewer.Viewer
 
MODIFY_DELETE_ATOMS - Static variable in class org.jmol.viewer.Viewer
 
MODIFY_DELETE_BONDS - Static variable in class org.jmol.viewer.Viewer
 
MODIFY_DELETE_MODEL - Static variable in class org.jmol.viewer.Viewer
 
MODIFY_SET_COORD - Static variable in class org.jmol.viewer.Viewer
 
modifyorcreate - Static variable in class org.jmol.script.T
 
modo - Static variable in class org.jmol.script.T
 
modScale - Variable in class org.jmol.util.Vibration
 
modt1 - Static variable in class org.jmol.script.T
 
modt2 - Static variable in class org.jmol.script.T
 
modt3 - Static variable in class org.jmol.script.T
 
modulateoccupancy - Static variable in class org.jmol.script.T
 
modulation - Static variable in class org.jmol.script.T
 
Modulation - Class in org.jmol.util
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
Modulation(char, char, double[], String, double[]) - Constructor for class org.jmol.util.Modulation
Each atomic modulation involves a fractional coordinate wave vector q, a Fourier power n, a modulation axis (x, y, or, z), and specified parameters that depend upon the type of function.
modulationscale - Static variable in class org.jmol.script.T
 
modulationScale - Variable in class org.jmol.viewer.GlobalSettings
 
ModulationSet - Class in org.jmol.util
A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy
ModulationSet() - Constructor for class org.jmol.util.ModulationSet
 
MODULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
modx - Static variable in class org.jmol.script.T
 
modxyz - Static variable in class org.jmol.script.T
 
mody - Static variable in class org.jmol.script.T
 
modz - Static variable in class org.jmol.script.T
 
MOEnergySorter() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
 
MOInfo() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
mol - Variable in class jme.JME
 
Mol2Reader - Class in org.jmol.adapter.readers.more
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
 
Mol3DReader - Class in org.jmol.adapter.readers.molxyz
3D only
Mol3DReader() - Constructor for class org.jmol.adapter.readers.molxyz.Mol3DReader
 
MoldenReader - Class in org.jmol.adapter.readers.quantum
A molecular structure and orbital reader for MolDen files.
MoldenReader() - Constructor for class org.jmol.adapter.readers.quantum.MoldenReader
 
molecular - Static variable in class org.jmol.script.T
 
MolecularOrbital - Class in org.jmol.shapesurface
 
MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
 
MolecularOrbitalRenderer - Class in org.jmol.rendersurface
 
MolecularOrbitalRenderer() - Constructor for class org.jmol.rendersurface.MolecularOrbitalRenderer
 
molecule - Static variable in class org.jmol.script.T
 
MOLECULE - Enum constant in enum class org.jmol.c.PAL
 
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_STEREO - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_FORMULA - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
moleculeCount - Variable in class org.jmol.modelset.BondCollection
 
moleculeCount - Variable in class org.jmol.modelset.Model
 
moleculeID - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
moleculeIndex - Variable in class org.jmol.util.JmolMolecule
 
molecules - Variable in class org.jmol.modelset.BondCollection
 
moleculeXml - Variable in class org.jmol.jvxl.data.JvxlData
 
molFile() - Method in class jme.JME
 
molform - Variable in class jspecview.export.AMLExporter
 
molform - Variable in class jspecview.export.CMLExporter
 
molForm - Variable in class jspecview.source.AnIMLReader
 
MolReader - Class in org.jmol.adapter.readers.molxyz
A reader for MDLI mol and sdf files.
MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
 
mols - Variable in class jme.JME
 
MOLWriter - Class in org.jmol.adapter.writers
 
MOLWriter() - Constructor for class org.jmol.adapter.writers.MOLWriter
 
monitorenergy - Static variable in class org.jmol.script.T
 
monomer - Static variable in class org.jmol.script.T
 
Monomer - Class in org.jmol.modelsetbio
A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
Monomer() - Constructor for class org.jmol.modelsetbio.Monomer
 
MONOMER - Enum constant in enum class org.jmol.c.PAL
 
monomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
 
monomerCount - Variable in class org.jmol.renderbio.BackboneRenderer
 
monomerCount - Variable in class org.jmol.renderbio.CartoonRenderer
 
monomerCount - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
monomerCount - Variable in class org.jmol.renderbio.RibbonsRenderer
 
monomerCount - Variable in class org.jmol.renderbio.RocketsRenderer
 
monomerCount - Variable in class org.jmol.renderbio.StrandsRenderer
 
monomerCount - Variable in class org.jmol.renderbio.TraceRenderer
 
monomerCount - Variable in class org.jmol.shape.AtomShape
 
monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomers - Variable in class org.jmol.modelsetbio.BioPolymer
 
monomers - Variable in class org.jmol.renderbio.BackboneRenderer
 
monomers - Variable in class org.jmol.renderbio.CartoonRenderer
 
monomers - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
monomers - Variable in class org.jmol.renderbio.RibbonsRenderer
 
monomers - Variable in class org.jmol.renderbio.RocketsRenderer
 
monomers - Variable in class org.jmol.renderbio.StrandsRenderer
 
monomers - Variable in class org.jmol.renderbio.TraceRenderer
 
monomers - Variable in class org.jmol.shapebio.BioShape
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
 
MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
MopacArchiveReader - Class in org.jmol.adapter.readers.simple
Mopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cell
MopacArchiveReader() - Constructor for class org.jmol.adapter.readers.simple.MopacArchiveReader
 
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.CsfReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
mopacBasis - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
GAMESS may need AM1, PMn, or RM1 zeta/coef data
MopacGraphfReader - Class in org.jmol.adapter.readers.quantum
Reads Mopac 2007 GRAPHF output files
MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
MopacReader - Class in org.jmol.adapter.readers.simple
Reads Mopac 93, 6, 7, 2002, or 2009 output files
MopacReader() - Constructor for class org.jmol.adapter.readers.simple.MopacReader
 
MOReader - Class in org.jmol.adapter.readers.quantum
General methods for reading molecular orbital data, including embedded output from the NBO program.
MOReader() - Constructor for class org.jmol.adapter.readers.quantum.MOReader
 
moreLabels(Map<String, String>) - Method in class org.openscience.jmol.app.janocchio.NmrGuiMap
See NMR_JmolPanel where "NMR." is processed, and ./Properties/Nmr.properties where they are defined
moreLabels(Map<String, String>) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
Add more labels if desired
morph - Static variable in class org.jmol.script.T
 
morph(float) - Method in class org.jmol.viewer.AnimationManager
 
morphTrajectories(int, int, float) - Method in class org.jmol.modelset.ModelSet
 
moSymmetry - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
motionDisabled - Variable in class org.molecularplayground.MPJmolApp
 
moTypes - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
mouse - Static variable in class org.jmol.script.T
 
Mouse - Class in org.jmol.awtjs2d
JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
Mouse(double, Viewer, Object) - Constructor for class org.jmol.awtjs2d.Mouse
 
MOUSE_DOWN - Static variable in class org.jmol.awtjs.Event
 
MOUSE_DRAG - Static variable in class org.jmol.awtjs.Event
 
MOUSE_ENTER - Static variable in class org.jmol.awtjs.Event
 
MOUSE_EXIT - Static variable in class org.jmol.awtjs.Event
 
MOUSE_LEFT - Static variable in class org.jmol.awtjs.Event
 
MOUSE_MIDDLE - Static variable in class org.jmol.awtjs.Event
 
MOUSE_MOVE - Static variable in class org.jmol.awtjs.Event
 
MOUSE_NONE - Static variable in class org.jmol.viewer.JC
 
MOUSE_RIGHT - Static variable in class org.jmol.awtjs.Event
 
MOUSE_UP - Static variable in class org.jmol.awtjs.Event
 
MOUSE_WHEEL - Static variable in class org.jmol.awtjs.Event
 
mouseAction(int, long, int, int, int, int) - Method in class jspecview.common.PanelData
 
mouseAction(int, long, int, int, int, int) - Method in interface org.jmol.api.EventManager
 
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.multitouch.ActionManagerMT
 
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.viewer.ActionManager
 
mouseClicked(MouseEvent) - Method in class jme.JME
 
mouseClicked(MouseEvent) - Method in class jspecview.app.GenericMouse
 
mouseClicked(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
 
mouseClicked(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseDown(MouseEvent, int, int) - Method in class jme.JME
 
mouseDrag(MouseEvent, int, int) - Method in class jme.JME
 
mousedragfactor - Static variable in class org.jmol.script.T
 
mouseDragFactor - Variable in class org.jmol.viewer.ActionManager
 
mouseDragged(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
mouseDragged(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mouseDragged(MouseEvent) - Method in class jme.JME
 
mouseDragged(MouseEvent) - Method in class jspecview.app.GenericMouse
 
mouseDragged(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseEntered(MouseEvent) - Method in class jme.JME
 
mouseEntered(MouseEvent) - Method in class jspecview.app.GenericMouse
 
mouseEntered(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
 
mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseEnterExit(long, int, int, boolean) - Method in class jspecview.common.PanelData
 
mouseEnterExit(long, int, int, boolean) - Method in interface org.jmol.api.EventManager
 
mouseEnterExit(long, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
 
mouseExited(MouseEvent) - Method in class jme.JME
 
mouseExited(MouseEvent) - Method in class jspecview.app.GenericMouse
 
mouseExited(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
 
mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
 
mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseListener - Variable in class org.jmol.awtjs.swing.Component
 
mouseMove(MouseEvent, int, int) - Method in class jme.JME
 
mouseMoved(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
mouseMoved(int, int) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
mouseMoved(MouseEvent) - Method in class jme.JME
 
mouseMoved(MouseEvent) - Method in class jspecview.app.GenericMouse
 
mouseMoved(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mousePressed(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
mousePressed(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mousePressed(MouseEvent) - Method in class jme.JME
 
mousePressed(MouseEvent) - Method in class jspecview.app.GenericMouse
 
mousePressed(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
 
mousePressed(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseReleased(long, int, int) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
mouseReleased(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mouseReleased(MouseEvent) - Method in class jme.JME
 
mouseReleased(MouseEvent) - Method in class jspecview.app.GenericMouse
 
mouseReleased(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
 
mouseReleased(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseShift - Variable in class jme.JME
 
MouseState - Class in org.jmol.viewer
 
mouseUp(MouseEvent, int, int) - Method in class jme.JME
 
mousewheelfactor - Static variable in class org.jmol.script.T
 
mouseWheelFactor - Variable in class org.jmol.viewer.ActionManager
 
mouseWheelMoved(MouseWheelEvent) - Method in class jspecview.app.GenericMouse
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseX - Variable in class jspecview.common.PanelData
 
mouseY - Variable in class jspecview.common.PanelData
 
movableBitSet - Variable in class org.jmol.viewer.Viewer
 
movableX - Variable in class org.jmol.modelset.Text
 
movableXPercent - Variable in class org.jmol.modelset.Text
 
movableY - Variable in class org.jmol.modelset.Text
 
movableYPercent - Variable in class org.jmol.modelset.Text
 
movableZ - Variable in class org.jmol.modelset.Text
 
movableZPercent - Variable in class org.jmol.modelset.Text
 
move - Static variable in class org.jmol.script.T
 
move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.Viewer
 
MOVE - Static variable in class com.sparshui.common.TouchState
 
MOVE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
moveAtoms(M4, M3, M3, V3, BS, P3, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
moveAtoms(M4, M3, M3, V3, P3, boolean, BS, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
moveAtomWithHydrogens(int, int, int, int, P3, BS) - Method in class org.jmol.viewer.Viewer
 
moved - Variable in class org.jmol.viewer.ActionManager
 
moved(long, int, int, int) - Method in class jspecview.app.GenericMouse
 
MOVED - Static variable in class org.jmol.awtjs.Event
 
moveMinConstrained(int, P3, BS) - Method in class org.jmol.modelkit.ModelKit
 
movePossible - Variable in class jme.JME
 
moveRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
 
moveto - Static variable in class org.jmol.script.T
 
moveto(int, int) - Method in class javajs.export.PDFCreator
 
moveTo(JmolScriptEvaluator, float, P3, V3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.Viewer
 
MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
moveToPyMOL(JmolScriptEvaluator, float, float[]) - Method in class org.jmol.viewer.TransformManager
 
movetoThread - Variable in class org.jmol.viewer.TransformManager
 
MoveToThread - Class in org.jmol.thread
 
MoveToThread() - Constructor for class org.jmol.thread.MoveToThread
 
moveUpdate(float) - Method in class org.jmol.viewer.Viewer
 
movie - Static variable in class org.jmol.script.T
 
mp - Variable in class jspecview.export.AMLExporter
 
mp - Variable in class jspecview.export.CMLExporter
 
mPending - Variable in class org.jmol.shape.Measures
 
MPJmolApp - Class in org.molecularplayground
 
MPJmolApp() - Constructor for class org.molecularplayground.MPJmolApp
 
MPJmolApp(int) - Constructor for class org.molecularplayground.MPJmolApp
 
mrc - Static variable in class org.jmol.script.T
 
ms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ms - Variable in class org.jmol.modelset.Measurement
 
ms - Variable in class org.jmol.modelset.Model
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
ms - Variable in class org.jmol.modelset.ModelLoader
 
ms - Variable in class org.jmol.render.ShapeRenderer
 
ms - Variable in class org.jmol.shape.Shape
 
ms - Variable in class org.jmol.viewer.Viewer
 
MSCifParser - Class in org.jmol.adapter.readers.cif
 
MSCifParser() - Constructor for class org.jmol.adapter.readers.cif.MSCifParser
 
msg - Variable in class org.jmol.jvxl.data.JvxlData
 
msInfo - Variable in class org.jmol.modelset.ModelSet
 
MSInterface - Interface in org.jmol.adapter.smarter
Modulated Structure Reader Interface
msms - Static variable in class org.jmol.script.T
 
MSRdr - Class in org.jmol.adapter.readers.cif
generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth, Legendre; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1
MSRdr() - Constructor for class org.jmol.adapter.readers.cif.MSRdr
 
mul - Static variable in class org.jmol.script.T
 
mul(float) - Method in class javajs.util.Quat
 
mul(M3) - Method in class javajs.util.M3
Sets the value of this matrix to the result of multiplying itself with matrix m1.
mul(M4) - Method in class javajs.util.M4
Sets the value of this matrix to the result of multiplying itself with matrix m1.
mul(Matrix) - Method in class javajs.util.Matrix
Linear algebraic matrix multiplication, A * B
mul2(M3, M3) - Method in class javajs.util.M3
Sets the value of this matrix to the result of multiplying the two argument matrices together.
mul2(M4, M4) - Method in class javajs.util.M4
Sets the value of this matrix to the result of multiplying the two argument matrices together.
mul3 - Static variable in class org.jmol.script.T
 
mul33(float) - Method in class javajs.util.M34
 
mulQ(Quat) - Method in class javajs.util.Quat
 
MULTI_POINT_DRAG_GESTURE - Static variable in class com.sparshui.GestureType
 
MULTI_POINT_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JC
 
MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JC
 
MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JC
 
MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JC
 
multipart - Variable in class jme.JME
 
MULTIPLE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
multiplebondbananas - Static variable in class org.jmol.script.T
 
multiplebondradiusfactor - Static variable in class org.jmol.script.T
 
multiplebondspacing - Static variable in class org.jmol.script.T
 
multiprocessor - Static variable in class org.jmol.script.T
 
mustBeConnected - Variable in class org.jmol.modelset.MeasurementData
 
mustFinalizeModelSet - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
mustNotBeConnected - Variable in class org.jmol.modelset.MeasurementData
 
mustResumeEval - Variable in class org.jmol.script.ScriptContext
 
mutate - Static variable in class org.jmol.script.T
 
mutate(BS, String, String[], String, float[]) - Method in class org.jmol.modelsetbio.BioModelSet
 
mxyz - Variable in class org.jmol.util.ModulationSet
the modulated magnetic spin
myAtoms - Variable in class org.jmol.util.ContactPair
 
mydeflater - Variable in class com.jcraft.jzlib.DeflaterOutputStream
 
MyFileFilter - Class in org.openscience.jmol.app.janocchio
 
MyFileFilter(String[], String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
 
MyFileFilter(String, String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
 
myFrame - Variable in class jme.JME
 
myinflater - Variable in class com.jcraft.jzlib.InflaterInputStream
 
myName - Variable in class org.jmol.script.SV
 
myName - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
myParams - Variable in class jspecview.common.MeasurementData
 
myParams - Variable in class jspecview.dialog.JSVDialog
 
myStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
myType - Variable in class org.jmol.shape.Shape
 
myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
 
myVisibilityFlag - Variable in class org.jmol.render.ShapeRenderer
 

N

n - Variable in class javajs.util.Matrix
 
n(int, int) - Static method in class org.jmol.script.T
 
N_GROUPS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
N_ITERS - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
NA - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
nada - Static variable in class org.jmol.script.T
 
NADA - Enum constant in enum class org.jmol.c.VDW
 
name - Variable in class jspecview.common.Parameters
 
name - Variable in class org.jmol.awtjs.swing.Component
 
name - Variable in class org.jmol.minimize.forcefield.ForceField
 
name - Static variable in class org.jmol.script.T
 
name - Variable in class org.jmol.symmetry.UnitCell
 
name - Variable in class org.jmol.thread.JmolThread
 
name - Variable in class org.jmol.viewer.binding.Binding
 
name - Variable in class org.jmol.viewer.MouseState
 
namedSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
 
nameOf(int) - Static method in class org.jmol.script.T
note: nameOf is a very inefficient mechanism for getting the name of a token.
NamfisReader - Class in org.openscience.jmol.app.janocchio
 
NamfisReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisReader
 
NamfisSaver - Class in org.openscience.jmol.app.janocchio
 
NamfisSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisSaver
 
nativeLanguage - Variable in class org.jmol.i18n.Language
 
natoms - Variable in class jme.JMEmol
 
nAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
 
nAtoms - Variable in class org.jmol.minimize.MMConstraint
 
nAtoms0 - Variable in class org.jmol.adapter.readers.cif.CifReader
 
NAV_MODE_IGNORE - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager
 
navfps - Static variable in class org.jmol.script.T
 
navFps - Variable in class org.jmol.viewer.TransformManager
 
navigate - Static variable in class org.jmol.script.T
 
navigateAxis(V3, float) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigateAxis(V3, float) - Method in class org.jmol.navigate.Navigator
 
navigateAxis(V3, float) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navigateAxis(V3, float) - Method in class org.jmol.viewer.Viewer
 
navigateKey(int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigateKey(int, int) - Method in class org.jmol.navigate.Navigator
 
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.navigate.Navigator
 
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.viewer.TransformManager
 
navigatePt(P3) - Method in class org.jmol.viewer.Viewer
 
navigatesurface - Static variable in class org.jmol.script.T
 
navigating - Variable in class org.jmol.viewer.TransformManager
 
navigationCenter - Variable in class org.jmol.viewer.TransformManager
 
navigationdepth - Static variable in class org.jmol.script.T
 
navigationDepthPercent - Variable in class org.jmol.viewer.TransformManager
 
navigationmode - Static variable in class org.jmol.script.T
 
navigationOffset - Variable in class org.jmol.viewer.TransformManager
 
navigationperiodic - Static variable in class org.jmol.script.T
 
navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
 
navigationslab - Static variable in class org.jmol.script.T
 
navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager
 
navigationspeed - Static variable in class org.jmol.script.T
 
Navigator - Class in org.jmol.navigate
Navigator is a user input mechanism that utilizes the keypad to drive through the model.
Navigator() - Constructor for class org.jmol.navigate.Navigator
 
navMode - Variable in class org.jmol.viewer.TransformManager
 
navOn - Variable in class org.jmol.viewer.TransformManager
 
navTranslatePercent(float, float) - Method in class org.jmol.viewer.Viewer
 
navTranslatePercentOrTo(float, float, float) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.navigate.Navigator
 
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.viewer.TransformManager
seconds invalid input: '<' 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"
navx - Static variable in class org.jmol.script.T
 
navX - Variable in class org.jmol.viewer.TransformManager
 
navy - Static variable in class org.jmol.script.T
 
navY - Variable in class org.jmol.viewer.TransformManager
 
NAVY - Static variable in class org.jmol.util.C
 
navz - Static variable in class org.jmol.script.T
 
navZ - Variable in class org.jmol.viewer.TransformManager
 
nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
 
nbo - Static variable in class org.jmol.script.T
 
NBO - Class in org.jmol.shapesurface
 
NBO() - Constructor for class org.jmol.shapesurface.NBO
 
NBO_CONFIG - Static variable in class org.jmol.viewer.JC
 
NBO_MODEL - Static variable in class org.jmol.viewer.JC
 
NBO_RUN - Static variable in class org.jmol.viewer.JC
 
NBO_SEARCH - Static variable in class org.jmol.viewer.JC
 
NBO_TYPES - Static variable in class org.jmol.viewer.JC
 
NBO_VIEW - Static variable in class org.jmol.viewer.JC
 
nbocharges - Static variable in class org.jmol.script.T
 
nbonds - Variable in class jme.JMEmol
 
nBonds - Variable in class org.jmol.minimize.MinAtom
 
NBOParser - Class in org.jmol.adapter.readers.quantum
 
NBOParser() - Constructor for class org.jmol.adapter.readers.quantum.NBOParser
 
NBORenderer - Class in org.jmol.rendersurface
 
NBORenderer() - Constructor for class org.jmol.rendersurface.NBORenderer
 
nBytes - Variable in class javajs.util.BinaryDocument
 
nBytes - Variable in class org.jmol.jvxl.data.JvxlData
 
nBytes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nci - Static variable in class org.jmol.script.T
 
NciCalculation - Class in org.jmol.quantum
 
NciCalculation() - Constructor for class org.jmol.quantum.NciCalculation
 
nCoef - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
nContours - Variable in class org.jmol.jvxl.data.JvxlData
 
nData - Variable in class org.jmol.jvxl.readers.JvxlReader
 
nData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
nData - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
nDataPoints - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
ndots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
ne - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
nEdges - Variable in class org.jmol.jvxl.data.JvxlData
 
needRecentering - Variable in class jme.JMEmol
 
needTranslucent - Variable in class org.jmol.render.MeshRenderer
 
negate() - Method in class javajs.util.Quat
 
negativeAtomCount - Variable in class org.jmol.jvxl.readers.JvxlReader
 
negativeAtomCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
negativeAtomCount - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
nElements - Variable in class org.jmol.util.JmolMolecule
 
nError - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
NetworkConfiguration - Class in com.sparshui.common
Defines the port the server will be listening for connections on.
NetworkConfiguration() - Constructor for class com.sparshui.common.NetworkConfiguration
 
new3(float, float, float) - Static method in class javajs.util.P3
 
new3(float, float, float) - Static method in class javajs.util.V3
 
new3(int, int, int) - Static method in class javajs.util.P3i
 
new4(float, float, float, float) - Static method in class javajs.util.A4
Constructs and initializes an AxisAngle4f from the specified x, y, z, and angle.
new4(float, float, float, float) - Static method in class javajs.util.P4
 
new4(float, float, float, float) - Static method in class javajs.util.Quat
Note that q0 is the last parameter here
newA(float[]) - Static method in class javajs.util.P3
 
newA(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
newA16(float[]) - Static method in class javajs.util.M4
Constructs and initializes a Matrix4f from the specified 16 element array.
newA9(float[]) - Static method in class javajs.util.M3
Constructs and initializes a Matrix3f from the specified 9 element array.
newAA(A4) - Static method in class javajs.util.A4
Constructs and initializes a AxisAngle4f from the specified AxisAngle4f.
newAA(A4) - Static method in class javajs.util.Quat
 
newAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
NewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
NewAction(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
newAndSetBit(int) - Static method in class org.jmol.util.BSUtil
 
newAntialiasing - Variable in class org.jmol.util.GData
 
newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
Create a new atoms set, clearing the atom map
newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
newAtomSetClear(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Create a new atom set, optionally clearing the atom map.
newBinding(Viewer, String) - Static method in class org.jmol.viewer.binding.Binding
 
newBitSet2(int, int) - Static method in class org.jmol.util.BSUtil
 
newBS(BS) - Static method in class org.jmol.modelset.BondSet
 
newBufferedImage(Object, int, int) - Method in class jspecview.java.AwtPlatform
 
newBufferedImage(Object, int, int) - Method in class jspecview.js2d.JsPlatform
 
newBufferedImage(Object, int, int) - Method in interface org.jmol.api.GenericPlatform
 
newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
 
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs.Platform
 
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs2d.Platform
 
newByte2(int) - Static method in class javajs.util.AU
 
newBZip2InputStream(InputStream) - Method in interface javajs.api.GenericZipTools
 
newBZip2InputStream(InputStream) - Method in class javajs.util.ZipTools
 
newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newDocument(int, int, boolean) - Method in class javajs.export.PDFCreator
 
newDouble2(int) - Static method in class javajs.util.AU
 
newDouble3n(int) - Static method in class javajs.util.AU
 
newEcho(Viewer, Font, String, short, int, int, float) - Static method in class org.jmol.modelset.Text
 
newF(float) - Static method in class org.jmol.script.SV
 
newFile(String) - Method in class jspecview.java.AwtPlatform
 
newFile(String) - Method in class jspecview.js2d.JsPlatform
 
newFile(String) - Method in interface org.jmol.api.GenericPlatform
 
newFile(String) - Method in class org.jmol.awt.Platform
 
newFile(String) - Method in class org.jmol.awtjs2d.Platform
 
newFileSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newFileSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
newFloat2(int) - Static method in class javajs.util.AU
 
newFloat3(int, int) - Static method in class javajs.util.AU
 
newFont(String, boolean, boolean, float) - Method in class jspecview.java.AwtPlatform
 
newFont(String, boolean, boolean, float) - Method in class jspecview.js2d.JsPlatform
 
newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.FontManager
 
newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
 
newFont(String, boolean, boolean, float) - Method in class org.jmol.awtjs2d.Platform
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface javajs.api.js.J2SObjectInterface
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.common.PDFWriter
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.java.AwtG2D
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class jspecview.js2d.JsG2D
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface org.jmol.api.GenericGraphics
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awt.AwtG2D
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awtjs2d.JsG2D
 
newGZIPInputStream(InputStream) - Method in interface javajs.api.GenericZipTools
 
newGZIPInputStream(InputStream) - Method in class javajs.util.ZipTools
 
newGZIPInputStream(InputStream) - Method in interface jspecview.api.JSVZipInterface
 
newGZIPInputStream(InputStream) - Method in class jspecview.common.JSVZipUtil
 
newI(int) - Static method in class org.jmol.script.SV
 
newI(int) - Static method in class org.jmol.util.Rgb16
 
newID(String) - Static method in class org.jmol.awtjs.swing.Component
 
newInt2(int) - Static method in class javajs.util.AU
 
newInt3(int, int) - Static method in class javajs.util.AU
 
newInt4(int) - Static method in class javajs.util.AU
 
newJButton(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJMenu(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
newJMenu(String) - Method in class org.jmol.console.JmolConsole
 
newJMenu(String) - Method in class org.jmol.consolejs.AppletConsole
 
newJMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJMenuItem(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
newJMenuItem(String) - Method in class org.jmol.console.JmolConsole
 
newJMenuItem(String) - Method in class org.jmol.consolejs.AppletConsole
 
newJMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJSVZipFileSequentialReader(InputStream, String[], String) - Method in interface jspecview.api.JSVZipInterface
 
newJSVZipFileSequentialReader(InputStream, String[], String) - Method in class jspecview.common.JSVZipUtil
 
newLabel(Viewer, Font, String, short, short, int, float) - Static method in class org.jmol.modelset.Text
 
newLatticePts - Variable in class org.jmol.util.BZone
 
newLine - Static variable in class jspecview.export.JDXExporter
 
newList() - Static method in class org.qcschema.QCSchemaUnits
 
newM(M3) - Static method in class javajs.util.Quat
 
newM3(M3) - Static method in class javajs.util.M3
Constructs a new matrix with the same values as the Matrix3f parameter.
newM4(M4) - Static method in class javajs.util.M4
Constructs a new matrix with the same values as the Matrix4f parameter.
newMeasure(Viewer, Font, short) - Static method in class org.jmol.modelset.Text
 
newMeasurementData(String, Lst<Object>) - Method in class org.jmol.viewer.Viewer
 
newMesh(boolean, T3[], int, int[][], T3[], int) - Static method in class org.jmol.util.MeshSurface
 
newModel(int) - Method in class org.jmol.adapter.readers.cif.CifReader
 
newMolecule - Variable in class jme.JME
 
newMV(M3, T3) - Static method in class javajs.util.M4
Constructs and initializes a Matrix4f from the rotation matrix and translation.
newN(int) - Static method in class javajs.util.BS
Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range 0 through nbits-1.
newN(int) - Static method in class javajs.util.SB
 
newOffScreenImage(int, int) - Method in class jspecview.java.AwtPlatform
 
newOffScreenImage(int, int) - Method in class jspecview.js2d.JsPlatform
 
newOffScreenImage(int, int) - Method in interface org.jmol.api.GenericPlatform
 
newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
 
newOffScreenImage(int, int) - Method in class org.jmol.awtjs.Platform
 
newOffScreenImage(int, int) - Method in class org.jmol.awtjs2d.Platform
 
newP(T3) - Static method in class javajs.util.P3
 
newP4(P4) - Static method in class javajs.util.Quat
 
newParams(float[], float) - Static method in class org.jmol.util.SimpleUnitCell
 
newPlanes - Variable in class org.jmol.util.BZone
 
newPt(P4) - Static method in class javajs.util.P4
 
newQ(Quat) - Static method in class javajs.util.Quat
 
newS(String) - Static method in class javajs.util.SB
 
newS(String) - Static method in class org.jmol.script.SV
 
newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
newSg() - Method in class org.jmol.shapesurface.Isosurface
 
newShort2(int) - Static method in class javajs.util.AU
 
newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in interface org.jmol.api.SymmetryInterface
 
newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in class org.jmol.symmetry.Symmetry
 
newSpectrum(Lst<Spectrum>) - Method in class jspecview.common.ViewData
 
newSpectrum(Spectrum, Coordinate[], String) - Static method in class jspecview.common.Spectrum
copy spectrum with new coordinates
newStereo(SmilesSearch) - Static method in class org.jmol.smiles.SmilesStereo
 
newT(T3, boolean) - Static method in class javajs.util.Matrix
 
newT(T) - Static method in class org.jmol.script.SV
 
newToolbar(String[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
newTreePath(Object[]) - Method in interface jspecview.api.JSVTree
 
newTreePath(Object[]) - Method in class jspecview.application.AwtTree
 
newTreePath(Object[]) - Method in class jspecview.tree.SimpleTree
 
newV(int, Object) - Static method in class org.jmol.script.SV
 
newV(T3) - Static method in class javajs.util.V3
 
newVA(T3, float) - Static method in class javajs.util.Quat
 
newVA(V3, float) - Static method in class javajs.util.A4
Constructs and initializes an AxisAngle4f from the specified axis and angle.
newVertex(P3, V3, float) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
newVertexBitSet() - Static method in class org.jmol.util.Normix
 
newVoxelDataCube() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
newVsub(T3, T3) - Static method in class javajs.util.V3
 
newwinAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
NewwinAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
 
newWindow(boolean) - Method in interface jspecview.api.AppletFrame
 
newWindow(boolean) - Method in class jspecview.appletjs.JSVApplet
 
newWindowHeight - Variable in class org.jmol.util.GData
 
newWindowWidth - Variable in class org.jmol.util.GData
 
newXYCoords - Variable in class jspecview.export.AMLExporter
 
newXYCoords - Variable in class jspecview.export.CMLExporter
 
newZipInputStream(InputStream) - Method in interface javajs.api.GenericZipTools
 
newZipInputStream(InputStream) - Method in class javajs.util.ZipTools
 
next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
next - Variable in class org.jmol.jvxl.readers.JvxlReader
 
next - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
next - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
next - Static variable in class org.jmol.script.T
 
next() - Method in class jspecview.source.JDXDecompressor
 
next() - Method in interface org.jmol.api.AtomIndexIterator
 
next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
next() - Method in interface org.jmol.modelset.BondIterator
 
next() - Method in class org.jmol.symmetry.UnitCellIterator
 
nextAtomSet() - Method in class org.jmol.adapter.readers.cif.CifReader
 
nextClearBit(int) - Method in class javajs.util.BS
Returns the index of the first bit that is set to false that occurs on or after the specified starting index.
nextData(StringTokenizer, String) - Static method in class jme.JMEmol
 
nextData(StringTokenizer, String) - Static method in class jme.JMEUtil
 
nextElement() - Method in class jspecview.tree.SimpleTreeEnumeration
 
nextElement() - Method in class org.jmol.bspt.CubeIterator
normal iterator method
nextEvent() - Method in class jspecview.source.XMLParser
 
nextFileName(String, int) - Method in class org.jmol.console.GenericConsole
 
nextFileName(String, int) - Method in class org.jmol.console.JmolConsole
 
nextFileName(String, int) - Method in class org.jmol.consolejs.AppletConsole
 
nextIndex() - Method in interface org.jmol.modelset.BondIterator
 
nextRandom8Bit() - Method in class org.jmol.util.Shader
Implements RANDU algorithm for random noise in lighting/shading.
nextSetBit(int) - Method in class javajs.util.BS
Returns the index of the first bit that is set to true that occurs on or after the specified starting index.
nextStartTag() - Method in class jspecview.source.XMLParser
 
nextTag() - Method in class jspecview.source.XMLParser
 
nextToken() - Method in class jspecview.common.ScriptTokenizer
 
nextValue() - Method in class jspecview.source.XMLParser
 
nextView() - Method in class jspecview.common.PanelData
Displays the next view zoomed
nextVoxel() - Method in class org.jmol.jvxl.readers.JvxlReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
nFast - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
nFrankList - Variable in class org.jmol.popup.JmolGenericPopup
 
nGaussians - Variable in class org.jmol.quantum.MOCalculation
 
nihresolverformat - Static variable in class org.jmol.script.T
 
nIn - Variable in class org.jmol.util.Shader
 
nioClosed(JsonNioServer) - Method in class org.molecularplayground.MPJmolApp
 
nioClosed(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
nioClosed(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
 
nioSync(Viewer, Map<String, Object>) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
process touch or gesture commands driven by hardware.
nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
nList - Variable in class org.jmol.shapecgo.CGOMesh
 
nmols - Variable in class jme.JME
 
nmr - Static variable in class org.jmol.script.T
 
Nmr - Class in org.openscience.jmol.app.janocchio
 
Nmr(String[]) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
 
Nmr(String[], NmrPlugin) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
 
NMR_DC - Static variable in class org.jmol.modelset.Measurement
 
NMR_DisplayPanel - Class in org.openscience.jmol.app.janocchio
 
NMR_JC - Static variable in class org.jmol.modelset.Measurement
 
NMR_JmolPanel - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
NMR_JmolPanel.DetachAppletAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.JumpBestFrameAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.LabelNmrAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.ReadNamfisAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.ReadNmrAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.ReattachAppletAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.ViewCoupleTableAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.ViewNoeTableAction - Class in org.openscience.jmol.app.janocchio
 
NMR_JmolPanel.WriteNamfisAction - Class in org.openscience.jmol.app.janocchio
 
NMR_NOE_OR_J - Static variable in class org.jmol.modelset.Measurement
 
NMR_NOT - Static variable in class org.jmol.modelset.Measurement
 
NMR_Viewer - Class in org.openscience.jmol.app.janocchio
Implements some lost interfaces.
NMR_Viewer(Map<String, Object>) - Constructor for class org.openscience.jmol.app.janocchio.NMR_Viewer
 
NmrApplet - Class in org.openscience.jmol.app.janocchio
 
NmrApplet() - Constructor for class org.openscience.jmol.app.janocchio.NmrApplet
 
NMRCalculation - Class in org.jmol.quantum
 
NMRCalculation() - Constructor for class org.jmol.quantum.NMRCalculation
 
NmrGuiMap - Class in org.openscience.jmol.app.janocchio
 
NmrGuiMap() - Constructor for class org.openscience.jmol.app.janocchio.NmrGuiMap
 
nmrMaxY - Variable in class jspecview.common.JSViewer
 
NmrMolecule - Class in org.openscience.jmol.app.janocchio
 
NmrMolecule(NMR_JmolPanel, BS, String[], boolean) - Constructor for class org.openscience.jmol.app.janocchio.NmrMolecule
 
NMRNoeMatrix - Class in org.jmol.quantum
Class for calculating NOE intensities by full matrix relaxation approach.
NMRNoeMatrix.NOEParams - Class in org.jmol.quantum
 
nmrPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
 
nmrPanel - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
NmrPlugin - Class in org.openscience.jmol.app.janocchio
 
NmrPlugin() - Constructor for class org.openscience.jmol.app.janocchio.NmrPlugin
 
nmrpredictformat - Static variable in class org.jmol.script.T
 
NmrReader - Class in org.openscience.jmol.app.janocchio
 
NmrReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrReader
 
NmrResourceHandler - Class in org.openscience.jmol.app.janocchio
Provides access to resources (for example, strings and images).
NmrSaver - Class in org.openscience.jmol.app.janocchio
 
NmrSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrSaver
 
nmrType(String) - Static method in class org.jmol.modelset.Measurement
 
nmrurlformat - Static variable in class org.jmol.script.T
 
NO_AUTOPLAY - Static variable in interface org.jmol.api.JmolScriptManager
 
NO_CONVERT - Enum constant in enum class jspecview.common.Spectrum.IRMode
 
NO_SCRIPT - Static variable in interface org.jmol.api.JmolScriptManager
 
NO_SUCH_PAGE - Static variable in class jspecview.common.JSViewer
 
noArgs - Static variable in class org.jmol.script.T
 
nobackshell - Static variable in class org.jmol.script.T
 
nocenter - Variable in class jme.JME
 
noColor - Variable in class org.jmol.export.__CartesianExporter
 
nocontourlines - Static variable in class org.jmol.script.T
 
noCopy(int, int) - Method in class org.jmol.script.ScriptEval
 
nocross - Static variable in class org.jmol.script.T
 
noCross - Variable in class org.jmol.shapespecial.Dipole
 
Node - Interface in org.jmol.util
 
nodebug - Static variable in class org.jmol.script.T
 
nodelay - Static variable in class org.jmol.script.T
 
noDelay - Variable in class org.jmol.viewer.GlobalSettings
ensures that ScriptManager.allowJSThreads is false so that ScriptManager.useThreads() returns false; Jmol 14.21.1
nodes - Variable in class org.jmol.util.JmolMolecule
 
nodots - Static variable in class org.jmol.script.T
 
noeColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
 
NoeColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
 
NoeColourSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
 
noedges - Static variable in class org.jmol.script.T
 
noeMatrix - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
 
noeParameterSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
 
NoeParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
 
NoeParameterSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
 
NOEParams() - Constructor for class org.jmol.quantum.NMRNoeMatrix.NOEParams
 
noeTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
NoeTable - Class in org.openscience.jmol.app.janocchio
 
NoeTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.NoeTable
Constructor
nofill - Static variable in class org.jmol.script.T
 
noFrankEcho - Variable in class org.jmol.viewer.Viewer
 
noGraphicsAllowed - Variable in class org.jmol.viewer.Viewer
 
nohead - Static variable in class org.jmol.script.T
 
noHead - Variable in class org.jmol.shapespecial.DrawMesh
 
NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
 
NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
 
noHydrogens - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
NOJMOL - Enum constant in enum class org.jmol.c.VDW
 
noLabelAtom - Variable in class jme.AtomDisplayLabel
 
noload - Static variable in class org.jmol.script.T
 
nomesh - Static variable in class org.jmol.script.T
 
noMinimize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
nonArrayString(Object) - Static method in class javajs.util.PT
Checks to see if an object is an array (including typed arrays), and if it is, returns null; otherwise it returns the string equivalent of that object.
none - Static variable in class org.jmol.script.T
 
NONE - Enum constant in enum class javajs.util.Encoding
 
NONE - Enum constant in enum class jspecview.common.Annotation.AType
 
NONE - Enum constant in enum class jspecview.common.PanelData.LinkMode
 
NONE - Enum constant in enum class org.jmol.c.PAL
 
NONE - Enum constant in enum class org.jmol.c.STER
 
NONE - Enum constant in enum class org.jmol.c.STR
 
NONE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
NONE - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
 
NONE - Static variable in interface javajs.api.GenericCifDataParser
 
NONE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
NONE - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
 
noneSelected - Variable in class org.jmol.viewer.SelectionManager
a flag to indicate that labels and fonts should be set to default values; set only by SELECT NONE;
nonisomericSmiles() - Method in class jme.JME
 
noPack - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
noplane - Static variable in class org.jmol.script.T
 
nOrbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
NORM_NBO - Static variable in class org.jmol.quantum.MOCalculation
 
NORM_NONE - Static variable in class org.jmol.quantum.MOCalculation
 
NORM_NWCHEM - Static variable in class org.jmol.quantum.MOCalculation
 
NORM_STANDARD - Static variable in class org.jmol.quantum.MOCalculation
 
normal - Static variable in class org.jmol.script.T
 
NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
 
normalCount - Variable in class org.jmol.util.MeshSurface
 
normalise(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
Normalises the y values of a spectrum to a certain range
normalize() - Method in class javajs.util.T3
Normalizes this vector in place.
normalize() - Method in class javajs.util.V3d
Normalizes this vector in place.
normalize12ths(V3) - Static method in class org.jmol.symmetry.SymmetryOperation
 
normalizeIntegral() - Method in class jspecview.common.PanelData
 
normalizeOperationToCentroid(int, M4, P3[], int, int) - Static method in class org.jmol.symmetry.SymmetryOperation
Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.
normalizeSimulation(double) - Method in class jspecview.source.JDXDataObject
 
normals - Variable in class org.jmol.util.MeshSurface
 
normalsTemp - Variable in class org.jmol.util.MeshSurface
 
Normix - Class in org.jmol.util
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Normix() - Constructor for class org.jmol.util.Normix
 
NORMIX_NULL - Static variable in class org.jmol.util.Normix
 
normixCount - Static variable in class org.jmol.util.GData
 
normixCount - Variable in class org.jmol.util.MeshSurface
 
normixes - Variable in class org.jmol.render.MeshRenderer
 
normixes - Variable in class org.jmol.shape.Mesh
 
normType - Variable in class org.jmol.quantum.MOCalculation
 
NORTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
 
NOT - Enum constant in enum class org.jmol.c.HB
 
NOT - Enum constant in enum class org.jmol.c.STR
 
NOT_LOADED - Enum constant in enum class org.jmol.c.FIL
 
NOT_SORTED - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
 
note - Variable in class org.jmol.modelset.MeasurementData
 
NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JC
 
notfrontonly - Static variable in class org.jmol.script.T
 
notify(int, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notify(int, Object[]) - Method in class org.jmol.console.ScriptEditor
 
notifyAtomPositionsChanged(int, BS, M4) - Method in class org.jmol.viewer.ShapeManager
 
notifyAtoms(String, BS[]) - Method in class org.jmol.viewer.ShapeManager
 
notifyAudioEnded(Object) - Method in interface org.jmol.api.JmolAppletInterface
 
notifyAudioEnded(Object) - Method in class org.jmol.util.GenericApplet
 
notifyAudioStatus(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
called from JmolAudio
notifyCallback(CBK, Object[]) - Method in interface org.jmol.api.JmolCallbackListener
 
notifyCallback(CBK, Object[]) - Method in class org.jmol.console.GenericConsole
 
notifyCallback(CBK, Object[]) - Method in class org.jmol.util.GenericApplet
 
notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyCallback(CBK, Object[]) - Method in interface org.openscience.jmol.app.JmolPlugin
 
notifyContext(ScriptContext, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notifyContext(ScriptContext, Object[]) - Method in class org.jmol.console.ScriptEditor
 
notifyEnabled(CBK) - Method in interface org.jmol.api.JmolCallbackListener
 
notifyEnabled(CBK) - Method in class org.jmol.console.GenericConsole
 
notifyEnabled(CBK) - Method in class org.jmol.util.GenericApplet
 
notifyEnabled(CBK) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyEndOfRendering() - Method in class jspecview.java.AwtPlatform
 
notifyEndOfRendering() - Method in class jspecview.js2d.JsPlatform
 
notifyEndOfRendering() - Method in interface org.jmol.api.GenericPlatform
 
notifyEndOfRendering() - Method in class org.jmol.awt.Platform
 
notifyEndOfRendering() - Method in class org.jmol.awtjs2d.Platform
 
notifyError(String, String, String) - Method in class org.jmol.viewer.Viewer
 
notifyListeners(Object) - Method in class jspecview.common.PanelData
 
notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
 
notifyMouseClicked(int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
notifyPeakPickedListeners(PeakPickEvent) - Method in class jspecview.common.PanelData
Notifies CoordinatePickedListeners
notifyResumeStatus() - Method in interface org.jmol.api.JmolScriptEvaluator
 
notifyResumeStatus() - Method in class org.jmol.script.ScriptEval
 
notifyScriptEditor(int, Object[]) - Method in class org.jmol.viewer.Viewer
 
notifyScriptStart() - Method in class org.jmol.console.ScriptEditor
 
notifyScriptTermination(String) - Method in class org.jmol.console.ScriptEditor
 
notifyStatusReady(boolean) - Method in class org.jmol.api.JmolViewer
 
notifyStatusReady(boolean) - Method in class org.jmol.viewer.Viewer
 
notifySubSpectrumChange(int, Spectrum) - Method in class jspecview.common.PanelData
 
notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifyViewerRepaintDone() - Method in class org.jmol.api.JmolViewer
 
notifyViewerRepaintDone() - Method in class org.jmol.viewer.Viewer
 
notInCentroid(ModelSet, BS, int[]) - Method in interface org.jmol.api.SymmetryInterface
 
notInCentroid(ModelSet, BS, int[]) - Method in class org.jmol.symmetry.Symmetry
 
notriangles - Static variable in class org.jmol.script.T
 
nOut - Variable in class org.jmol.util.Shader
 
now - Static variable in class org.jmol.script.T
 
npoints - Variable in class jspecview.export.AMLExporter
 
npoints - Variable in class jspecview.export.CMLExporter
 
npoints - Variable in class jspecview.source.AnIMLReader
 
nPoints - Variable in class org.jmol.jvxl.data.VolumeData
 
nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsX - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsY - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsZ - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nProcessors - Static variable in class org.jmol.viewer.Viewer
 
nRes - Variable in class org.jmol.modelsetbio.ProteinStructure
 
nSets - Variable in class org.jmol.util.MeshSurface
 
nSkipX - Variable in class org.jmol.jvxl.readers.JvxlReader
 
nSkipX - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
nSkipX - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
nSkipY - Variable in class org.jmol.jvxl.readers.JvxlReader
 
nSkipY - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
nSkipY - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
nSkipZ - Variable in class org.jmol.jvxl.readers.JvxlReader
 
nSkipZ - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
nSkipZ - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
 
nSurfaces - Variable in class org.jmol.jvxl.readers.JvxlReader
 
nSurfaces - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
nSurfaces - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
nTab - Variable in class org.jmol.console.GenericConsole
 
nTokens - Variable in class org.jmol.script.ScriptCompiler
 
nTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
nucleic - Static variable in class org.jmol.script.T
 
NUCLEIC - Enum constant in enum class org.jmol.c.PAL
 
NUCLEIC - Static variable in class org.jmol.util.ColorEncoder
 
NucleicMonomer - Class in org.jmol.modelsetbio
 
NucleicPolymer - Class in org.jmol.modelsetbio
 
NucleicRenderer - Class in org.jmol.renderbio
extends CartoonRenderer for nucleics
NucleicRenderer() - Constructor for class org.jmol.renderbio.NucleicRenderer
 
nucleusX - Variable in class jspecview.source.JDXDataObject
 
nucleusY - Variable in class jspecview.source.JDXDataObject
 
nullDeletedAtoms - Static variable in class org.jmol.viewer.Viewer
 
nullPeakInfo - Static variable in class jspecview.common.PeakInfo
 
nullString - Variable in class javajs.util.CifDataParser
string to return for CIF data value .
NUM_OVERSHOOT_BYTES - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
number - Variable in class jme.JME
 
numberAtoms() - Method in class jme.JMEmol
 
numberOutOfRange(float, float) - Method in class org.jmol.script.ScriptError
 
numCached - Variable in class org.jmol.modelset.BondCollection
 
numSet - Variable in class org.jmol.modelset.MeasurementPending
 
numWindows - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
nUnnamed - Variable in class org.jmol.shape.MeshCollection
 
nVertexColors - Variable in class org.jmol.jvxl.data.JvxlData
 
NWChemReader - Class in org.jmol.adapter.readers.quantum
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
NWChemReader() - Constructor for class org.jmol.adapter.readers.quantum.NWChemReader
 
nX - Variable in class org.jmol.quantum.QuantumCalculation
 
nXX - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
nY - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
nY - Variable in class org.jmol.quantum.QuantumCalculation
 
nZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
nZ - Variable in class org.jmol.quantum.QuantumCalculation
 

O

o(int, Object) - Static method in class org.jmol.script.T
 
o(String, Object) - Static method in class org.jmol.i18n.GT
 
oabc - Variable in class org.jmol.jvxl.data.VolumeData
 
oabc - Variable in class org.jmol.util.MeshSurface
 
obFreq - Variable in class jspecview.export.AMLExporter
 
obFreq - Variable in class jspecview.export.CMLExporter
 
obFreq - Variable in class jspecview.source.AnIMLReader
 
obj - Static variable in class org.jmol.script.T
 
OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
 
OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
 
object - Static variable in class org.jmol.script.T
 
objectNameParameter(int) - Method in class org.jmol.script.ScriptParam
 
objects - Variable in class org.jmol.shape.TextShape
 
obNucleus - Variable in class jspecview.export.AMLExporter
 
obNucleus - Variable in class jspecview.export.CMLExporter
 
obNucleus - Variable in class jspecview.source.AnIMLReader
 
OBSCURE - Enum constant in enum class jspecview.common.ScriptToken
 
obscureTitleFromUser - Variable in class jspecview.common.JSViewer
 
oc - Variable in class org.jmol.adapter.writers.CMLWriter
 
oc - Variable in class org.jmol.util.JSONWriter
 
OC - Class in javajs.util
A generic output method.
OC() - Constructor for class javajs.util.OC
 
OC(String) - Constructor for class javajs.util.OC
 
occupancies - Variable in class org.jmol.modelset.AtomCollection
 
occupancy - Static variable in class org.jmol.script.T
 
OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
 
OdysseyReader - Class in org.jmol.adapter.readers.spartan
 
OdysseyReader() - Constructor for class org.jmol.adapter.readers.spartan.OdysseyReader
 
off - Static variable in class org.jmol.script.T
 
OFF - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
officialRelease - Static variable in class org.jmol.viewer.JC
 
offset - Static variable in class org.jmol.script.T
 
offset - Variable in class org.jmol.util.MeshSurface
 
offset(BS, int, int) - Static method in class org.jmol.util.BSUtil
offset the bitset in place by the specified number of bits starting at a given position
OFFSET - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
 
offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
 
offsetPt - Variable in class org.jmol.shapespecial.Dipole
 
offsets - Variable in class org.jmol.modelsetbio.Monomer
 
offsets - Variable in class org.jmol.shape.Labels
 
offsetside - Static variable in class org.jmol.script.T
 
offsetSide - Variable in class org.jmol.shapespecial.Dipole
 
offsetX - Variable in class org.jmol.modelset.Text
 
offsetY - Variable in class org.jmol.modelset.Text
 
ok() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
OK - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
OLIVE - Static variable in class org.jmol.util.C
 
omega - Static variable in class org.jmol.script.T
 
on - Static variable in class org.jmol.script.T
 
ON - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
once - Static variable in class org.jmol.script.T
 
ONE_OVER_D - Static variable in class org.jmol.quantum.MepCalculation
 
ONE_OVER_ONE_PLUS_D - Static variable in class org.jmol.quantum.MepCalculation
 
onFailure(Throwable) - Method in class jme.JMEUtil.JSME_RunAsyncCallback
 
onFailure(Throwable) - Method in interface jme.JMEUtil.RunAsyncCallback
Called when, for some reason, the necessary code cannot be loaded.
onFailure(Throwable) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
Called when, for some reason, the necessary code cannot be loaded.
onFocus() - Method in class jspecview.js2d.JsDialog
 
only - Static variable in class org.jmol.script.T
 
onSuccess() - Method in interface jme.JMEUtil.RunAsyncCallback
Called once the necessary code for it has been loaded.
onSuccess(String) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
Called once the necessary code for it has been loaded.
onWarning(String) - Method in interface jme.JMEUtil.RunWhenDataReadyCallback
 
oops(Exception) - Method in class org.jmol.minimize.MinimizationThread
 
oops(Exception) - Method in class org.jmol.navigate.Navigator
 
oops(Exception) - Method in class org.jmol.thread.JmolThread
 
opacityFractionalFromArgb(int) - Static method in class org.jmol.export.___Exporter
 
opacityFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
 
opAnd - Static variable in class org.jmol.script.T
 
opAND - Static variable in class org.jmol.script.T
 
opaque - Static variable in class org.jmol.script.T
 
OPAQUE_MASK - Static variable in class org.jmol.util.C
 
open() - Method in class org.jmol.console.ScriptEditor
 
openAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
 
openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openConnection(URL) - Method in class javajs.util.AjaxURLStreamHandler
 
openDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String) - Method in class jspecview.common.JSViewer
 
openDocument(SB) - Static method in class javajs.util.XmlUtil
 
openDocument(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
 
openDOM(Object) - Method in class org.jmol.api.JmolViewer
 
openDOM(Object) - Method in class org.jmol.viewer.Viewer
applet DOM method -- does not preserve state
openExportChannel(double, String, boolean) - Method in class org.jmol.viewer.Viewer
 
openFile(String) - Method in class jspecview.appletjs.JSVApplet
possibly called from JSmolJSV.js upon start up
openFile(String) - Method in class org.jmol.api.JmolViewer
 
openFile(String) - Method in class org.jmol.util.GenericApplet
possibly called from JSmolApplet.js upon start up
openFile(String) - Method in class org.jmol.viewer.Viewer
for JmolSimpleViewer -- external applications only (and no-script JavaScript)
openFile(String, boolean) - Method in class jspecview.common.JSViewer
Opens and displays a file
openFileAsync(String) - Method in class org.jmol.api.JmolViewer
 
openFileAsync(String, int, String) - Method in interface org.jmol.api.JmolScriptManager
 
openFileAsync(String, int, String) - Method in class org.jmol.script.ScriptManager
From file dropping.
openFileAsyncSpecial(String, int) - Method in interface javajs.api.JSInterface
 
openFileAsyncSpecial(String, int) - Method in class jspecview.appletjs.JSVApplet
 
openFileAsyncSpecial(String, int) - Method in class jspecview.common.JSViewer
 
openFileAsyncSpecial(String, int) - Method in class org.jmol.api.JmolViewer
 
openFileAsyncSpecial(String, int) - Method in class org.jmol.util.GenericApplet
 
openFileAsyncSpecial(String, int) - Method in class org.jmol.viewer.Viewer
opens a file as a model, a script, or a surface via the creation of a script that is queued.
openFileAsyncSpecialType(String, int, String) - Method in interface javajs.api.JSInterface
 
openFileAsyncSpecialType(String, int, String) - Method in class jspecview.appletjs.JSVApplet
 
openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.api.JmolViewer
 
openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.util.GenericApplet
 
openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.viewer.Viewer
 
openFileFromDialog(boolean, boolean, String, String) - Method in class jspecview.common.JSViewer
 
openFiles(String[]) - Method in class org.jmol.api.JmolViewer
 
openFiles(String[]) - Method in class org.jmol.viewer.Viewer
for JmolSimpleViewer -- external applications only
openmolAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenMolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
 
openpdbAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenPdbAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
 
openReader(String, Object) - Method in class org.jmol.api.JmolViewer
Opens the file and creates the model set, given the reader.
openReader(String, String, Object) - Method in class org.jmol.api.JmolViewer
Opens the file and creates the model set, given the reader.
openReader(String, String, Object) - Method in class org.jmol.viewer.Viewer
Opens the file, given an already-created reader.
openSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
openStringInline(String) - Method in class org.jmol.api.JmolViewer
 
openStringInline(String) - Method in class org.jmol.viewer.Viewer
only used by file dropper.
openStringInlineParamsAppend(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
openTag(SB, String) - Static method in class javajs.util.XmlUtil
 
openTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
 
openTagAttr(SB, String, Object[]) - Static method in class javajs.util.XmlUtil
 
openurlAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenUrlAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
opEQ - Static variable in class org.jmol.script.T
 
operations - Variable in class org.jmol.symmetry.SpaceGroup
 
opGE - Static variable in class org.jmol.script.T
 
opGT - Static variable in class org.jmol.script.T
 
opIf - Static variable in class org.jmol.script.T
 
opIsLong - Variable in class org.jmol.symmetry.SymmetryOperation
 
opLE - Static variable in class org.jmol.script.T
 
opLIKE - Static variable in class org.jmol.script.T
 
opLT - Static variable in class org.jmol.script.T
 
opNE - Static variable in class org.jmol.script.T
 
opNot - Static variable in class org.jmol.script.T
 
opOr - Static variable in class org.jmol.script.T
 
oPt - Variable in class org.jmol.script.ScriptMathProcessor
 
OptimadeReader - Class in org.jmol.adapter.readers.xtal
A (preliminary) reader for OPTIMADE resources.
OptimadeReader() - Constructor for class org.jmol.adapter.readers.xtal.OptimadeReader
 
optimize2D - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
optionKey - Variable in class jspecview.dialog.JSVDialog
 
optionKey - Variable in class jspecview.java.AwtDialog
 
optionKey - Variable in class jspecview.js2d.JsDialog
 
options - Variable in class jspecview.common.PanelData
 
options - Variable in class jspecview.dialog.JSVDialog
 
options - Variable in class jspecview.java.AwtDialog
 
options - Variable in class jspecview.js2d.JsDialog
 
options - Static variable in class org.jmol.script.T
 
options - Variable in class org.jmol.shapespecial.Ellipsoid
 
options(String) - Method in class jme.JME
 
optionsSaved - Variable in class jspecview.common.PanelData
 
opToggle - Static variable in class org.jmol.script.T
 
optOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
optParameterAsString(int) - Method in class org.jmol.script.ScriptParam
 
opXor - Static variable in class org.jmol.script.T
 
or(BS) - Method in class javajs.util.BS
Performs a logical OR of this bit set with the bit set argument.
ORANGE - Static variable in class org.jmol.util.C
 
orbital - Static variable in class org.jmol.script.T
 
orbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
Orbitals - Class in org.openscience.jmol.app.webexport
 
Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
 
orbitalsRead - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
orbitalType - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
OrcaReader - Class in org.jmol.adapter.readers.quantum
Reads ORCA input and output files
OrcaReader - Class in org.jmol.adapter.readers.simple
Reads ORCA input and output files
OrcaReader() - Constructor for class org.jmol.adapter.readers.quantum.OrcaReader
 
OrcaReader() - Constructor for class org.jmol.adapter.readers.simple.OrcaReader
 
order - Variable in class org.jmol.adapter.smarter.Bond
 
order - Variable in class org.jmol.minimize.MinBond
 
order - Variable in class org.jmol.util.Edge
 
ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_HEX - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_QUAD - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_QUINT - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PYMOL_MULT - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PYMOL_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_EITHER - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
 
org.apache.tools.bzip2 - package org.apache.tools.bzip2
 
org.jmol.adapter.readers.cif - package org.jmol.adapter.readers.cif
 
org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
 
org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
 
org.jmol.adapter.readers.pdb - package org.jmol.adapter.readers.pdb
 
org.jmol.adapter.readers.pymol - package org.jmol.adapter.readers.pymol
 
org.jmol.adapter.readers.quantum - package org.jmol.adapter.readers.quantum
 
org.jmol.adapter.readers.simple - package org.jmol.adapter.readers.simple
 
org.jmol.adapter.readers.spartan - package org.jmol.adapter.readers.spartan
 
org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
 
org.jmol.adapter.readers.xtal - package org.jmol.adapter.readers.xtal
 
org.jmol.adapter.smarter - package org.jmol.adapter.smarter
 
org.jmol.adapter.writers - package org.jmol.adapter.writers
 
org.jmol.api - package org.jmol.api
 
org.jmol.api.js - package org.jmol.api.js
 
org.jmol.appletjs - package org.jmol.appletjs
 
org.jmol.atomdata - package org.jmol.atomdata
 
org.jmol.awt - package org.jmol.awt
 
org.jmol.awtjs - package org.jmol.awtjs
 
org.jmol.awtjs.swing - package org.jmol.awtjs.swing
 
org.jmol.awtjs2d - package org.jmol.awtjs2d
 
org.jmol.bspt - package org.jmol.bspt
Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
org.jmol.c - package org.jmol.c
 
org.jmol.console - package org.jmol.console
 
org.jmol.consolejs - package org.jmol.consolejs
 
org.jmol.dialog - package org.jmol.dialog
 
org.jmol.dssx - package org.jmol.dssx
 
org.jmol.export - package org.jmol.export
 
org.jmol.g3d - package org.jmol.g3d
Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
org.jmol.geodesic - package org.jmol.geodesic
 
org.jmol.i18n - package org.jmol.i18n
 
org.jmol.image - package org.jmol.image
 
org.jmol.inchi - package org.jmol.inchi
 
org.jmol.io - package org.jmol.io
 
org.jmol.jsv - package org.jmol.jsv
 
org.jmol.jvxl.api - package org.jmol.jvxl.api
 
org.jmol.jvxl.calc - package org.jmol.jvxl.calc
 
org.jmol.jvxl.data - package org.jmol.jvxl.data
 
org.jmol.jvxl.readers - package org.jmol.jvxl.readers
 
org.jmol.minimize - package org.jmol.minimize
 
org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
 
org.jmol.modelkit - package org.jmol.modelkit
 
org.jmol.modelset - package org.jmol.modelset
 
org.jmol.modelsetbio - package org.jmol.modelsetbio
 
org.jmol.multitouch - package org.jmol.multitouch
 
org.jmol.multitouch.jni - package org.jmol.multitouch.jni
 
org.jmol.multitouch.sparshui - package org.jmol.multitouch.sparshui
 
org.jmol.navigate - package org.jmol.navigate
 
org.jmol.popup - package org.jmol.popup
 
org.jmol.quantum - package org.jmol.quantum
 
org.jmol.quantum.mo - package org.jmol.quantum.mo
 
org.jmol.render - package org.jmol.render
 
org.jmol.renderbio - package org.jmol.renderbio
 
org.jmol.rendercgo - package org.jmol.rendercgo
 
org.jmol.renderspecial - package org.jmol.renderspecial
 
org.jmol.rendersurface - package org.jmol.rendersurface
 
org.jmol.script - package org.jmol.script
 
org.jmol.scriptext - package org.jmol.scriptext
 
org.jmol.shape - package org.jmol.shape
 
org.jmol.shapebio - package org.jmol.shapebio
 
org.jmol.shapecgo - package org.jmol.shapecgo
 
org.jmol.shapespecial - package org.jmol.shapespecial
 
org.jmol.shapesurface - package org.jmol.shapesurface
 
org.jmol.smiles - package org.jmol.smiles
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
org.jmol.symmetry - package org.jmol.symmetry
 
org.jmol.thread - package org.jmol.thread
 
org.jmol.translation - package org.jmol.translation
 
org.jmol.util - package org.jmol.util
 
org.jmol.viewer - package org.jmol.viewer
 
org.jmol.viewer.binding - package org.jmol.viewer.binding
 
org.molecularplayground - package org.molecularplayground
 
org.openscience.jmol.app - package org.openscience.jmol.app
 
org.openscience.jmol.app.janocchio - package org.openscience.jmol.app.janocchio
 
org.openscience.jmol.app.jmolpanel - package org.openscience.jmol.app.jmolpanel
 
org.openscience.jmol.app.jmolpanel.console - package org.openscience.jmol.app.jmolpanel.console
 
org.openscience.jmol.app.jsonkiosk - package org.openscience.jmol.app.jsonkiosk
 
org.openscience.jmol.app.surfacetool - package org.openscience.jmol.app.surfacetool
 
org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
 
org.openscience.jvxl - package org.openscience.jvxl
 
org.openscience.jvxl.simplewriter - package org.openscience.jvxl.simplewriter
 
org.qcschema - package org.qcschema
 
orientation - Variable in class org.jmol.modelset.Model
 
orientation - Static variable in class org.jmol.script.T
 
Orientation - Class in org.jmol.modelset
 
Orientation(Viewer, boolean, float[]) - Constructor for class org.jmol.modelset.Orientation
 
origin - Variable in class jspecview.export.AMLExporter
 
origin - Variable in class jspecview.export.CMLExporter
 
origin - Variable in class jspecview.source.JDXHeader
 
origin - Variable in class jspecview.source.AnIMLReader
 
origin - Variable in class org.jmol.jvxl.data.VolumeData
 
origin - Variable in class org.jmol.jvxl.readers.Parameters
 
origin - Static variable in class org.jmol.script.T
 
origin - Variable in class org.jmol.shapespecial.Dipole
 
originBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
originPoint - Variable in class org.jmol.shape.Axes
 
OS_AMIGA - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_ATARI - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_CPM - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_MACOS - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_MSDOS - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_OS2 - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_QDOS - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_RISCOS - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_TOPS20 - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_UNIX - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_UNKNOWN - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_VMCMS - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_VMS - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_WIN32 - Static variable in class com.jcraft.jzlib.GZIPHeader
 
OS_ZSYSTEM - Static variable in class com.jcraft.jzlib.GZIPHeader
 
out - Variable in class javajs.img.ImageEncoder
 
out - Variable in class javajs.util.BinaryDocument
 
out - Variable in class jspecview.export.AMLExporter
 
out - Variable in class jspecview.export.CMLExporter
 
out - Variable in class jspecview.export.SVGExporter
 
out - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
out - Variable in class org.jmol.export.___Exporter
 
out - Variable in class org.jmol.jvxl.readers.JvxlReader
 
out - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
out - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
out - Static variable in class org.jmol.script.T
 
output - Variable in class org.jmol.console.GenericConsole
 
output(String) - Method in class org.jmol.console.ScriptEditor
 
output(String) - Method in class org.jmol.export.___Exporter
 
output(String) - Method in class org.jmol.export._StlExporter
 
output(String) - Method in class org.jmol.util.GenericApplet
 
output(T3) - Method in class org.jmol.export.___Exporter
 
output(T3) - Method in class org.jmol.export._IdtfExporter
 
output(T3) - Method in class org.jmol.export._MayaExporter
 
output(T3) - Method in class org.jmol.export._ObjExporter
 
output(T3) - Method in class org.jmol.export._PovrayExporter
 
output(T3) - Method in class org.jmol.export._TachyonExporter
 
output(T3) - Method in class org.jmol.export._VrmlExporter
 
output(T3) - Method in class org.jmol.export.JSExporter
 
outputAppearance(short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputAppearance(short, boolean) - Method in class org.jmol.export._X3dExporter
 
outputAttr(String, float, float, float) - Method in class org.jmol.export._StlExporter
 
outputAttr(String, float, float, float) - Method in class org.jmol.export._VrmlExporter
 
outputAttr(String, float, float, float) - Method in class org.jmol.export._X3dExporter
 
outputAttrPt(String, T3) - Method in class org.jmol.export._StlExporter
 
outputAttrPt(String, T3) - Method in class org.jmol.export._VrmlExporter
 
outputAttrPt(String, T3) - Method in class org.jmol.export._X3dExporter
 
outputBuffer - Variable in class org.jmol.script.ScriptContext
 
outputBuffer - Variable in class org.jmol.script.ScriptEval
 
outputBytes(byte[]) - Method in class javajs.util.AjaxURLConnection
 
outputChildClose() - Method in class org.jmol.export._StlExporter
 
outputChildClose() - Method in class org.jmol.export._VrmlExporter
 
outputChildClose() - Method in class org.jmol.export._X3dExporter
 
outputChildShapeClose() - Method in class org.jmol.export._VrmlExporter
 
outputChildShapeClose() - Method in class org.jmol.export._X3dExporter
 
outputChildShapeStart() - Method in class org.jmol.export._VrmlExporter
 
outputChildShapeStart() - Method in class org.jmol.export._X3dExporter
 
outputChildStart() - Method in class org.jmol.export._StlExporter
 
outputChildStart() - Method in class org.jmol.export._VrmlExporter
 
outputChildStart() - Method in class org.jmol.export._X3dExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._StlExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._X3dExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
 
outputCloseTag() - Method in class org.jmol.export._VrmlExporter
 
outputCloseTag() - Method in class org.jmol.export._X3dExporter
 
outputColorIndices(int[][], int, BS, int, Map<Short, Integer>, short[], short[]) - Method in class org.jmol.export._VrmlExporter
 
outputColors(Lst<Short>) - Method in class org.jmol.export._VrmlExporter
 
outputComment(String) - Method in class org.jmol.export.___Exporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export.__CartesianExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._IdtfExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._MayaExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._VrmlExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export.JSExporter
 
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._MayaExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._ObjExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.JSExporter
 
outputCylinderChildScaled(short, byte) - Method in class org.jmol.export._VrmlExporter
 
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._PovrayExporter
 
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._TachyonExporter
 
outputDefChildFaceSet(String) - Method in class org.jmol.export._VrmlExporter
 
outputDefChildFaceSet(String) - Method in class org.jmol.export._X3dExporter
 
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._PovrayExporter
 
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._TachyonExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.__CartesianExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._IdtfExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._MayaExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._ObjExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._VrmlExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.JSExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export.__CartesianExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._IdtfExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._MayaExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._ObjExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._VrmlExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export.JSExporter
 
outputFaceSetClose() - Method in class org.jmol.export._VrmlExporter
 
outputFaceSetClose() - Method in class org.jmol.export._X3dExporter
 
outputFaceSetStart() - Method in class org.jmol.export._VrmlExporter
 
outputFaceSetStart() - Method in class org.jmol.export._X3dExporter
 
outputFileName - Variable in class org.jmol.dialog.Dialog
 
outputFooter() - Method in class org.jmol.export.___Exporter
 
outputFooter() - Method in class org.jmol.export._IdtfExporter
 
outputFooter() - Method in class org.jmol.export._TachyonExporter
 
outputFooter() - Method in class org.jmol.export._VrmlExporter
 
outputFooter() - Method in class org.jmol.export._X3dExporter
 
outputFooter() - Method in class org.jmol.export.JSExporter
 
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._StlExporter
 
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
 
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._X3dExporter
 
outputHeader() - Method in class org.jmol.export.___Exporter
 
outputHeader() - Method in class org.jmol.export._IdtfExporter
 
outputHeader() - Method in class org.jmol.export._MayaExporter
 
outputHeader() - Method in class org.jmol.export._ObjExporter
 
outputHeader() - Method in class org.jmol.export._PovrayExporter
 
outputHeader() - Method in class org.jmol.export._StlExporter
 
outputHeader() - Method in class org.jmol.export._TachyonExporter
 
outputHeader() - Method in class org.jmol.export._VrmlExporter
 
outputHeader() - Method in class org.jmol.export._X3dExporter
 
outputHeader() - Method in class org.jmol.export.JSExporter
 
outputIndices(int[][], int[], int, BS, int) - Method in class org.jmol.export.__CartesianExporter
 
outputInitialTransform() - Method in class org.jmol.export._VrmlExporter
 
outputJmolPerspective() - Method in class org.jmol.export.___Exporter
 
OutputManagerAwt - Class in org.jmol.viewer
 
OutputManagerAwt() - Constructor for class org.jmol.viewer.OutputManagerAwt
 
OutputManagerJS - Class in org.jmol.viewer
 
OutputManagerJS() - Constructor for class org.jmol.viewer.OutputManagerJS
 
outputNormals(Lst<String>) - Method in class org.jmol.export._VrmlExporter
 
outputQuaternionFrame(P3, P3, P3, P3, float, float, float) - Method in class org.jmol.export._VrmlExporter
 
outputRotation(A4) - Method in class org.jmol.export._StlExporter
 
outputRotation(A4) - Method in class org.jmol.export._VrmlExporter
 
outputRotation(A4) - Method in class org.jmol.export._X3dExporter
 
outputShapeClose() - Method in class org.jmol.export._VrmlExporter
 
outputShapeClose() - Method in class org.jmol.export._X3dExporter
 
outputShapeStart() - Method in class org.jmol.export._VrmlExporter
 
outputShapeStart() - Method in class org.jmol.export._X3dExporter
 
outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export.__CartesianExporter
 
outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export._VrmlExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._TachyonExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
 
outputString(String) - Method in class javajs.util.AjaxURLConnection
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.___Exporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._IdtfExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._MayaExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._PovrayExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._TachyonExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.JSExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._TachyonExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export.__CartesianExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._IdtfExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._MayaExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._ObjExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._VrmlExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._X3dExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export.JSExporter
 
outputToFile(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
 
outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
outputTransRot(P3, P3, int, int, int) - Method in class org.jmol.export._VrmlExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__CartesianExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._IdtfExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._MayaExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._PovrayExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._TachyonExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._X3dExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.JSExporter
 
outputUseChildClose(String) - Method in class org.jmol.export._VrmlExporter
 
outputUseChildClose(String) - Method in class org.jmol.export._X3dExporter
 
outputVertex(T3, T3) - Method in class org.jmol.export.___Exporter
 
outputVertex(T3, T3) - Method in class org.jmol.export._PovrayExporter
 
outputVertex(T3, T3) - Method in class org.jmol.export._TachyonExporter
 
outputVertices(T3[], int, T3) - Method in class org.jmol.export.___Exporter
 
outSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
OUTSOCKET - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OUTSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
oValue(Object) - Static method in class org.jmol.script.SV
 
overlaps(double, double) - Method in class jspecview.common.Measurement
 
OVERLAY - Enum constant in enum class jspecview.common.ScriptToken
 
OVERLAY_DIALOG - Static variable in class jspecview.common.JSViewer
 
OVERLAY_OFFSET - Static variable in class jspecview.common.JSViewer
 
OverlayLegend - Enum constant in enum class jspecview.common.Annotation.AType
 
OverlayLegendDialog - Class in jspecview.dialog
Dialog for showing the legend or key for overlaid plots in a JSVPanel.
OverlayLegendDialog() - Constructor for class jspecview.dialog.OverlayLegendDialog
 
OVERLAYSTACKED - Enum constant in enum class jspecview.common.ScriptToken
 
owner - Variable in class jspecview.export.AMLExporter
 
owner - Variable in class jspecview.export.CMLExporter
 
owner - Variable in class jspecview.source.JDXHeader
 
owner - Variable in class jspecview.source.AnIMLReader
 

P

P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
P - Static variable in class org.jmol.quantum.QS
 
P_CHECK - Static variable in class org.jmol.util.MeshSurface
 
P_CONTOUR - Static variable in class org.jmol.util.MeshSurface
 
P_EXPLICIT_COLOR - Static variable in class org.jmol.util.MeshSurface
 
P2nReader - Class in org.jmol.adapter.readers.pdb
P2N file reader.
P2nReader() - Constructor for class org.jmol.adapter.readers.pdb.P2nReader
 
P3 - Class in javajs.util
A 3 element point that is represented by single precision floating point x,y,z coordinates.
P3() - Constructor for class javajs.util.P3
 
P3i - Class in javajs.util
A 3 element point that is represented by signed integer x,y,z coordinates.
P3i() - Constructor for class javajs.util.P3i
 
p3Screens - Variable in class org.jmol.render.AxesRenderer
 
p3Screens - Variable in class org.jmol.render.BbcageRenderer
 
p3Screens - Variable in class org.jmol.render.UccageRenderer
 
p3Screens - Variable in class org.jmol.render.MeshRenderer
 
P4 - Class in javajs.util
A 4 element point that is represented by single precision floating point x,y,z,w coordinates.
P4() - Constructor for class javajs.util.P4
 
PAC - Enum constant in enum class jspecview.common.ExportType
 
pack() - Method in interface jspecview.api.PlatformDialog
 
pack() - Method in class org.jmol.awtjs.swing.JDialog
 
packageJSON(String, String) - Static method in class javajs.util.PT
 
packed - Static variable in class org.jmol.script.T
 
PAGE_EXISTS - Static variable in class jspecview.common.JSViewer
 
paint(Graphics) - Method in class jme.JME
 
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
paintComponent(Graphics) - Method in class jspecview.java.AwtPanel
Overrides paintComponent in class JPanel in order to draw the spectrum
paintComponent(Object) - Method in interface jspecview.api.JSVPanel
 
paintComponent(Object) - Method in class jspecview.java.AwtPanel
 
paintComponent(Object) - Method in class jspecview.js2d.JsPanel
Overrides paintComponent in class JPanel in order to draw the spectrum
paintMolecularArea(BufferedImage) - Method in class jme.JME
 
PAL - Enum Class in org.jmol.c
Enum for animation mode.
PALETTE_ALTLOC - Static variable in enum class org.jmol.c.PAL
 
PALETTE_AMINO - Static variable in enum class org.jmol.c.PAL
 
PALETTE_CHAIN - Static variable in enum class org.jmol.c.PAL
 
PALETTE_CPK - Static variable in enum class org.jmol.c.PAL
 
PALETTE_ENERGY - Static variable in enum class org.jmol.c.PAL
 
PALETTE_FIXEDTEMP - Static variable in enum class org.jmol.c.PAL
 
PALETTE_FORMAL_CHARGE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_GROUP - Static variable in enum class org.jmol.c.PAL
 
PALETTE_INSERTION - Static variable in enum class org.jmol.c.PAL
 
PALETTE_JMOL - Static variable in enum class org.jmol.c.PAL
 
PALETTE_MOLECULE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_MONOMER - Static variable in enum class org.jmol.c.PAL
 
PALETTE_NONE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_NUCLEIC - Static variable in enum class org.jmol.c.PAL
 
PALETTE_PARTIAL_CHARGE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_POLYMER - Static variable in enum class org.jmol.c.PAL
 
PALETTE_PROPERTY - Static variable in enum class org.jmol.c.PAL
 
PALETTE_RASMOL - Static variable in enum class org.jmol.c.PAL
 
PALETTE_SHAPELY - Static variable in enum class org.jmol.c.PAL
 
PALETTE_STRAIGHTNESS - Static variable in enum class org.jmol.c.PAL
 
PALETTE_STRUCTURE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_SURFACE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_TEMP - Static variable in enum class org.jmol.c.PAL
 
PALETTE_TYPE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_VARIABLE - Static variable in enum class org.jmol.c.PAL
 
PALETTE_VOLATILE - Static variable in enum class org.jmol.c.PAL
 
paletteID - Variable in class org.jmol.modelset.Atom
 
paletteIDs - Variable in class org.jmol.shape.AtomShape
 
palindrome - Static variable in class org.jmol.script.T
 
panel() - Method in class org.openscience.jmol.app.webexport.Test
 
PanelData - Class in jspecview.common
JSVPanel class draws a plot from the data contained a instance of a Graph.
PanelData(JSVPanel, JSViewer) - Constructor for class jspecview.common.PanelData
 
PanelData.LinkMode - Enum Class in jspecview.common
 
panelEvent(Object) - Method in interface jspecview.api.PanelListener
 
panelEvent(Object) - Method in class jspecview.app.JSVApp
called by notifyPeakPickedListeners in JSVPanel
panelEvent(Object) - Method in class jspecview.application.MainFrame
 
PanelListener - Interface in jspecview.api
 
panelNode - Variable in class jspecview.application.AwtTreeNode
 
panelNode - Variable in class jspecview.tree.SimpleTreeNode
 
PanelNode - Class in jspecview.common
 
PanelNode(String, String, JDXSource, JSVPanel) - Constructor for class jspecview.common.PanelNode
 
panelNodes - Variable in class jspecview.common.JSViewer
 
paper - Variable in class jspecview.common.PrintLayout
The size of the paper to be printed on
paperHeight - Variable in class jspecview.common.PrintLayout
 
paperWidth - Variable in class jspecview.common.PrintLayout
 
parabolicInterpolation(Coordinate[], int) - Static method in class jspecview.common.Coordinate
see https://ccrma.stanford.edu/~jos/sasp/Quadratic_Interpolation_Spectral_Peaks.html
parallel - Static variable in class org.jmol.script.T
 
PARAM_COUNT - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_M33 - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_M4 - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_OXYZ - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_SCALE - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_SLOP - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_STD - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_SUPERCELL - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_VAX - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_VBX - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_VCX - Static variable in class org.jmol.util.SimpleUnitCell
 
PARAM_VCZ - Static variable in class org.jmol.util.SimpleUnitCell
 
paramAsStr(int) - Method in class org.jmol.script.ScriptParam
 
paramAsStr(int) - Method in class org.jmol.scriptext.ScriptExt
 
parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptEval
 
parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptEval
 
parameterExpressionSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptEval
 
parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptEval
 
parameterExpressionToken(int) - Method in class org.jmol.script.ScriptEval
 
parameters - Variable in class jspecview.common.JSViewer
 
parameters - Static variable in class org.jmol.script.T
 
Parameters - Class in jspecview.common
 
Parameters - Class in org.jmol.jvxl.readers
 
Parameters() - Constructor for class jspecview.common.Parameters
 
Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
 
params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
params - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
params(int, int) - Method in class com.jcraft.jzlib.Deflater
 
paramsCentroid - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
paramsLattice - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
paramTypes - Static variable in class org.jmol.script.T
 
parBorU - Variable in class org.jmol.util.Tensor
 
parent - Variable in class jspecview.source.JDXDataObject
 
parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
parent - Variable in class org.jmol.awtjs.swing.Component
 
parentContext - Variable in class org.jmol.script.ScriptContext
 
parse(String, boolean) - Method in class javajs.util.JSJSONParser
Could return Integer, Float, Boolean, String, Mapinvalid input: '<'String, Object>, Lst, or null
parseCartesianField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
 
parseCartesianField() - Method in class org.jmol.adapter.readers.cif.CifReader
 
parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
 
parseDataBlockParameters(String[], String, String, int[], int[]) - Method in interface javajs.api.GenericCifDataParser
 
parseDataBlockParameters(String[], String, String, int[], int[]) - Method in class javajs.util.CifDataParser
Process a data block, with or without a loop_.
parsedContext - Variable in class org.jmol.console.ScriptEditor
 
parsedData - Variable in class org.jmol.console.ScriptEditor
 
parseDSV(String, double, double) - Static method in class jspecview.common.Coordinate
Parses data stored in x, y format
parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat() - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseFloat() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseFloat() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseFloat(String) - Static method in class javajs.util.PT
 
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseFloatArray(String) - Static method in class javajs.util.PT
 
parseFloatArrayBsData(String[], BS, float[]) - Static method in class org.jmol.util.Parser
 
parseFloatArrayData(String[], float[]) - Static method in class javajs.util.PT
parses a string array for floats.
parseFloatArrayDataN(String[], float[], int) - Static method in class javajs.util.PT
parses a string array for floats.
parseFloatArrayFromMatchAndField(String, BS, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
the major lifter here.
parseFloatArrayInfested(String[], float[]) - Static method in class javajs.util.PT
 
parseFloatArrayNext(String, int[], float[], String, String) - Static method in class javajs.util.PT
 
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseFloatChecked(String, int, int[], boolean) - Static method in class javajs.util.PT
A float parser that is 30% faster than Float.parseFloat(x) and also accepts x.yD+-n
parseFloatField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
 
parseFloatField() - Method in class org.jmol.adapter.readers.cif.CifReader
 
parseFloatFraction(String) - Static method in class javajs.util.PT
parse a float or "float/float"
parseFloatNext(String, int[]) - Static method in class javajs.util.PT
 
parseFloatRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseFloatRange(String, int, int[]) - Static method in class javajs.util.PT
 
parseFloatStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseFloatStrict(String) - Static method in class javajs.util.PT
 
parseInitScript(String) - Method in class jspecview.common.JSViewer
Parses the JavaScript call parameters and executes them accordingly
parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt() - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseInt() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseInt() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseInt(String) - Static method in class javajs.util.PT
 
parseIntAt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseIntChecked(String, int, int[]) - Static method in class javajs.util.PT
 
parseIntField() - Method in class org.jmol.adapter.readers.cif.BCIFReader
 
parseIntField() - Method in class org.jmol.adapter.readers.cif.CifReader
 
parseIntFieldTok(byte) - Method in class org.jmol.adapter.readers.cif.BCIFReader
Get a specific column's item for this category on this row.
parseIntFieldTok(byte) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
parseIntNext(String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseIntNext(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseIntNext(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseIntNext(String, int[]) - Static method in class javajs.util.PT
 
parseIntRadix(String, int) - Static method in class javajs.util.PT
 
parseIntRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseIntRange(String, int, int[]) - Static method in class javajs.util.PT
 
parseIntStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseIntStr(String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
parseIntStr(String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
parseIntStr(String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
parseJSON(String) - Method in class org.jmol.viewer.Viewer
 
parseJSONArray(String) - Method in class org.jmol.viewer.Viewer
 
parseJSONMap(String) - Method in class org.jmol.viewer.Viewer
 
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.BCIFReader
This is the callback the that the MMCifReader and CifReader process.....() methods call initially.
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
sets up arrays and variables for tokenizer.getData() after the first tag of the loop has been checked.
parseMap(String, boolean) - Method in class javajs.util.JSJSONParser
requires { "key":"value", "key":"value",....}
parsePrecision(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
Track the precision (count of y digits in "xx.yyyy") for setting cellSlop.
parser - Variable in class jspecview.source.AnIMLReader
 
Parser - Class in org.jmol.util
 
Parser() - Constructor for class org.jmol.util.Parser
 
parseScript(String, int) - Method in class org.jmol.console.ScriptEditor
 
parseStringInfestedFloatArray(String, BS, float[]) - Static method in class org.jmol.util.Parser
parses a "dirty" string for floats.
parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseToken(String) - Static method in class javajs.util.PT
 
parseTokenChecked(String, int, int[]) - Static method in class javajs.util.PT
 
parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTokenNext(String, int[]) - Static method in class javajs.util.PT
 
parseTokenRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTokenRange(String, int, int[]) - Static method in class javajs.util.PT
 
parseTokenStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTrimmed(String) - Static method in class javajs.util.PT
 
parseTrimmedAt(String, int) - Static method in class javajs.util.PT
 
parseTrimmedChecked(String, int, int) - Static method in class javajs.util.PT
 
parseTrimmedRange(String, int, int) - Static method in class javajs.util.PT
 
PARTIAL_CHARGE - Enum constant in enum class org.jmol.c.PAL
 
PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
 
PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JC
 
partialcharge - Static variable in class org.jmol.script.T
 
partialCharge - Variable in class org.jmol.adapter.smarter.Atom
 
partialCharge - Variable in class org.jmol.minimize.MinAtom
 
partialdots - Static variable in class org.jmol.script.T
 
particleradius - Static variable in class org.jmol.script.T
 
pass2Flag01 - Variable in class org.jmol.g3d.Graphics3D
 
pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PasteClipboardAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
 
pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
path - Static variable in class org.jmol.script.T
 
path - Static variable in class org.openscience.jmol.app.janocchio.Nmr
 
PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
AtomSetCollectionReader.readData() will close any BufferedReader
PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
pathforallfiles - Static variable in class org.jmol.script.T
 
pathlength - Variable in class jspecview.export.AMLExporter
 
pathlength - Variable in class jspecview.export.CMLExporter
 
pathlength - Variable in class jspecview.source.AnIMLReader
 
pattern - Static variable in class org.jmol.script.T
 
PatternMatcher - Class in org.jmol.util
 
PatternMatcher() - Constructor for class org.jmol.util.PatternMatcher
 
PatternMatcher.JSPattern - Class in org.jmol.util
Super-simplified for JavaScript
pause - Static variable in class org.jmol.script.T
 
pauseExecution(boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
pauseExecution(boolean) - Method in class org.jmol.script.ScriptEval
 
pauseScript(Viewer, boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
 
pbuf - Variable in class org.jmol.g3d.Graphics3D
 
pbufT - Variable in class org.jmol.g3d.Graphics3D
 
pc - Variable in class org.jmol.script.ScriptContext
 
pc - Variable in class org.jmol.script.ScriptEval
 
pc - Variable in class org.jmol.util.MeshSurface
polygon count
pc0 - Variable in class org.jmol.script.ScriptContext
 
pcEnd - Variable in class org.jmol.script.ScriptContext
 
pcResume - Variable in class org.jmol.script.ScriptEval
 
pcs - Variable in class org.jmol.util.MeshSurface
polygon color index "colix" array
pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
pd - Variable in class jspecview.app.GenericMouse
 
pd() - Method in class jspecview.common.JSViewer
 
pd() - Method in class jspecview.common.PanelNode
 
pdb - Static variable in class org.jmol.script.T
 
PDB_ANNOTATIONS - Static variable in class org.jmol.viewer.JC
 
PDB_CARTOONS - Static variable in interface org.jmol.api.JmolScriptManager
 
pdbaddhydrogens - Static variable in class org.jmol.script.T
 
pdbBondInfo - Static variable in class org.jmol.modelsetbio.BioResolver
pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid.
pdbgetheader - Static variable in class org.jmol.script.T
 
pdbheader - Static variable in class org.jmol.script.T
 
pdbID - Variable in class org.jmol.adapter.readers.cif.CifReader
 
pdbID - Variable in class org.jmol.modelset.Model
 
PdbReader - Class in org.jmol.adapter.readers.pdb
PDB file reader.
PdbReader() - Constructor for class org.jmol.adapter.readers.pdb.PdbReader
 
pdbsequential - Static variable in class org.jmol.script.T
 
PDBWriter - Class in org.jmol.adapter.writers
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
PDBWriter() - Constructor for class org.jmol.adapter.writers.PDBWriter
 
PDF - Enum constant in enum class jspecview.common.ExportType
 
PDFCreator - Class in javajs.export
 
PDFCreator() - Constructor for class javajs.export.PDFCreator
 
PdfEncoder - Class in javajs.img
A relatively primitive PDF generator that just makes a document with an image in it.
PdfEncoder() - Constructor for class javajs.img.PdfEncoder
 
PDFWriter - Class in jspecview.common
A class that creates the PDF document specific to JSpecView using javajs.export.PDFCreator.
PDFWriter() - Constructor for class jspecview.common.PDFWriter
 
PEAK - Enum constant in enum class jspecview.common.ScriptToken
 
PEAKCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
 
peakCount - Variable in class jspecview.source.JDXSource
 
PeakData - Class in jspecview.common
a data structure for peak lists
PeakData(Annotation.AType, Spectrum) - Constructor for class jspecview.common.PeakData
 
PeakInfo - Class in jspecview.common
 
PeakInfo() - Constructor for class jspecview.common.PeakInfo
 
PeakInfo(String) - Constructor for class jspecview.common.PeakInfo
 
PeakList - Enum constant in enum class jspecview.common.Annotation.AType
 
PEAKLIST - Enum constant in enum class jspecview.common.ScriptToken
 
PeakListDialog - Class in jspecview.dialog
Dialog for managing the peak listing for a Spectrum within a GraphSet
PeakListDialog() - Constructor for class jspecview.dialog.PeakListDialog
 
peakListInterpolation - Variable in class jspecview.common.Parameters
 
peakListThreshold - Variable in class jspecview.common.Parameters
 
PeakPickEvent - Class in jspecview.common
 
PeakPickEvent(Object, Coordinate, PeakInfo) - Constructor for class jspecview.common.PeakPickEvent
 
peakTabColor - Variable in class jspecview.common.PanelData
 
PEAKTABCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
peakTabsOn - Variable in class jspecview.common.PanelData
 
PEAKTABSON - Enum constant in enum class jspecview.common.ScriptToken
 
peek() - Method in class jspecview.source.XMLParser
 
peekToken() - Method in interface javajs.api.GenericCifDataParser
 
peekToken() - Method in class javajs.util.CifDataParser
Just look at the next token.
per - Static variable in class org.jmol.script.T
 
percent - Static variable in class org.jmol.script.T
 
percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
 
percentvdwatom - Static variable in class org.jmol.script.T
 
period - Static variable in class org.jmol.script.T
 
PeriodicVolumeFileReader - Class in org.jmol.jvxl.readers
 
PeriodicVolumeFileReader() - Constructor for class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
perpendicular - Static variable in class org.jmol.script.T
 
perper - Static variable in class org.jmol.script.T
 
perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
perspectivedepth - Static variable in class org.jmol.script.T
 
perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
 
perspectivemodel - Static variable in class org.jmol.script.T
 
perspectiveModel - Variable in class org.jmol.viewer.TransformManager
 
perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
 
perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
 
PfaatBinding - Class in org.jmol.viewer.binding
 
PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
 
phase - Static variable in class org.jmol.script.T
 
phi - Static variable in class org.jmol.script.T
 
phongexponent - Static variable in class org.jmol.script.T
 
PhosphorusMonomer - Class in org.jmol.modelsetbio
 
PhosphorusMonomer() - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
 
PhosphorusPolymer - Class in org.jmol.modelsetbio
 
PICK - Enum constant in enum class org.jmol.c.CBK
 
PICK_COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
 
pickedMesh - Variable in class org.jmol.shape.MeshCollection
 
pickedModel - Variable in class org.jmol.shape.MeshCollection
 
pickedPt - Variable in class org.jmol.shape.MeshCollection
 
pickedVertex - Variable in class org.jmol.shape.MeshCollection
 
picking - Static variable in class org.jmol.script.T
 
PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_LIGAND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MODEL - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MK_RESET - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SYMOP - Static variable in class org.jmol.viewer.ActionManager
 
pickingspinrate - Static variable in class org.jmol.script.T
 
pickingstyle - Static variable in class org.jmol.script.T
 
PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
picking styles
PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
 
picklabel - Static variable in class org.jmol.script.T
 
pidOf(Object) - Static method in enum class org.jmol.c.PAL
 
ping() - Method in class jme.JME
 
PINK - Static variable in class org.jmol.util.C
 
pis - Variable in class org.jmol.util.MeshSurface
polygon indexes
pivot - Static variable in class org.jmol.script.T
 
pivot2 - Static variable in class org.jmol.script.T
 
pixelLocation(Location) - Static method in class com.sparshui.common.Location
 
pixels - Variable in class javajs.img.ImageEncoder
 
PLAIN_MESSAGE - Static variable in class jspecview.dialog.DialogManager
 
planarparam - Static variable in class org.jmol.script.T
 
plane - Static variable in class org.jmol.script.T
 
PLANE - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
planeParameter(int, boolean) - Method in class org.jmol.script.ScriptParam
 
planeValue(T) - Method in class org.jmol.script.ScriptParam
 
Platform - Class in org.jmol.awt
 
Platform - Class in org.jmol.awtjs
WebGL interface
Platform - Class in org.jmol.awtjs2d
JavaScript 2D canvas version requires Ajax-based URL stream processing.
Platform() - Constructor for class org.jmol.awt.Platform
 
Platform() - Constructor for class org.jmol.awtjs.Platform
 
Platform() - Constructor for class org.jmol.awtjs2d.Platform
 
PlatformDialog - Interface in jspecview.api
 
platformspeed - Static variable in class org.jmol.script.T
 
PlatformViewer - Interface in org.jmol.api
 
play - Static variable in class org.jmol.script.T
 
playAudio(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
 
playAudio(JSmolAppletObject, Map<String, Object>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
 
playAudio(Viewer, Map<String, Object>) - Method in class org.jmol.util.JmolAudio
WAV only for application
playrev - Static variable in class org.jmol.script.T
 
plLabel - Variable in class jspecview.source.AnIMLReader
 
plot - Static variable in class org.jmol.script.T
 
plot3d - Static variable in class org.jmol.script.T
 
Plot3D - Class in org.jmol.shapesurface
 
Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
 
Plot3DRenderer - Class in org.jmol.rendersurface
 
Plot3DRenderer() - Constructor for class org.jmol.rendersurface.Plot3DRenderer
 
plotAreaColor - Variable in class jspecview.common.PanelData
 
PLOTAREACOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
PLOTCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
plotColors - Variable in class jspecview.common.ColorParameters
 
PLOTCOLORS - Enum constant in enum class jspecview.common.ScriptToken
 
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.util.GData
 
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in interface org.jmol.api.JmolRendererInterface
 
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.export.Export3D
 
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClippedP3i(P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
plotPixelClippedP3i(P3i) - Method in class org.jmol.export.Export3D
 
plotPixelClippedP3i(P3i) - Method in class org.jmol.g3d.Graphics3D
 
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.util.GData
 
pluginFile - Variable in class org.openscience.jmol.app.JmolApp
 
pluginFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
plus - Static variable in class org.jmol.script.T
 
plusPlus - Static variable in class org.jmol.script.T
 
pmesh - Static variable in class org.jmol.script.T
 
Pmesh - Class in org.jmol.shapesurface
 
Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
 
PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.viewer.FileManager
 
PmeshRenderer - Class in org.jmol.rendersurface
 
PmeshRenderer() - Constructor for class org.jmol.rendersurface.PmeshRenderer
 
PMeshWriter - Class in org.jmol.shapesurface
A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
PMeshWriter() - Constructor for class org.jmol.shapesurface.PMeshWriter
 
PNG - Enum constant in enum class jspecview.common.ExportType
 
pngBytes - Variable in class javajs.img.PngEncoder
 
PngEncoder - Class in javajs.img
Modified by Bob Hanson hansonr@stolaf.edu to be a subclass of ImageEncoder and to use javajs.util.OutputChannel instead of just returning bytes.
PngEncoder() - Constructor for class javajs.img.PngEncoder
 
pngjCache - Variable in class org.jmol.viewer.FileManager
 
PO - Class in org.jmol.translation
Just a marker for resourceClass.getClass().getResource(resourceName); Jmol now reads the PO files directly for its translations.
PO() - Constructor for class org.jmol.translation.PO
 
pocket - Static variable in class org.jmol.script.T
 
point - Static variable in class org.jmol.script.T
 
POINT - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
point3f - Static variable in class org.jmol.script.T
 
Point3fi - Class in org.jmol.util
the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points)
Point3fi() - Constructor for class org.jmol.util.Point3fi
 
point4f - Static variable in class org.jmol.script.T
 
pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pointer - Variable in class org.jmol.modelset.Text
 
pointerPt - Variable in class org.jmol.modelset.Text
 
pointgroup - Static variable in class org.jmol.script.T
 
pointGroup - Variable in class org.jmol.modelset.AtomCollection
 
pointgroupdistancetolerance - Static variable in class org.jmol.script.T
 
pointgrouplineartolerance - Static variable in class org.jmol.script.T
 
PointIterator - Class in org.jmol.bspt
 
PointIterator() - Constructor for class org.jmol.bspt.PointIterator
 
pointPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d, boolean) - Static method in class org.jmol.minimize.Util
calculates angle of a to plane bcd, returning a value > pi/2 in highly distorted trigonal pyramidal situations
points - Variable in class org.jmol.jvxl.readers.Parameters
 
points - Variable in class org.jmol.modelset.MeasurementData
 
points - Variable in class org.jmol.quantum.QuantumCalculation
 
pointScale - Variable in class org.jmol.shapespecial.Polyhedron
 
pointSize - Variable in class org.jmol.jvxl.data.JvxlData
 
pointSize - Variable in class org.jmol.jvxl.readers.Parameters
 
POINTSONLY - Enum constant in enum class jspecview.common.ScriptToken
 
pointsperangstrom - Static variable in class org.jmol.script.T
 
pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
 
pointT - Variable in class org.jmol.render.FontLineShapeRenderer
 
pointT2 - Variable in class org.jmol.render.FontLineShapeRenderer
 
pointT3 - Variable in class org.jmol.render.FontLineShapeRenderer
 
polarnitro - Variable in class jme.JME
 
polygon - Static variable in class org.jmol.script.T
 
POLYGON - Enum constant in enum class org.jmol.shapespecial.Draw.EnumDrawType
 
polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
 
polygonCount0 - Variable in class org.jmol.util.MeshSurface
 
polyhedra - Static variable in class org.jmol.script.T
 
Polyhedra - Class in org.jmol.shapespecial
 
Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
 
POLYHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
 
PolyhedraRenderer - Class in org.jmol.renderspecial
 
PolyhedraRenderer() - Constructor for class org.jmol.renderspecial.PolyhedraRenderer
 
Polyhedron - Class in org.jmol.shapespecial
 
polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
 
polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
 
polyhedronStereo - Variable in class org.jmol.smiles.SmilesSearch
indicates that we have [XxPHn] with no connected atoms
polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in class org.jmol.smiles.SmilesMatcher
Generate a topological SMILES string from a set of faces
polymer - Static variable in class org.jmol.script.T
 
POLYMER - Enum constant in enum class org.jmol.c.PAL
 
polymerlength - Static variable in class org.jmol.script.T
 
polySmiles - Variable in class org.jmol.shapespecial.Polyhedron
 
polySmilesCenter - Variable in class org.jmol.smiles.SmilesGenerator
 
pop - Static variable in class org.jmol.script.T
 
popHoldRepaint(boolean, String) - Method in interface org.jmol.api.JmolRepaintManager
 
popHoldRepaint(boolean, String) - Method in class org.jmol.render.RepaintManager
 
popHoldRepaint(String) - Method in class org.jmol.api.JmolViewer
 
popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
 
popMatrix() - Method in class org.jmol.export._StlExporter
 
popMatrix() - Method in class org.jmol.export._VrmlExporter
 
popMatrix() - Method in class org.jmol.export._X3dExporter
 
popStack(int) - Method in class org.jmol.viewer.StateManager
Remove the last item on the specified stack, and save the current state to the other stack provided that state is not null.
popState() - Method in class org.jmol.util.CommandHistory
 
popState() - Method in class org.jmol.viewer.Viewer
 
populateVariables() - Method in class jspecview.source.AnIMLReader
 
populationDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
PopulationDisplay - Class in org.openscience.jmol.app.janocchio
 
PopulationDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.PopulationDisplay
Constructor
PopupHelper - Interface in org.jmol.popup
 
popupMenu - Variable in class org.jmol.popup.GenericPopup
 
PopupResource - Class in org.jmol.popup
 
PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
 
port - Variable in class org.openscience.jmol.app.JmolApp
The data model.
port - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
PORTRAIT - Static variable in class jspecview.common.JSViewer
 
position - Variable in class jspecview.common.PrintLayout
The position of the graph on the paper ("center", "default", "fit to page")
postByteArray(String, byte[]) - Method in interface javajs.api.BytePoster
 
postByteArray(String, byte[]) - Static method in class jspecview.common.JSVFileManager
 
postByteArray(String, byte[]) - Method in class jspecview.common.JSViewer
 
postByteArray(String, byte[]) - Method in class org.jmol.viewer.FileManager
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PovrayAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
 
povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
A dialog for controling the creation of a povray input file from a Chemframe and a display.
PovrayDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
Creates a dialog for getting info related to output frames in povray format.
povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
PpmEncoder - Class in javajs.img
see http://netpbm.sourceforge.net/doc/ppm.html
PpmEncoder() - Constructor for class javajs.img.PpmEncoder
 
PqrReader - Class in org.jmol.adapter.readers.pdb
PQR file reader.
PqrReader() - Constructor for class org.jmol.adapter.readers.pdb.PqrReader
 
precision - Variable in class jspecview.common.MeasurementData
 
precision - Variable in class jspecview.common.Parameters
 
precision - Variable in class jspecview.common.ScaleData
The precision (number of decimal places) of the X and Y values
precision - Variable in class jspecview.dialog.JSVDialog
 
precision - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
maximum of the decimal length of unit cell lengths and fractional coordinates
precision - Variable in class org.jmol.adapter.writers.XtlWriter
 
PrecisionRenderer - Class in org.jmol.g3d
Note added 4/2015 BH: Well, it turns out that the calculation of the intermediate pixel z value in all methods involving rasterization of lines is incorrect and has been incorrect since Jmol's inception.
PrecisionRenderer() - Constructor for class org.jmol.g3d.PrecisionRenderer
 
predefinedset - Static variable in class org.jmol.script.T
 
predefinedStatic - Static variable in class org.jmol.viewer.JC
 
predefinedVariable - Static variable in class org.jmol.viewer.JC
 
preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PreferencesDialog - Class in jspecview.application
Dialog to change the preferences for the application.
PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
 
PreferencesDialog(Frame, JSViewer, String, boolean, DisplaySchemesProcessor) - Constructor for class jspecview.application.PreferencesDialog
Initialises the PreferencesDialog
PreferencesDialog(JmolPanel, JFrame, GuiMap, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
prepareBinaryOutput(SV) - Method in class org.jmol.scriptext.CmdExt
 
prepareNextLine() - Method in class javajs.util.CifDataParser
sets the string for parsing to be from the next line when the token buffer is empty, and if ';' is at the beginning of that line, extends the string to include that full multiline string.
preprocessSemiString() - Method in class javajs.util.CifDataParser
Encapsulate a multi-line ; ....
preprocessString() - Method in class javajs.util.CifDataParser
Preprocess the string on a line starting with a semicolon to produce a string with a \1 ...
preprocessString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
initial processing; returns a string bounded by \1
preservestate - Static variable in class org.jmol.script.T
 
preserveState - Variable in class org.jmol.modelset.AtomCollection
 
preserveState - Variable in class org.jmol.viewer.GlobalSettings
 
pressed(long, int, int, int, boolean) - Method in class jspecview.app.GenericMouse
 
PRESSED - Static variable in class org.jmol.awtjs.Event
 
pressedCount - Variable in class org.jmol.viewer.ActionManager
 
prev - Static variable in class org.jmol.script.T
 
prevBondCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
 
previousMeshID - Variable in class org.jmol.shape.MeshCollection
 
previousMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
previousView() - Method in class jspecview.common.PanelData
Displays the previous view zoomed
previousX - Variable in class org.jmol.viewer.TransformManager
 
previousY - Variable in class org.jmol.viewer.TransformManager
 
prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
 
primitiveToCrystal - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
print - Static variable in class org.jmol.script.T
 
print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
added print command, so that it can be used by RasmolScriptHandler
print(Graphics, PageFormat, int) - Method in class jspecview.java.AwtPanel
Implements method print in interface printable
print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
print(Object, double, double, double, double, double, double, boolean, int) - Method in class jspecview.common.PanelData
 
print(String) - Method in interface jspecview.api.JSVAppletInterface
 
print(String) - Method in class jspecview.app.JSVApp
 
print(String) - Method in class jspecview.appletjs.JSVApplet
 
print(String) - Method in class jspecview.application.MainFrame
 
print(String) - Method in class jspecview.common.JSViewer
 
PRINT - Enum constant in enum class jspecview.common.ScriptToken
 
printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PrintAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
 
printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
printFilePath(Object, int, int, String) - Method in class jspecview.common.PanelData
 
printGraphPosition - Variable in class jspecview.common.PanelData
 
printingFontName - Variable in class jspecview.common.PanelData
 
printJobTitle - Variable in class jspecview.common.PanelData
 
PrintLayout - Class in jspecview.common
PrintLayout class stores all the information needed from the PrintLayoutDialog
PrintLayout(PanelData) - Constructor for class jspecview.common.PrintLayout
 
printPanel(PrintLayout, OutputStream, String) - Method in interface jspecview.api.JSVPanel
 
printPanel(PrintLayout, OutputStream, String) - Method in class jspecview.java.AwtPanel
Send a print job of the spectrum to the default printer on the system
printPanel(PrintLayout, OutputStream, String) - Method in class jspecview.js2d.JsPanel
Send a print job of the spectrum to the default printer on the system
printPdf(GenericGraphics, PrintLayout) - Method in class jspecview.common.PanelData
from jspecview.export.PDFCreator -- does not use iText --
printPDF(JSViewer, String) - Method in interface jspecview.export.ExportInterface
 
printVersion(Object, int) - Method in class jspecview.common.PanelData
 
privat - Static variable in class org.jmol.script.T
 
privateFuncs - Variable in class org.jmol.script.ScriptContext
 
privateFuncs - Variable in class org.jmol.script.ScriptEval
 
privateKey - Variable in class org.jmol.export.___Exporter
 
privateKey - Variable in class org.jmol.viewer.OutputManagerAwt
 
privateKey - Variable in class org.jmol.viewer.OutputManagerJS
 
probe - Static variable in class org.jmol.script.T
 
probes - Variable in class org.jmol.jvxl.readers.Parameters
 
probeValues - Variable in class org.jmol.jvxl.readers.Parameters
 
probeValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
process - Static variable in class org.jmol.script.T
 
process() - Method in class org.jmol.quantum.MepCalculation
 
process() - Method in class org.jmol.quantum.MOCalculation
 
process() - Method in class org.jmol.quantum.NciCalculation
 
process() - Method in class org.jmol.quantum.QuantumCalculation
 
process(int, boolean) - Method in class jspecview.source.AnIMLReader
Process the audit XML events
process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
process(int, int, float) - Method in class org.jmol.quantum.QuantumPlaneCalculation
Data mapping function to radically increase speed and reduce memory requirements of mapping data when the mapping comes from the same data set as the points, so isosurface creation and data mapping can be carried out both in the first (and only) pass.
process(Lst<Spectrum>, Spectrum.IRMode) - Static method in class jspecview.common.Spectrum
 
processAssemblyGenBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processAtom(Atom, String, char, String, int, int, char, boolean, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
processAtom2(Atom, int, float, float, float, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.BCIFReader
The primare method initiating this reader
processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.MMTFReader
 
processBinaryDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
processBinaryDocument() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
processBinaryDocument() - Method in class org.jmol.adapter.readers.xtal.CmdfReader
 
processBinaryDocument() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processBlock(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
 
processCellParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
unit cell parameters -- two options, so we use MOD 6
processChange(List<TouchPoint>, TouchPoint) - Method in interface com.sparshui.gestures.Gesture
Process a touch point change in the gesture.
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
incorporates double-click gesture
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
a general name definition field.
processCitationListBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
 
processClick(String) - Method in class jspecview.dialog.DialogManager
processing click event from platform DialogManager
processCompBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processDOM(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processDOM(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
processEnd2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processEndMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
 
processEndTag(int) - Method in class jspecview.source.AnIMLReader
 
processEntry() - Method in class org.jmol.adapter.readers.cif.MSCifParser
 
processError(int) - Method in class com.sparshui.server.ServerToClientProtocol
Send an error message to the client.
processErrors(String) - Method in class jspecview.source.AnIMLReader
 
processEvent(int, int, int, int, long) - Method in class jspecview.app.GenericMouse
 
processEvent(int, int, int, int, long) - Method in interface org.jmol.api.GenericMouseInterface
 
processEvent(int, int, int, int, long) - Method in class org.jmol.awtjs2d.Mouse
 
processEvent(int, Event) - Method in interface com.sparshui.client.SparshClient
This method processes events from the Gesture Server.
processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
Translate the specialized Sparsh UI information into a format that Jmol's ActionManager can understand without any special classes.
processEvents(int, Lst<Event>) - Method in class com.sparshui.server.ServerToClientProtocol
Instruct the client to process the events that have been generated by a group.
processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processKey(int, int, boolean) - Method in class org.jmol.console.GenericConsole
 
processKeyEvent(Object) - Method in interface javajs.api.JSInterface
 
processKeyEvent(Object) - Method in interface jspecview.api.JSVPanel
 
processKeyEvent(Object) - Method in class jspecview.app.GenericMouse
 
processKeyEvent(Object) - Method in class jspecview.appletjs.JSVApplet
 
processKeyEvent(Object) - Method in class jspecview.java.AwtPanel
 
processKeyEvent(Object) - Method in class jspecview.js2d.JsPanel
 
processKeyEvent(Object) - Method in interface org.jmol.api.GenericMouseInterface
 
processKeyEvent(Object) - Method in class org.jmol.awtjs2d.Mouse
 
processKeyEvent(Object) - Method in class org.jmol.util.GenericApplet
 
processKeyEvent(Object) - Method in class org.jmol.viewer.Viewer
 
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
processes loop_ blocks of interest or skips the data
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifParser
creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.
processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
processMKPropertyItem(String, boolean) - Method in class org.jmol.modelkit.ModelKit
 
processModelData(String, String, String, String, String, float, float, boolean) - Method in class jspecview.source.JDXReader
 
processModelData(String, String, String, String, String, float, float, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
processModelData(String, String, String, String, String, float, float, boolean) - Method in interface org.jmol.api.JmolJDXMOLReader
 
processMouseEvent(int, int, int, int, long) - Method in interface javajs.api.JSInterface
 
processMouseEvent(int, int, int, int, long) - Method in interface jspecview.api.JSVPanel
 
processMouseEvent(int, int, int, int, long) - Method in class jspecview.appletjs.JSVApplet
 
processMouseEvent(int, int, int, int, long) - Method in class jspecview.common.JSViewer
called by JSmol.js mouse event
processMouseEvent(int, int, int, int, long) - Method in class jspecview.java.AwtPanel
 
processMouseEvent(int, int, int, int, long) - Method in class jspecview.js2d.JsPanel
called only by JavaScript
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.util.GenericApplet
 
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.viewer.Viewer
 
processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.multitouch.ActionManagerMT
 
processMultitouchEvent(int, int, int, int, P3, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.viewer.ActionManager
Specific to ActionManagerMT -- for processing SparshUI gestures
processNextMeasure(MeasurementData, Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
 
processNextMeasure(MeasurementData, Measurement) - Method in class org.jmol.modelset.MeasurementData
if this is the client, then this method is called by MeasurementData when a measurement is ready
processNextMeasure(MeasurementData, Measurement) - Method in class org.jmol.shape.Measures
 
processNioMessage(byte[]) - Method in class org.molecularplayground.MPJmolApp
 
processNioMessage(byte[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
processNioMessage(byte[]) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
 
processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
processPeakPickEvent(Object, boolean) - Method in class jspecview.common.JSViewer
this method is called as a result of the user clicking on a peak (eventObject instanceof PeakPickEvent) or from PEAK command execution
processPoints() - Method in class org.jmol.quantum.MOCalculation
 
processPoints() - Method in class org.jmol.quantum.QuantumCalculation
 
processPt(T3) - Method in class org.jmol.quantum.QuantumCalculation
 
ProcessRecord(String, String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
process _topol_node.id 1
processRequest(SparshClient) - Method in class com.sparshui.client.ClientToServerProtocol
Processes a request from the Gesture Server
processSemiString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
Sets a multiline semicolon-eclipsed string to be parsed from the beginning, allowing for CIF 2.0-type prefixed text lines and removing line folding.
processSequence() - Method in class org.jmol.adapter.readers.cif.MMCifReader
get canonical 1-letter DNA/RNA sequence code from 3-letter code.
processService(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
service is expected to return a value in the "ret" key
processStart2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processStartMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
 
processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
identifies ranges for HELIX and TURN
processStructConnLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processStructOperListBlock(boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
identifies sheet ranges
processStructSiteBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
identifies structure sites
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.CifReader
 
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
 
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processSymop(String, boolean) - Method in class org.jmol.modelkit.ModelKit
 
processSync(String, int) - Method in interface org.jmol.api.JmolJSpecView
 
processSync(String, int) - Method in class org.jmol.jsv.JSpecView
 
processTableEvent(String, int, int, boolean) - Method in class jspecview.dialog.DialogManager
processing table cell click event from platform DialogManager; takes two hits in AWT -- one a row, the other a column
processTag(int) - Method in class jspecview.source.AnIMLReader
Process the XML events.
processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
processTwoPointGesture(float[][][]) - Method in interface javajs.api.JSInterface
 
processTwoPointGesture(float[][][]) - Method in interface jspecview.api.JSVPanel
 
processTwoPointGesture(float[][][]) - Method in class jspecview.app.GenericMouse
 
processTwoPointGesture(float[][][]) - Method in class jspecview.appletjs.JSVApplet
 
processTwoPointGesture(float[][][]) - Method in class jspecview.common.JSViewer
 
processTwoPointGesture(float[][][]) - Method in class jspecview.java.AwtPanel
 
processTwoPointGesture(float[][][]) - Method in class jspecview.js2d.JsPanel
 
processTwoPointGesture(float[][][]) - Method in interface org.jmol.api.GenericMouseInterface
 
processTwoPointGesture(float[][][]) - Method in class org.jmol.awtjs2d.Mouse
called by JSmol as processTwoPointGesture(canvas.touches);
processTwoPointGesture(float[][][]) - Method in class org.jmol.util.GenericApplet
 
processTwoPointGesture(float[][][]) - Method in class org.jmol.viewer.Viewer
 
processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cif.CifReader
the PDB transformation matrix cartesian --> fractional key and field have been set already
processUpdate(String) - Method in class org.jmol.util.JmolAudio
 
processWindowClosing(String) - Method in class jspecview.dialog.DialogManager
processing window closing event from platform DialogManager
processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
from eval write command only includes option to write set of files
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCdxReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
the current state
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processXML(int, int) - Method in class jspecview.source.AnIMLReader
 
processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.more.CDXReader
 
processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
programInfo - Variable in class org.jmol.atomdata.AtomData
 
projectOntoAxis(P3, P3, V3, V3) - Static method in class javajs.util.Measure
project point onto a line containing ptA and having axis unitVector axisUnitVector, returning the result in point and a vector from ptA to pt in vectorProjection
prompt - Static variable in class org.jmol.script.T
 
prompt(String, String, String[], boolean) - Method in class jspecview.java.AwtPlatform
 
prompt(String, String, String[], boolean) - Method in class jspecview.js2d.JsPlatform
 
prompt(String, String, String[], boolean) - Method in interface org.jmol.api.GenericPlatform
 
prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
 
prompt(String, String, String[], boolean) - Method in class org.jmol.awtjs2d.Platform
 
prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
 
PROP_ATOMS_DELETED - Static variable in class org.jmol.viewer.JC
 
PROP_ATOMS_MOVED - Static variable in class org.jmol.viewer.JC
 
PROP_DELETE_MODEL_ATOMS - Static variable in class org.jmol.viewer.JC
 
properties - Variable in class jspecview.common.JSViewer
 
properties - Variable in class org.jmol.modelset.Model
 
property - Variable in class org.jmol.modelset.Measurement
 
property - Variable in class org.jmol.modelset.MeasurementData
 
property - Static variable in class org.jmol.script.T
 
PROPERTY - Enum constant in enum class org.jmol.c.PAL
 
propertyatomnumbercolumncount - Static variable in class org.jmol.script.T
 
propertyatomnumberfield - Static variable in class org.jmol.script.T
 
propertyChange(PropertyChangeEvent) - Method in class org.jmol.dialog.FilePreview
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
propertycolorscheme - Static variable in class org.jmol.script.T
 
propertydatacolumncount - Static variable in class org.jmol.script.T
 
propertydatafield - Static variable in class org.jmol.script.T
 
propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
 
PROPERTYFLAGS - Static variable in class org.jmol.script.T
 
PropertyManager - Class in org.jmol.viewer
The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
 
propselector - Static variable in class org.jmol.script.T
 
protein - Static variable in class org.jmol.script.T
 
proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
ProteinStructure - Class in org.jmol.modelsetbio
 
ProteinStructure() - Constructor for class org.jmol.modelsetbio.ProteinStructure
 
proteinStructureTainted - Variable in class org.jmol.modelset.ModelSet
 
PS_CLOSEPATH - Static variable in class org.jmol.shapecgo.CGOMesh
 
PS_LINETO - Static variable in class org.jmol.shapecgo.CGOMesh
 
PS_MOVETO - Static variable in class org.jmol.shapecgo.CGOMesh
 
PS_NEWPATH - Static variable in class org.jmol.shapecgo.CGOMesh
 
PS_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
 
PS_SETLINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
 
PS_SHOWPAGE - Static variable in class org.jmol.shapecgo.CGOMesh
 
PS_STROKE - Static variable in class org.jmol.shapecgo.CGOMesh
 
psi - Static variable in class org.jmol.script.T
 
psi_monteCarloCount - Variable in class org.jmol.jvxl.readers.Parameters
 
PsiReader - Class in org.jmol.adapter.readers.quantum
Reader for Psi3 output files.
PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
 
pt - Variable in enum class org.jmol.c.VDW
 
pt - Variable in class org.jmol.util.ContactPair
 
PT - Class in javajs.util
a combination of Parsing and Text-related utility classes
PT() - Constructor for class javajs.util.PT
 
PT_INT_LABEL - Static variable in class jspecview.common.Measurement
 
PT_ON_LINE - Static variable in class jspecview.common.Measurement
 
PT_ON_LINE1 - Static variable in class jspecview.common.Measurement
 
PT_ON_LINE2 - Static variable in class jspecview.common.Measurement
 
PT_XY1 - Static variable in class jspecview.common.Measurement
 
PT_XY2 - Static variable in class jspecview.common.Measurement
 
pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pt0 - Variable in class org.jmol.modelsetbio.AlphaPolymer
Specifically for mmTF bitset setting of structures
pt0 - Variable in class org.jmol.render.FontLineShapeRenderer
 
pt0 - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt0i - Variable in class org.jmol.render.FontLineShapeRenderer
 
pt0i - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt1 - Variable in class org.jmol.render.FontLineShapeRenderer
 
pt1 - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt1f - Variable in class org.jmol.render.MeshRenderer
 
pt1i - Variable in class org.jmol.render.MeshRenderer
 
pt2 - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt2f - Variable in class org.jmol.render.MeshRenderer
 
pt2i - Variable in class org.jmol.render.FontLineShapeRenderer
 
pt2i - Variable in class org.jmol.render.MeshRenderer
 
pt3i - Variable in class org.jmol.render.MeshRenderer
 
pt4Value(SV) - Static method in class org.jmol.script.SV
 
ptCenter - Variable in class org.jmol.shape.Mesh
 
pTemp - Variable in class org.jmol.render.LabelsRenderer
 
ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ptMark - Variable in class javajs.util.DataReader
 
ptNewSetModifier - Variable in class org.jmol.script.ScriptCompiler
 
pts - Variable in class org.jmol.modelset.Measurement
 
ptSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
ptTest1 - Variable in class org.jmol.viewer.TransformManager
 
ptTest2 - Variable in class org.jmol.viewer.TransformManager
 
ptTest3 - Variable in class org.jmol.viewer.TransformManager
 
ptToIJK(T3, int) - Static method in class org.jmol.util.SimpleUnitCell
Convert user's {3 2 1} to {1500500500, 1503502501, 0 or 1, 1500501}
ptValue(SV) - Static method in class org.jmol.script.SV
 
ptValue(SV, BS) - Method in class org.jmol.script.ScriptMathProcessor
 
purine - Static variable in class org.jmol.script.T
 
PURINE_MASK - Static variable in class org.jmol.viewer.JC
 
PURPLE - Static variable in class org.jmol.util.C
 
push - Static variable in class org.jmol.script.T
 
pushContextDown(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
pushContextDown(String) - Method in class org.jmol.script.ScriptEval
 
pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
 
pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
 
pushHoldRepaint(String) - Method in interface org.jmol.api.JmolRepaintManager
 
pushHoldRepaint(String) - Method in class org.jmol.render.RepaintManager
 
pushHoldRepaintWhy(String) - Method in class org.jmol.viewer.Viewer
 
pushMatrix() - Method in class org.jmol.export._StlExporter
 
pushMatrix() - Method in class org.jmol.export._VrmlExporter
 
pushMatrix() - Method in class org.jmol.export._X3dExporter
 
pushPop(SV, SV) - Method in class org.jmol.script.SV
Script variables are pushed after cloning, because the name comes with them when we do otherwise they are not mutable anyway.
pushState() - Method in class org.jmol.viewer.Viewer
 
pushState(String) - Method in class org.jmol.util.CommandHistory
 
put(int, int) - Method in class org.jmol.util.Int2IntHash
 
putBox(int, float[]) - Method in class org.jmol.shape.Labels
 
putByte(int) - Method in class javajs.img.ImageEncoder
 
putCoord(V3d, double[]) - Static method in class org.jmol.minimize.Util
 
putInfo(String, Map<String, Object>, String, Object) - Static method in class jspecview.common.Parameters
 
putLabel(int, Text) - Method in class org.jmol.shape.Labels
 
putP(T3) - Method in class javajs.util.T3
 
putString(String) - Method in class javajs.img.ImageEncoder
 
PWmatReader - Class in org.jmol.adapter.readers.xtal
crude PWmat atom.config reader http://pwmatus.com/manual
PWmatReader() - Constructor for class org.jmol.adapter.readers.xtal.PWmatReader
 
PWMATWriter - Class in org.jmol.adapter.writers
A writer for PWMAT atom.config files.
PWMATWriter() - Constructor for class org.jmol.adapter.writers.PWMATWriter
 
Pwr2 - Static variable in class org.jmol.util.TriangleData
 
pymol - Static variable in class org.jmol.script.T
 
PYMOL_LABEL_OFFSET_ABS_ANG - Static variable in class org.jmol.modelset.Text
 
PYMOL_LABEL_OFFSET_ABS_PIX - Static variable in class org.jmol.modelset.Text
 
PYMOL_LABEL_OFFSET_JMOL - Static variable in class org.jmol.modelset.Text
 
PYMOL_LABEL_OFFSET_PIX - Static variable in class org.jmol.modelset.Text
 
PYMOL_LABEL_OFFSET_REL - Static variable in class org.jmol.modelset.Text
 
PYMOL_LABEL_OFFSET_REL_ANG - Static variable in class org.jmol.modelset.Text
 
PYMOL_LABEL_OFFSET_REL_PIX - Static variable in class org.jmol.modelset.Text
 
PymolAtomReader - Interface in org.jmol.api
 
pymolOffset - Variable in class org.jmol.modelset.Text
 
PyMOLReader - Class in org.jmol.adapter.readers.pymol
PyMOL PSE (binary Python session) file reader.
PyMOLReader() - Constructor for class org.jmol.adapter.readers.pymol.PyMOLReader
 
pyrimidine - Static variable in class org.jmol.script.T
 
PYRIMIDINE_MASK - Static variable in class org.jmol.viewer.JC
 

Q

q0 - Variable in class javajs.util.Quat
 
q1 - Variable in class javajs.util.Quat
 
q2 - Variable in class javajs.util.Quat
 
q3 - Variable in class javajs.util.Quat
 
QchemReader - Class in org.jmol.adapter.readers.quantum
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
QchemReader() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader
 
QchemReader.MOInfo - Class in org.jmol.adapter.readers.quantum
 
QCJSONReader - Class in org.jmol.adapter.readers.quantum
A molecular structure and orbital reader for MolDen files.
QCJSONReader() - Constructor for class org.jmol.adapter.readers.quantum.QCJSONReader
 
QCJSONWriter - Class in org.jmol.adapter.writers
A very experimental class for writing QCJSON files.
QCJSONWriter() - Constructor for class org.jmol.adapter.writers.QCJSONWriter
 
QCJSONWriter.SparseArray - Class in org.jmol.adapter.writers
 
QCSchemaUnits - Class in org.qcschema
A general Java class for working with QCShema units and array types.
QCSchemaUnits() - Constructor for class org.qcschema.QCSchemaUnits
 
qmAtoms - Variable in class org.jmol.quantum.QuantumCalculation
 
qpc - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
QS - Class in org.jmol.quantum
Constants and static methods for quantum shells.
QS() - Constructor for class org.jmol.quantum.QS
 
QUADRIC - Static variable in class org.jmol.shapecgo.CGOMesh
 
qualifiedValue() - Method in class jspecview.source.XMLParser
for <xxxx> value </xxxx>
quality - Variable in class javajs.img.ImageEncoder
 
qualityJ - Variable in class org.jmol.dialog.Dialog
 
qualityJPG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
QualityListener(boolean, JSlider) - Constructor for class org.jmol.dialog.Dialog.QualityListener
 
qualityP - Variable in class org.jmol.dialog.Dialog
 
qualityPNG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
quantize(float, boolean) - Method in class org.jmol.util.ColorEncoder
gets the value at the color boundary for this color range fraction
quantize4(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
 
QuantumCalculation - Class in org.jmol.quantum
 
QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
 
QuantumPlaneCalculation - Class in org.jmol.quantum
Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
QuantumPlaneCalculation() - Constructor for class org.jmol.quantum.QuantumPlaneCalculation
 
Quat - Class in javajs.util
 
Quat() - Constructor for class javajs.util.Quat
 
quaternion - Static variable in class org.jmol.script.T
 
quaternionframe - Static variable in class org.jmol.script.T
 
query - Variable in class jme.JME
 
QUESTION_MESSAGE - Static variable in class jspecview.dialog.DialogManager
 
queueOnHold - Variable in class org.jmol.viewer.Viewer
 
queueThreadFinished(int) - Method in interface org.jmol.api.JmolScriptManager
 
queueThreadFinished(int) - Method in class org.jmol.script.ScriptManager
 
quiet - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
quit - Static variable in class org.jmol.script.T
 

R

r - Variable in class org.jmol.quantum.SlaterData
 
r - Variable in class org.jmol.util.Rgb16
 
R3 - Static variable in class org.jmol.minimize.forcefield.ForceField
 
R4 - Static variable in class org.jmol.minimize.forcefield.ForceField
 
R5 - Static variable in class org.jmol.minimize.forcefield.ForceField
 
rad - Static variable in class org.jmol.script.T
 
RAD_COV_BODR_2014_02_22 - Static variable in class org.jmol.util.Elements
 
RAD_COV_IONIC_OB1_100_1 - Static variable in class org.jmol.util.Elements
 
RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
 
radiansPerDegree - Static variable in class javajs.util.Measure
 
radiansPerDegree - Static variable in class org.jmol.viewer.JC
 
radical - Static variable in class org.jmol.script.T
 
radii - Variable in class org.jmol.util.ContactPair
 
radius - Variable in class org.jmol.adapter.smarter.Atom
 
radius - Variable in class org.jmol.adapter.smarter.Bond
 
radius - Static variable in class org.jmol.script.T
 
RADIUS_GLOBAL - Static variable in class org.jmol.modelset.Atom
 
RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
 
RADIUS_MAX - Static variable in class org.jmol.shape.Shape
 
radiusData - Variable in class org.jmol.atomdata.AtomData
 
radiusData - Variable in class org.jmol.modelset.MeasurementData
 
RadiusData - Class in org.jmol.atomdata
 
RadiusData(float[], float, RadiusData.EnumType, VDW) - Constructor for class org.jmol.atomdata.RadiusData
 
RadiusData.EnumType - Enum Class in org.jmol.atomdata
 
ramachandran - Static variable in class org.jmol.script.T
 
random - Static variable in class org.jmol.script.T
 
randomPoint() - Static method in class org.jmol.shapespecial.Draw
 
randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
 
range - Static variable in class org.jmol.script.T
 
rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
 
rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeselected - Static variable in class org.jmol.script.T
 
rangeSelected - Variable in class org.jmol.viewer.GlobalSettings
 
Raromatic - Static variable in class org.jmol.minimize.forcefield.ForceField
 
rasmol - Static variable in class org.jmol.script.T
 
RASMOL - Enum constant in enum class org.jmol.c.PAL
 
RASMOL - Enum constant in enum class org.jmol.c.VDW
 
RASMOL - Static variable in class org.jmol.util.ColorEncoder
 
RasmolBinding - Class in org.jmol.viewer.binding
 
RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
 
rawBondCount - Variable in class org.jmol.minimize.Minimizer
 
rawIndex - Variable in class org.jmol.minimize.MinBond
 
rawLine - Variable in class jspecview.source.JDXSourceStreamTokenizer
 
RBOND - Static variable in class jme.JMEmol
 
rButton - Variable in class jme.JME
 
rd - Variable in class org.jmol.viewer.Viewer
 
rd() - Method in class jspecview.source.JDXReader
 
rd() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
rd() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
rd() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
rd() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
filter out unnecessary lines
rd() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
rd() - Method in interface org.jmol.api.JmolJDXMOLReader
 
rd() - Method in class org.jmol.jvxl.readers.JvxlReader
 
rd() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
rd() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
rdline() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
Rdr - Class in javajs.util
A general helper class for a variety of stream and reader functionality including: stream and byte magic-number decoding for PNG, PNGJ, ZIP, and GZIP streams various stream/reader methods, including UTF-encoded stream reading reflection-protected access to a CIF parser and ZIP tools
Rdr(BufferedReader) - Constructor for class javajs.util.Rdr
 
Rdr.StreamReader - Class in javajs.util
 
rdSiesta() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
reaction - Variable in class jme.JME
 
reactionPart() - Method in class jme.JMEmol
 
read() - Method in class org.apache.tools.bzip2.CBZip2InputStream
read(byte[], int, int) - Method in class com.jcraft.jzlib.InflaterInputStream
 
read(byte[], int, int) - Method in class org.apache.tools.bzip2.CBZip2InputStream
 
read(char[], int, int) - Method in class javajs.util.ArrayDataReader
 
read(char[], int, int) - Method in class javajs.util.ListDataReader
 
read(char[], int, int) - Method in class jspecview.common.JSVZipFileSequentialReader
 
read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
readACDAssignments(int, boolean) - Method in interface org.jmol.api.JmolJDXMOLParser
 
readACDAssignments(int, boolean) - Method in class org.jmol.jsv.JDXMOLParser
 
readACDMolFile() - Method in interface org.jmol.api.JmolJDXMOLParser
 
readACDMolFile() - Method in class org.jmol.jsv.JDXMOLParser
MOL file embedded in JDX file
readAllAsString(BufferedReader, int, boolean, String[], int) - Static method in class javajs.util.Rdr
This method fills data[i] with string data from a file that may or may not be binary even though it is being read by a reader.
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readBonds() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readBrukerDir(String) - Method in class jspecview.source.BrukerReader
Read through a Bruker directory (Java only) looking for title, acqus, procs, 1r, 1i, 2rr.
readBrukerZip(byte[], String) - Method in class jspecview.source.BrukerReader
Read through a ZIP file (Java or JavaScript) looking for title, acqus, procs, 1r, 1i, 2rr.
readBuf(char[], int, int) - Method in class javajs.util.DataReader
 
readByte() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readByte() - Method in class javajs.util.BinaryDocument
 
readByteArray(byte[], int, int) - Method in interface javajs.api.GenericBinaryDocument
 
readByteArray(byte[], int, int) - Method in class javajs.util.BinaryDocument
 
readByteAsInt() - Method in class com.jcraft.jzlib.InflaterInputStream
 
readByteAsInt() - Method in class org.apache.tools.bzip2.CBZip2InputStream
 
readBytes(int) - Method in interface javajs.api.GenericBinaryDocumentReader
 
readBytes(int) - Method in class javajs.util.BinaryDocument
 
readCifData(String, Object, String) - Method in interface org.jmol.atomdata.AtomDataServer
 
readCifData(String, Object, String) - Method in class org.jmol.viewer.Viewer
 
readCifData(String, String) - Method in class org.jmol.viewer.Viewer
 
readCifData(GenericCifDataParser, BufferedReader) - Static method in class javajs.util.Rdr
 
readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
readDataObject(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readDouble() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readDouble() - Method in class javajs.util.BinaryDocument
 
readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readEnergy() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
READER_NOT_FOUND - Static variable in class org.jmol.viewer.JC
 
readerClosed - Variable in class org.jmol.jvxl.readers.JvxlReader
 
readerClosed - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
readerClosed - Variable in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readFileAsMap(BufferedInputStream, Map<String, Object>, String) - Method in interface javajs.api.GenericZipTools
 
readFileAsMap(BufferedInputStream, Map<String, Object>, String) - Method in class javajs.util.ZipTools
 
readFileAsMap(BufferedInputStream, Map<String, Object>, String) - Method in class org.jmol.viewer.Viewer
 
readFloat() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readFloat() - Method in class javajs.util.BinaryDocument
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readFrequencies(String, boolean) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Interprets the Harmonic frequencies section.
readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readHeader() - Method in class com.jcraft.jzlib.InflaterInputStream
 
readInf(byte[], int, int) - Method in class com.jcraft.jzlib.InflaterInputStream
 
readInputRecords() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
 
readInt() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readInt() - Method in class javajs.util.BinaryDocument
 
readIntLE() - Method in interface javajs.api.GenericBinaryDocument
 
readIntLE() - Method in class javajs.util.BinaryDocument
 
readLine() - Method in interface javajs.api.GenericCifDataParser
 
readLine() - Method in class javajs.util.ArrayDataReader
 
readLine() - Method in class javajs.util.CifDataParser
 
readLine() - Method in class javajs.util.ListDataReader
 
readLine() - Method in class jspecview.common.JSVZipFileSequentialReader
 
readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readLineTrimmed() - Method in class jspecview.source.JDXSourceStreamTokenizer
 
readLineWithNewline() - Method in class javajs.util.LimitedLineReader
 
readList() - Method in class javajs.util.CifDataParser
Read a CIF 2.0 list structure, converting it to either a JSON string or to a Java data structure
readLong() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readLong() - Method in class javajs.util.BinaryDocument
 
readMap() - Method in class javajs.util.MessagePackReader
 
readModels() - Method in interface org.jmol.api.JmolJDXMOLParser
 
readModels() - Method in class org.jmol.jsv.JDXMOLParser
 
readMolecularFormula() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
try various ways to read the optional atom labels.
readMolecularObitals() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readMolecule(String) - Method in class jme.JME
 
readMolFile(String) - Method in class jme.JME
 
ReadNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
 
readNBOCoefficients(Map<String, Object>, String, Viewer) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
Called by setNBOType in IsoExt when use issues NBO TYPE xxx
readNextLine() - Method in interface javajs.api.GenericLineReader
 
readNextLine() - Method in class javajs.util.Rdr
 
readNextLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ReadNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
 
readNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
readNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
readOldFrequency() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
 
readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readParameters() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readPeaks(boolean, int) - Method in interface org.jmol.api.JmolJDXMOLParser
 
readPeaks(boolean, int) - Method in class org.jmol.jsv.JDXMOLParser
 
readShort() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readShort() - Method in class javajs.util.BinaryDocument
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
READSPT - Enum constant in enum class org.jmol.viewer.Viewer.ACCESS
 
readString(int) - Method in interface javajs.api.GenericBinaryDocumentReader
 
readString(int) - Method in class javajs.util.BinaryDocument
 
readStructure(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readSurfaceDataJXR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readSurfaceDataXML() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readTable() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
Read a CIF 2.0 table into either a JSON string or a java data structure
readUInt8() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readUInt8() - Method in class javajs.util.BinaryDocument
 
readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
readUnsignedShort() - Method in interface javajs.api.GenericBinaryDocumentReader
 
readUnsignedShort() - Method in class javajs.util.BinaryDocument
 
readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
ReattachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
 
rebond() - Method in class org.jmol.api.JmolViewer
 
rebond() - Method in class org.jmol.viewer.Viewer
 
rebondState(boolean) - Method in class org.jmol.viewer.Viewer
 
recachePngjBytes(String, byte[]) - Method in class org.jmol.viewer.FileManager
 
recalcAltVertices - Variable in class org.jmol.shape.Mesh
 
reCalculate(BS, M3) - Method in class org.jmol.geodesic.EnvelopeCalculation
problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
recalculateAllPolymers(BS, Group[]) - Method in class org.jmol.modelsetbio.BioModelSet
 
recalculateEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
 
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelSet
 
recalculatePoints(int) - Method in class org.jmol.modelsetbio.BioModelSet
 
recalculatePolymers(BS) - Method in class org.jmol.modelset.ModelSet
 
recalculatePositionDependentQuantities(BS, M4) - Method in class org.jmol.modelset.ModelSet
 
recallCommand(boolean, boolean) - Method in class org.jmol.console.GenericConsole
 
recallCommand(boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
Recall command history.
recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
RecentFilesAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
 
recordData(float) - Method in class org.jmol.jvxl.readers.JvxlReader
 
recordData(float) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
recordData(float) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
Rectangle - Class in org.jmol.util
 
Rectangle() - Constructor for class org.jmol.util.Rectangle
 
rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
RED - Static variable in class jspecview.common.ColorParameters
 
RED - Static variable in class org.jmol.util.C
 
REDBLUE - Enum constant in enum class org.jmol.c.STER
 
REDCYAN - Enum constant in enum class org.jmol.c.STER
 
REDGREEN - Enum constant in enum class org.jmol.c.STER
 
redo - Static variable in class org.jmol.script.T
 
redomove - Static variable in class org.jmol.script.T
 
reducedAnisotropy() - Method in class org.jmol.util.Tensor
reduced anisotropy = largest difference from isotropy (may be negative)
reEnable() - Method in class jspecview.dialog.JSVDialog
 
REF_TYPE_BRUKER - Static variable in class jspecview.source.JDXDataObject
 
REF_TYPE_STANDARD - Static variable in class jspecview.source.JDXDataObject
 
REF_TYPE_UNSPECIFIED - Static variable in class jspecview.source.JDXDataObject
 
REF_TYPE_VARIAN - Static variable in class jspecview.source.JDXDataObject
 
reference - Variable in class org.jmol.modelset.TickInfo
 
reference - Static variable in class org.jmol.script.T
 
referenceCenter - Variable in class org.jmol.export.___Exporter
 
referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
 
reformatDistanceIfSelected(boolean) - Method in class org.jmol.modelset.Measurement
 
refPoint - Variable in class jspecview.source.AnIMLReader
 
refresh - Static variable in class org.jmol.script.T
 
refresh() - Method in class jspecview.common.PanelData
 
refresh() - Method in class jspecview.common.RepaintManager
 
refresh(boolean) - Method in class org.jmol.script.ScriptEval
Refresh the display NOW
refresh(int, String) - Method in class org.jmol.api.JmolViewer
 
refresh(int, String) - Method in class org.jmol.viewer.Viewer
initiate a repaint/update sequence if it has not already been requested.
refresh(Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
REFRESH_REPAINT - Static variable in class org.jmol.viewer.Viewer
 
REFRESH_REPAINT_NO_MOTION_ONLY - Static variable in class org.jmol.viewer.Viewer
 
REFRESH_SEND_WEBGL_NEW_ORIENTATION - Static variable in class org.jmol.viewer.Viewer
 
REFRESH_SYNC - Static variable in class org.jmol.viewer.Viewer
 
REFRESH_SYNC_MASK - Static variable in class org.jmol.viewer.Viewer
 
refreshing - Static variable in class org.jmol.script.T
 
refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
 
regainFocus() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
regainFocus() - Method in class org.jmol.console.AppletConsole
 
regainFocus() - Method in class org.jmol.consolejs.AppletConsole
 
regainFocus() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
register(String, JmolSyncInterface) - Method in class jspecview.application.MainFrame
called by Jmol's StatusListener to register itself, indicating to JSpecView that it needs to synchronize with it
register(String, JmolSyncInterface) - Method in interface org.jmol.api.JmolSyncInterface
 
register(String, JmolSyncInterface) - Method in class org.jmol.util.GenericApplet
 
register(String, JmolSyncInterface) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
register(Component, String) - Method in interface org.jmol.awtjs.swing.SwingController
Set c's id to a unique identifier and add it to an associative array that will associate that id with c.
registerAudio(String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
 
registerDialog(JSVDialog) - Method in class jspecview.dialog.DialogManager
register the JSV dialog with a unique key to be used as an ID in callbacks optionKeys ending with "!" are one-of-a-kind, such as "views"
registerSelector(String, Object) - Method in class jspecview.dialog.DialogManager
 
registryKey - Variable in class jspecview.java.AwtDialog
 
registryKey - Variable in class jspecview.js2d.JsDialog
 
reinitializeLightingAndColor(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
reinitShape() - Method in class org.jmol.shape.Axes
 
reinstateMenu(JMenuItem, MenuElement[]) - Method in class org.jmol.awt.AwtPopupHelper
Cause the menu to persist in its open state.
rejectAtomName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
Related Documentation - Search tag in package org.jmol.g3d
Section
RELATIVE_DRAG_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
RELATIVE_DRAG_EVENT - Static variable in class com.sparshui.GestureType
 
RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
RELATIVE_DRAG_GESTURE - Static variable in class com.sparshui.GestureType
 
RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
RelativeDragEvent - Class in com.sparshui.common.messages.events
 
RelativeDragEvent() - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
 
RelativeDragEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
Constructs a dragEvent from a complete serialized version of the drag event.
RelativeDragEvent(float, float) - Constructor for class com.sparshui.common.messages.events.RelativeDragEvent
 
relativeStereo - Variable in class jme.JME
 
release() - Method in interface org.jmol.api.AtomIndexIterator
 
release() - Method in class org.jmol.bspt.CubeIterator
nulls internal references
release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
release() - Method in class org.jmol.symmetry.UnitCellIterator
 
released(long, int, int, int) - Method in class jspecview.app.GenericMouse
 
RELEASED - Static variable in class org.jmol.awtjs.Event
 
releaseModelSet() - Method in class org.jmol.modelset.ModelSet
 
releaseModelSetAC() - Method in class org.jmol.modelset.AtomCollection
 
releaseModelSetBC() - Method in class org.jmol.modelset.BondCollection
 
releaseScreenImage() - Method in class org.jmol.api.JmolViewer
 
releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
 
releaseScreenImage() - Method in class org.jmol.util.GData
 
releaseScreenImage() - Method in class org.jmol.viewer.Viewer
 
releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
 
remove - Static variable in class org.jmol.script.T
 
remove() - Method in class jspecview.source.JDXDecompressor
 
remove(int) - Method in class javajs.util.Lst
 
remove(int) - Method in class jspecview.common.IntegralData
 
remove(int) - Method in interface org.jmol.api.SC
 
remove(int) - Method in class org.jmol.awt.AwtSwingComponent
 
remove(int) - Method in class org.jmol.awtjs.swing.Container
 
remove(Object) - Method in class javajs.util.Lst
Deprecated.
removeAll() - Method in interface org.jmol.api.SC
 
removeAll() - Method in class org.jmol.awt.AwtSwingComponent
 
removeAll() - Method in class org.jmol.awtjs.swing.Container
 
removeAllHighlights() - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that removes all highlights from the plot area of a JSVPanel
removeAllHighlights() - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that removes all highlights from the plot area of a JSVPanel
removeAllHighlights() - Method in class jspecview.appletjs.JSVApplet
 
removeAllHighlights() - Method in class jspecview.application.MainFrame
 
removeAllHighlights() - Method in class jspecview.common.PanelData
Removes all highlights from the display
removeAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
note that sets must be iterated from LAST to FIRST not a general method -- would mess up if we had unit cells
removeCommand() - Method in class org.jmol.util.CommandHistory
 
removeCommand() - Method in class org.jmol.viewer.Viewer
Removes one command from the command history
removeCommand(int) - Method in class org.jmol.util.CommandHistory
 
removeCurrentAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
removeDialog(JSVDialog) - Method in class jspecview.common.PanelData
 
removeDuplicates(ModelSet, BS, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
removeDuplicates(ModelSet, BS, boolean) - Method in class org.jmol.symmetry.Symmetry
 
removeFunction(String) - Method in class org.jmol.viewer.Viewer
 
removeHighlight(double, double) - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that removes a highlight from the plot area of a JSVPanel
removeHighlight(double, double) - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that removes a highlight from the plot area of a JSVPanel
removeHighlight(double, double) - Method in class jspecview.appletjs.JSVApplet
 
removeHighlight(double, double) - Method in class jspecview.application.MainFrame
 
removeHighlight(double, double) - Method in class jspecview.common.PanelData
Remove the highlight specified by the starting and ending x value
removeItemAt(int) - Method in class javajs.util.Lst
 
removeLastUnselectedAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
removeMapKeys(Map<String, ?>, String) - Static method in class javajs.util.AU
remove all keys from a map that start with given root
removeNodeFromParent(JSVTreeNode) - Method in class jspecview.tree.SimpleTreeModel
 
removeObj(Object) - Method in class javajs.util.Lst
 
removePacking(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
removeParam(String) - Method in class org.jmol.viewer.GlobalSettings
 
removePropertyChangeListener(PropertyChangeListener) - Method in class jspecview.java.FileDropperJmol
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
 
removeScale(Coordinate[], double, double) - Static method in class jspecview.common.Coordinate
Removes the scale factor from the coordinates
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
 
removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
 
render() - Method in class org.jmol.render.AxesRenderer
 
render() - Method in class org.jmol.render.BallsRenderer
 
render() - Method in class org.jmol.render.BbcageRenderer
 
render() - Method in class org.jmol.render.EchoRenderer
 
render() - Method in class org.jmol.render.FrankRenderer
 
render() - Method in class org.jmol.render.HalosRenderer
 
render() - Method in class org.jmol.render.HoverRenderer
 
render() - Method in class org.jmol.render.LabelsRenderer
 
render() - Method in class org.jmol.render.MeasuresRenderer
 
render() - Method in class org.jmol.render.ShapeRenderer
 
render() - Method in class org.jmol.render.StarsRenderer
 
render() - Method in class org.jmol.render.SticksRenderer
 
render() - Method in class org.jmol.render.UccageRenderer
 
render() - Method in class org.jmol.renderbio.BioMeshRenderer
 
render() - Method in class org.jmol.renderbio.BackboneRenderer
 
render() - Method in class org.jmol.renderbio.CartoonRenderer
 
render() - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
render() - Method in class org.jmol.renderbio.RibbonsRenderer
 
render() - Method in class org.jmol.renderbio.RocketsRenderer
 
render() - Method in class org.jmol.renderbio.StrandsRenderer
 
render() - Method in class org.jmol.renderbio.TraceRenderer
 
render() - Method in class org.jmol.rendercgo.CGORenderer
 
render() - Method in class org.jmol.renderspecial.DipolesRenderer
 
render() - Method in class org.jmol.renderspecial.DotsRenderer
 
render() - Method in class org.jmol.renderspecial.DrawRenderer
 
render() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
render() - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
 
render() - Method in class org.jmol.renderspecial.PolyhedraRenderer
 
render() - Method in class org.jmol.renderspecial.VectorsRenderer
 
render() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
render() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
 
render() - Method in class org.jmol.rendersurface.PmeshRenderer
 
render(GData, ModelSet, boolean, int[]) - Method in interface org.jmol.api.JmolRepaintManager
 
render(GData, ModelSet, boolean, int[]) - Method in class org.jmol.render.RepaintManager
 
render1(Dots) - Method in class org.jmol.renderspecial.DotsRenderer
 
render2(boolean) - Method in class org.jmol.render.MeshRenderer
Overridden in DrawRenderer and IsosurfaceRenderer
render2(boolean) - Method in class org.jmol.renderspecial.DrawRenderer
 
render2(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
render2b(boolean) - Method in class org.jmol.render.MeshRenderer
 
render2Strand(boolean, float, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderAllStrings(Object) - Method in interface org.jmol.api.JmolGraphicsInterface
 
renderAllStrings(Object) - Method in class org.jmol.export.Export3D
 
renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
 
renderAllStrings(Object) - Method in class org.jmol.util.GData
 
renderArc - Variable in class org.jmol.modelset.Measurement
 
renderArrowHeads - Variable in class org.jmol.renderbio.RocketsRenderer
 
renderAxis - Variable in class org.jmol.modelset.Measurement
 
renderBackground(JmolRendererInterface) - Method in interface org.jmol.api.JmolRendererInterface
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.export.Export3D
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.util.GData
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.BackboneRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.CartoonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RibbonsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RocketsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.StrandsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.TraceRenderer
 
renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.AxesRenderer
 
renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.BbcageRenderer
 
renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.UccageRenderer
 
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.DotsRenderer
generic renderer -- dots and geosurface
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
 
renderCrossHairs(int[], int, int, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
 
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.export.Export3D
 
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.g3d.Graphics3D
 
renderDots(int) - Method in class org.jmol.renderspecial.DotsRenderer
also called by GeoSurface when in motion
renderExport(GData, ModelSet, Map<String, Object>) - Method in interface org.jmol.api.JmolRepaintManager
 
renderExport(GData, ModelSet, Map<String, Object>) - Method in class org.jmol.render.RepaintManager
 
renderHeight - Variable in class org.jmol.awtjs.swing.Component
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.BackboneRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.CartoonRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.RibbonsRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.RocketsRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.StrandsRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.TraceRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.BackboneRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.CartoonRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.RibbonsRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.RocketsRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.StrandsRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.TraceRenderer
 
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.BackboneRenderer
 
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.CartoonRenderer
 
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.RibbonsRenderer
 
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.RocketsRenderer
 
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.StrandsRenderer
 
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.TraceRenderer
 
renderHermiteRibbon(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, int) - Method in class org.jmol.g3d.HermiteRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.BackboneRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.CartoonRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.RibbonsRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.StrandsRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.TraceRenderer
 
renderHermiteRope(boolean, int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.HermiteRenderer
 
renderInfo() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderInfo() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
 
rendering - Variable in class org.jmol.jvxl.data.JvxlData
 
renderIso() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderLabelOrMeasure(Text, String) - Method in class org.jmol.render.LabelsRenderer
 
renderLine(P3, P3, int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
 
renderLow - Variable in class org.jmol.render.MeshRenderer
 
renderMesh2(Mesh) - Method in class org.jmol.render.MeshRenderer
overridden in BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
renderMeshes() - Method in class org.jmol.renderbio.BioMeshRenderer
 
renderMeshRibbon() - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderPass2(short) - Static method in class org.jmol.util.C
 
renderPoints() - Method in class org.jmol.render.MeshRenderer
 
renderPoints() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderRockets() - Method in class org.jmol.renderbio.RocketsRenderer
 
renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolViewer
 
renderScreenImage(Object, int, int) - Method in class org.jmol.viewer.Viewer
JmolViewer interface uses this, but that is all
renderScreenImage(Object, Object) - Method in class jspecview.java.AwtPlatform
legacy apps will use this
renderScreenImage(Object, Object) - Method in class jspecview.js2d.JsPlatform
legacy apps will use this
renderScreenImage(Object, Object) - Method in interface org.jmol.api.GenericPlatform
Deprecated.
renderScreenImage(Object, Object) - Method in class org.jmol.awt.Platform
legacy apps will use this
renderScreenImage(Object, Object) - Method in class org.jmol.awtjs2d.Platform
legacy apps will use this
renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
Deprecated.
renderScreenImageStereo(Object, boolean, int, int) - Method in class org.jmol.viewer.Viewer
 
renderShape(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
 
renderStrands() - Method in class org.jmol.renderbio.StrandsRenderer
 
renderStrandShape() - Method in class org.jmol.renderbio.StrandsRenderer
 
renderTrace() - Method in class org.jmol.renderbio.TraceRenderer
 
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.render.MeshRenderer
 
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderWidth - Variable in class org.jmol.awtjs.swing.Component
 
rep(String, String, String) - Static method in class javajs.util.PT
Does a clean ITERATIVE replace of strFrom in str with strTo.
repaint() - Method in interface jspecview.api.AppletFrame
 
repaint() - Method in interface jspecview.api.JSVPanel
 
repaint() - Method in interface jspecview.api.PlatformDialog
 
repaint() - Method in interface jspecview.api.ScriptInterface
 
repaint() - Method in class jspecview.app.JSVApp
 
repaint() - Method in class jspecview.appletjs.JSVApplet
 
repaint() - Method in class jspecview.application.JSpecView
 
repaint() - Method in class jspecview.common.PanelData
 
repaint() - Method in class jspecview.dialog.JSVDialog
 
repaint() - Method in class jspecview.js2d.JsPanel
 
repaint() - Method in class org.jmol.awtjs.swing.Component
 
repaint() - Method in class org.jmol.awtjs.swing.JDialog
 
repaint(Object) - Method in class jspecview.java.AwtPlatform
 
repaint(Object) - Method in class jspecview.js2d.JsPlatform
 
repaint(Object) - Method in interface org.jmol.api.GenericPlatform
 
repaint(Object) - Method in class org.jmol.awt.Platform
 
repaint(Object) - Method in class org.jmol.awtjs2d.Platform
 
repaint(JSAppletObject, boolean) - Method in interface javajs.api.js.J2SObjectInterface
 
REPAINT_IGNORE - Static variable in class org.jmol.viewer.JC
 
repaintDone() - Method in class jspecview.common.JSViewer
 
repaintDone() - Method in class jspecview.common.RepaintManager
 
repaintDone() - Method in interface org.jmol.api.JmolRepaintManager
 
repaintDone() - Method in class org.jmol.render.RepaintManager
 
repaintIfReady(String) - Method in interface org.jmol.api.JmolRepaintManager
 
repaintIfReady(String) - Method in class org.jmol.render.RepaintManager
 
repaintManager - Variable in class jspecview.common.JSViewer
 
RepaintManager - Class in jspecview.common
 
RepaintManager - Class in org.jmol.render
 
RepaintManager() - Constructor for class org.jmol.render.RepaintManager
 
RepaintManager(JSViewer) - Constructor for class jspecview.common.RepaintManager
 
repaintwaitms - Static variable in class org.jmol.script.T
 
repaintWaitMs - Variable in class org.jmol.viewer.GlobalSettings
 
replace - Static variable in class org.jmol.script.T
 
replace(int, int, String) - Method in class javajs.util.SB
 
replaceAllCharacters(String, String, String) - Static method in class javajs.util.PT
Does a clean replace of any of the characters in str with strTo If strTo contains strFrom, then only a single pass is done.
replaceGroup(Group, Group) - Method in class org.jmol.shape.Shape
 
replaceGroup(Group, Group) - Method in class org.jmol.shapebio.BioShapeCollection
 
replaceGroup(Group, Group) - Method in class org.jmol.viewer.ShapeManager
 
replaceQuotedStrings(String, Lst<String>, Lst<String>) - Static method in class javajs.util.PT
 
replaceStrings(String, Lst<String>, Lst<String>) - Static method in class javajs.util.PT
 
replaceTransformMatrix(M4) - Method in interface org.jmol.api.SymmetryInterface
 
replaceTransformMatrix(M4) - Method in class org.jmol.symmetry.Symmetry
 
replaceWithCharacter(String, String, char) - Static method in class javajs.util.PT
Does a clean replace of any of the characters in str with chrTo If strTo contains strFrom, then only a single pass is done.
reply(int, Object) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
reply(int, Object) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
report(String, boolean) - Method in class org.jmol.minimize.Minimizer
 
report(String, boolean) - Method in class org.jmol.script.ScriptEval
 
reportAll - Variable in class org.jmol.shape.Sticks
 
reportSelection(int) - Method in class org.jmol.viewer.ChimeMessenger
report atom selection in Chime format
reportSelection(int) - Method in interface org.jmol.viewer.JmolChimeMessenger
 
repositionWindow(String, Component) - Method in class org.openscience.jmol.app.HistoryFile
Uses the informations in the history to reposition the window.
repositionWindow(String, Component, int, int, boolean) - Method in class org.openscience.jmol.app.HistoryFile
Uses the informations in the history to reposition the window.
requestFocusInWindow(Object) - Method in class jspecview.java.AwtPlatform
 
requestFocusInWindow(Object) - Method in class jspecview.js2d.JsPlatform
 
requestFocusInWindow(Object) - Method in interface org.jmol.api.GenericPlatform
 
requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
 
requestFocusInWindow(Object) - Method in class org.jmol.awtjs2d.Platform
 
requestRepaint() - Method in class jspecview.common.JSViewer
 
requestRepaintAndWait(String) - Method in interface org.jmol.api.JmolRepaintManager
 
requestRepaintAndWait(String) - Method in class org.jmol.render.RepaintManager
 
requestRepaintAndWait(String) - Method in class org.jmol.viewer.Viewer
 
RequestThread() - Constructor for class jspecview.java.AwtPanel.RequestThread
 
requiresBSFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
requiresEndTag() - Method in class jspecview.source.XMLParser
 
reset - Static variable in class org.jmol.script.T
 
reset() - Method in class com.jcraft.jzlib.Adler32
 
reset() - Method in interface com.jcraft.jzlib.Checksum
 
reset() - Method in class com.jcraft.jzlib.CRC32
 
reset() - Method in class com.jcraft.jzlib.Inflater
 
reset() - Method in class com.jcraft.jzlib.InflaterInputStream
 
reset() - Method in interface javajs.api.GenericOutputChannel
 
reset() - Method in class javajs.util.ArrayDataReader
 
reset() - Method in class javajs.util.ListDataReader
 
reset() - Method in class javajs.util.OC
 
reset() - Method in class jme.JME
 
reset() - Method in class jspecview.common.JSVZipFileSequentialReader
 
reset() - Method in class org.jmol.thread.JmolThread
 
reset() - Method in class org.jmol.util.BoxInfo
 
reset(boolean) - Method in class org.jmol.viewer.Viewer
 
reset(int) - Method in class org.jmol.util.CommandHistory
Resets instance.
RESET_NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
 
resetAromatic() - Method in class org.jmol.modelset.BondCollection
 
resetAtomPickType() - Method in class org.jmol.modelkit.ModelKit
 
resetBioshapes(BS) - Method in class org.jmol.viewer.ShapeManager
 
resetBoundCount() - Method in class org.jmol.modelset.Model
 
resetChanged() - Method in class com.sparshui.server.TouchPoint
Reset the changed flag.
resetDSSR(boolean) - Method in class org.jmol.modelset.Model
Something has changed; clear the DSSR cache and possibly remove DSSR entirely.
resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
reset some parameters at the "MAP" keyword or initially
resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
 
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
resetLighting() - Method in class org.jmol.viewer.StateManager
Reset lighting to Jmol defaults
resetLong(long) - Method in class com.jcraft.jzlib.Adler32
 
resetLong(long) - Method in interface com.jcraft.jzlib.Checksum
 
resetLong(long) - Method in class com.jcraft.jzlib.CRC32
 
resetMolecules() - Method in class org.jmol.modelset.ModelSet
 
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
something has arisen that requires resetting of the navigation point.
resetObjects() - Method in class org.jmol.shape.MeshCollection
 
resetRasmolBonds(BS, int) - Method in class org.jmol.modelsetbio.BioModel
from Trajectory.setAtomPositions base models only; not trajectories
resetRotation() - Method in class org.jmol.viewer.TransformManager
 
resetRotation() - Method in class org.jmol.viewer.TransformManager4D
 
resetScaleFactors() - Method in class jspecview.common.ViewData
 
resetShapes(boolean) - Method in class org.jmol.viewer.ShapeManager
 
resetShapes(boolean) - Method in class org.jmol.viewer.Viewer
 
resetSlab() - Method in class org.jmol.util.MeshSurface
 
resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
resetView() - Method in class jspecview.common.PanelData
Resets the spectrum to it's original view
residue - Static variable in class org.jmol.script.T
 
RESIZE - Enum constant in enum class org.jmol.c.CBK
 
resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ResizeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
 
resizeApplet(Object, int[]) - Method in interface javajs.api.js.J2SObjectInterface
 
resizeInnerPanel(int, int) - Method in class org.jmol.api.JmolViewer
 
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.StatusManager
 
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.Viewer
 
resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
 
resizeInnerPanel(String) - Method in class org.jmol.util.GenericApplet
 
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
resizeInnerPanelString(String) - Method in class org.jmol.viewer.StatusManager
called by file droppers
resLabel - Variable in class jspecview.source.AnIMLReader
 
resno - Static variable in class org.jmol.script.T
 
resolution - Variable in class jspecview.export.AMLExporter
 
resolution - Variable in class jspecview.export.CMLExporter
 
resolution - Variable in class jspecview.source.AnIMLReader
 
resolution - Variable in class org.jmol.jvxl.readers.Parameters
 
resolution - Static variable in class org.jmol.script.T
 
resolveDataBase(String, String, String) - Static method in class org.jmol.viewer.JC
 
resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
Resolver - Class in org.jmol.adapter.smarter
 
Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
 
resourceName - Variable in class org.jmol.quantum.MepCalculation
 
restorativeForceAndAngleRadians(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndDistance(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndOutOfPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndTorsionAngleRadians(V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restore - Static variable in class org.jmol.script.T
 
restore(float, boolean) - Method in class org.jmol.modelset.Orientation
 
restoreAtomPositions(P3[]) - Method in class org.jmol.modelset.ModelSet
 
restoreBonds(String) - Method in class org.jmol.viewer.StateManager
 
restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
 
restoreScene(String, float) - Method in class org.jmol.viewer.StateManager
 
restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
restoreSelection(String) - Method in class org.jmol.viewer.StateManager
 
restoreUnitCell(String) - Method in class org.jmol.viewer.StateManager
 
restoreXY(double[][]) - Method in class jme.JMEmol
 
restrict - Static variable in class org.jmol.script.T
 
restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
restrictSelected(boolean, boolean) - Method in class org.jmol.viewer.ShapeManager
 
restrictToModel(BS, int) - Method in class org.jmol.viewer.Viewer
Restrict this bitset to the current model or its initial atom's model.
RESU - Static variable in class org.jmol.util.ColorEncoder
 
resume - Static variable in class org.jmol.script.T
 
resumeEval() - Method in class org.jmol.thread.JmolThread
 
resumeEval(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
 
resumeEval(Object) - Method in class org.jmol.script.ScriptEval
From dispatchCommands and JmolThread resumeEval.
resumePausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
 
resumePausedExecution() - Method in class org.jmol.script.ScriptEval
 
returncmd - Static variable in class org.jmol.script.T
 
reverse - Static variable in class org.jmol.script.T
 
reverse(Coordinate[]) - Static method in class jspecview.common.Coordinate
 
reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
Note, this may be incompatible with [$(select(..))] THIS IS NOT DEPENDABLE.
reversecolor - Static variable in class org.jmol.script.T
 
reverseColor - Variable in class org.jmol.shape.Mesh
 
reversed - Variable in class org.jmol.modelsetbio.BioPolymer
 
reverseModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
reversePlot() - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that toggles reversing the plot on a JSVPanel
reversePlot() - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that toggles reversing the plot on a JSVPanel
reversePlot() - Method in class jspecview.appletjs.JSVApplet
 
reversePlot() - Method in class jspecview.application.MainFrame
 
REVERSEPLOT - Enum constant in enum class jspecview.common.ScriptToken
 
revertStereo - Variable in class jme.JME
 
rewind - Static variable in class org.jmol.script.T
 
rgb(int, int, int) - Static method in class javajs.util.CU
 
Rgb16 - Class in org.jmol.util
 
Rgb16() - Constructor for class org.jmol.util.Rgb16
 
rgbFractionalFromArgb(int) - Method in class org.jmol.export.___Exporter
 
rgbFractionalFromColix(short) - Method in class org.jmol.export.___Exporter
 
rgbToHSL(P3, boolean) - Static method in class javajs.util.CU
Convert RGB values to HSL (hue/saturation/lightness)
rgbToXyz(P3, P3) - Method in class javajs.img.GifEncoder
 
RHOMB_TO_HEX - Static variable in class org.jmol.util.SimpleUnitCell
 
ribbon - Static variable in class org.jmol.script.T
 
ribbonaspectratio - Static variable in class org.jmol.script.T
 
ribbonborder - Static variable in class org.jmol.script.T
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.BackboneRenderer
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.CartoonRenderer
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.RocketsRenderer
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.StrandsRenderer
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.TraceRenderer
 
Ribbons - Class in org.jmol.shapebio
 
Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
 
RibbonsRenderer - Class in org.jmol.renderbio
 
RibbonsRenderer() - Constructor for class org.jmol.renderbio.RibbonsRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.BackboneRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.CartoonRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.RibbonsRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.RocketsRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.StrandsRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.TraceRenderer
 
right - Variable in class jspecview.common.PanelData
 
right - Static variable in class org.jmol.script.T
 
RIGHT - Static variable in class org.jmol.awtjs.swing.SwingConstants
 
RIGHT - Static variable in class org.jmol.viewer.binding.Binding
 
rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
rightbrace - Static variable in class org.jmol.script.T
 
rightDifference(Quat) - Method in class javajs.util.Quat
 
rightJustify(String, String) - Static method in class jme.JMEUtil
 
rightJustify(SB, String, String) - Static method in class javajs.util.PT
 
rightMargin - Static variable in class jspecview.common.PanelData
 
rightparen - Static variable in class org.jmol.script.T
 
rightsquare - Static variable in class org.jmol.script.T
 
RL() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
rldecode32(byte[], int) - Static method in class javajs.util.MessagePackReader
mmtf type 7 Decode an array of int32 using run-length decoding.
rldecode32Delta(byte[], int) - Static method in class javajs.util.MessagePackReader
mmtf type 8 Decode an array of int32 using run-length decoding of a difference array.
rldecode32ToChar(byte[], int) - Static method in class javajs.util.MessagePackReader
mmtf type 6 Decode an array of int32 using run-length decoding to one char per int.
rldecode32ToStr(byte[]) - Static method in class javajs.util.MessagePackReader
mmtf type 5 Decode each four bytes as a 1- to 4-character string label where a 0 byte indicates end-of-string.
rldecodef(byte[], int, float) - Static method in class javajs.util.MessagePackReader
mmtf type 9 Decode an array of int32 using run-length decoding and divide by a divisor to give a float32.
rmsd - Static variable in class org.jmol.script.T
 
rna - Static variable in class org.jmol.script.T
 
RNA - Enum constant in enum class org.jmol.c.STR
 
RNA_MASK - Static variable in class org.jmol.viewer.JC
 
rna3d - Static variable in class org.jmol.script.T
 
rNums - Static variable in interface org.apache.tools.bzip2.BZip2Constants
This array really shouldn't be here.
rock - Static variable in class org.jmol.script.T
 
rocket - Static variable in class org.jmol.script.T
 
rocketbarrels - Static variable in class org.jmol.script.T
 
RocketRenderer - Class in org.jmol.renderbio
 
RocketRenderer() - Constructor for class org.jmol.renderbio.RocketRenderer
 
Rockets - Class in org.jmol.shapebio
 
Rockets() - Constructor for class org.jmol.shapebio.Rockets
 
RocketsRenderer - Class in org.jmol.renderbio
 
RocketsRenderer() - Constructor for class org.jmol.renderbio.RocketsRenderer
 
ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
 
rotate - Static variable in class org.jmol.script.T
 
rotate(T3) - Method in class javajs.util.M34
 
ROTATE_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
ROTATE_EVENT - Static variable in class com.sparshui.GestureType
 
ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
ROTATE_GESTURE - Static variable in class com.sparshui.GestureType
 
ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
rotate2(T3, T3) - Method in class javajs.util.M34
Transform the vector vec using this Matrix3f and place the result into vecOut.
rotate3DBall(float, float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotate45 - Static variable in class org.jmol.script.T
 
rotate4DBall(float, float, float) - Method in class org.jmol.viewer.TransformManager4D
 
rotateAboutPointsInternal(JmolScriptEvaluator, P3, P3, float, float, boolean, BS, V3, Lst<P3>, float[], M4, boolean) - Method in class org.jmol.viewer.Viewer
 
rotateAxes(int, V3[], P3, M3) - Method in interface org.jmol.api.SymmetryInterface
 
rotateAxes(int, V3[], P3, M3) - Method in class org.jmol.symmetry.Symmetry
 
rotateAxisAngle(V3, float) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.Viewer
 
rotateAxisAngleRadiansFixed(float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleRadiansInternal(float, BS, M4, boolean) - Method in class org.jmol.viewer.TransformManager
 
RotateEvent - Class in com.sparshui.common.messages.events
 
RotateEvent() - Constructor for class com.sparshui.common.messages.events.RotateEvent
 
RotateEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.RotateEvent
Constructs a new Rotate Event based on a serial representation of a rotate event.
RotateEvent(float, Location, long) - Constructor for class com.sparshui.common.messages.events.RotateEvent
 
rotateFront() - Method in class org.jmol.api.JmolViewer
 
rotateFront() - Method in class org.jmol.viewer.Viewer
 
rotateHexCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
rotatePoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
 
rotateSelected - Static variable in class org.jmol.script.T
 
rotateTranslate(Quat, T3, boolean) - Method in class org.jmol.shape.Mesh
 
rotateXRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager4D
 
rotateYRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
 
rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
 
rotation - Static variable in class org.jmol.script.T
 
rotationradius - Static variable in class org.jmol.script.T
 
rotTrans(T3) - Method in class javajs.util.M4
Transforms the point parameter with this Matrix4f and places the result back into point.
rotTrans2(T3, T3) - Method in class javajs.util.M4
Transforms the point parameter with this Matrix4f and places the result into pointOut.
round() - Method in class org.openscience.jmol.app.janocchio.Measure
 
round(double) - Static method in class org.jmol.export.___Exporter
 
round(float) - Method in class javajs.util.M4
 
round(T3) - Static method in class org.jmol.export.___Exporter
 
roundInt(int) - Static method in class org.jmol.util.GData
JavaScript won't really have an integer here after integer division.
row - Static variable in class org.jmol.script.T
 
ROYGB - Static variable in class org.jmol.util.ColorEncoder
 
rubberband - Static variable in class org.jmol.script.T
 
run() - Method in class com.sparshui.client.ClientServerConnection
Begin processing requests.
run() - Method in class com.sparshui.server.GestureServer
Start accepting connections.
run() - Method in class com.sparshui.server.InputDeviceConnection
Begin receiving data from the input device.
run() - Method in class jspecview.java.AwtPanel.RequestThread
 
run() - Method in class org.jmol.io.FileReader
 
run() - Method in class org.jmol.io.FilesReader
 
run() - Method in class org.jmol.script.CommandWatcherThread
 
run() - Method in class org.jmol.script.ScriptProcessRunnable
 
run() - Method in class org.jmol.thread.JmolThread
 
run() - Method in class org.openscience.jmol.app.InputScannerThread
 
run() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
 
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
 
run1(int) - Method in class org.jmol.minimize.MinimizationThread
 
run1(int) - Method in class org.jmol.navigate.Navigator
 
run1(int) - Method in class org.jmol.script.CommandWatcherThread
 
run1(int) - Method in class org.jmol.script.ScriptQueueThread
 
run1(int) - Method in class org.jmol.thread.AnimationThread
 
run1(int) - Method in class org.jmol.thread.HoverWatcherThread
 
run1(int) - Method in class org.jmol.thread.JmolThread
 
run1(int) - Method in class org.jmol.thread.MoveToThread
 
run1(int) - Method in class org.jmol.thread.SpinThread
Java: run1(INIT) while(!interrupted()) { run1(MAIN) } run1(FINISH) JavaScript: run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or run1(FINISH) and return
run1(int) - Method in class org.jmol.thread.TimeoutThread
 
run1(int) - Method in class org.jmol.thread.VibrationThread
 
RUNA - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
runAllProcesses(Viewer) - Method in interface org.jmol.api.JmolParallelProcessor
 
runAllProcesses(Viewer) - Method in class org.jmol.script.ScriptParallelProcessor
 
runAsync(JMEUtil.RunAsyncCallback) - Static method in class jme.JMEUtil
 
RUNB - Static variable in interface org.apache.tools.bzip2.BZip2Constants
 
runBufferedSafely(String, SB) - Method in class org.jmol.script.ScriptEval
 
runButton - Variable in class org.jmol.console.GenericConsole
 
runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
runScript(String) - Method in interface jspecview.api.JSVAppletInterface
runs a script in proper order as listed
runScript(String) - Method in interface jspecview.api.ScriptInterface
 
runScript(String) - Method in class jspecview.app.JSVApp
 
runScript(String) - Method in class jspecview.appletjs.JSVApplet
 
runScript(String) - Method in class jspecview.application.JSpecView
for the applet, this is queued
runScript(String) - Method in class jspecview.application.MainFrame
ScriptInterface requires this.
runScript(String) - Method in class jspecview.common.JSViewer
 
runScript(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
runScript(String) - Method in class org.jmol.api.JmolViewer
starting with 14.8.2-beta-2017-02-06, uses script(xxxx) function; see runScriptCautiously for the older version
runScript(String) - Method in interface org.jmol.api.JSVInterface
 
runScript(String) - Method in class org.jmol.script.ScriptEval
 
runScript(String) - Method in class org.jmol.viewer.Viewer
Run a script immediately using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )
runScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
no queuing here -- called by MainFrame
runScriptBuffer(String, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
runScriptBuffer(String, SB, boolean) - Method in class org.jmol.script.ScriptEval
runs a script immediately and sends selected output to a provided SB
runScriptCautiously(String) - Method in class org.jmol.api.JmolViewer
Formerly runScript(script).
runScriptCautiously(String) - Method in class org.jmol.viewer.Viewer
formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script.
runScriptFromThread(Lst<Object>) - Method in class org.jmol.script.ScriptManager
 
runScriptNow() - Method in class org.jmol.script.ScriptManager
 
runScriptNow(String) - Method in interface jspecview.api.JSVAppletInterface
 
runScriptNow(String) - Method in interface jspecview.api.ScriptInterface
 
runScriptNow(String) - Method in class jspecview.app.JSVApp
 
runScriptNow(String) - Method in class jspecview.appletjs.JSVApplet
 
runScriptNow(String) - Method in class jspecview.application.JSpecView
 
runScriptNow(String) - Method in class jspecview.application.MainFrame
 
runScriptNow(String) - Method in class jspecview.common.JSViewer
 
runSleep(int, int) - Method in class org.jmol.thread.JmolThread
 
runsmi - Variable in class jme.JME
 
runUserAction(String, Object[], Viewer) - Static method in class org.jmol.script.ScriptEval
 
RWB - Static variable in class org.jmol.util.ColorEncoder
 
rxyz - Static variable in class org.jmol.script.T
 

S

S - Static variable in class org.jmol.quantum.QS
 
s1 - Variable in class org.jmol.render.FontLineShapeRenderer
 
s2 - Variable in class org.jmol.render.FontLineShapeRenderer
 
safeJSON(String, Object) - Static method in class org.jmol.script.SV
Safely create a JSON key - object pair, allowing for already-named arrays
safeTruncate(float, int) - Static method in class javajs.util.PT
 
sameAs(int, int) - Method in class org.jmol.modelset.Measurement
 
sameAsPoints(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
sampleID - Variable in class jspecview.source.AnIMLReader
 
samplenum - Variable in class jspecview.source.AnIMLReader
 
sampleowner - Variable in class jspecview.source.AnIMLReader
 
sampleRefNum - Variable in class jspecview.source.AnIMLReader
 
sasurface - Static variable in class org.jmol.script.T
 
SAUSAGE - Static variable in class org.jmol.shapecgo.CGOMesh
 
save - Static variable in class org.jmol.script.T
 
save() - Method in class org.openscience.jmol.app.HistoryFile
Saves properties to the history file.
saveAtomPositions() - Method in class org.jmol.modelset.ModelSet
 
saveBonds(String) - Method in class org.jmol.viewer.StateManager
 
saveContext(String, Object) - Method in class org.jmol.viewer.StateManager
 
saveCoordinates(String, BS) - Method in class org.jmol.viewer.StateManager
 
saved - Static variable in class org.jmol.script.T
 
saved - Variable in class org.jmol.viewer.StateManager
 
saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
saveImage(String, GenericFileInterface, OC) - Method in interface jspecview.api.JSVPanel
 
saveImage(String, GenericFileInterface, OC) - Method in class jspecview.java.AwtPanel
 
saveImage(String, GenericFileInterface, OC) - Method in class jspecview.js2d.JsPanel
 
saveImage(JSAppletObject, String, String) - Method in interface javajs.api.js.J2SObjectInterface
 
saveModelOrientation(int, Orientation) - Method in class org.jmol.modelset.ModelSet
 
saveName - Variable in class org.jmol.modelset.Orientation
 
saveOrientation(String, float[]) - Method in class org.jmol.viewer.StateManager
 
savePathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
saveProperties(Properties) - Method in class jspecview.app.JSVAppPro
 
saveProperties(Properties) - Method in class jspecview.application.JSpecView
 
saveProperties(Properties) - Method in interface org.jmol.api.JSVInterface
 
saveProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
saveproteinstructurestate - Static variable in class org.jmol.script.T
 
saveScene(String, Map<String, Object>) - Method in class org.jmol.viewer.StateManager
 
saveSelection(String, BS) - Method in class org.jmol.viewer.StateManager
 
saveState(String) - Method in class org.jmol.viewer.StateManager
 
saveStructure(String) - Method in class org.jmol.viewer.StateManager
 
saveUnitCell(String) - Method in class org.jmol.viewer.StateManager
 
saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
saveWindowSizes() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
saveWindowSizes() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
saveXY() - Method in class jme.JMEmol
 
saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Saves the currently active collection as a multistep XYZ file.
say(String) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SB - Class in javajs.util
Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
SB() - Constructor for class javajs.util.SB
 
sbKey - Variable in class org.jmol.minimize.MinAngle
 
sbOut - Variable in class org.jmol.jvxl.data.JvxlData
 
sbOut - Variable in class org.jmol.jvxl.readers.Parameters
 
sbType - Variable in class org.jmol.minimize.MinAngle
 
sc - Variable in class org.jmol.thread.JmolThread
 
SC - Interface in org.jmol.api
SwingComponent interface common to javax.swing and org.jmol.awtjs.swing Can be augmented as needed, provided classes of org.jmol.awtjs.swing are also updated.
scale - Variable in class org.jmol.modelset.TickInfo
 
scale - Static variable in class org.jmol.script.T
 
scale - Variable in class org.jmol.shape.Axes
 
scale - Variable in class org.jmol.shapespecial.DrawMesh
 
scale - Variable in class org.jmol.shapespecial.Polyhedron
 
scale(double) - Method in class javajs.util.T3d
Sets the value of this tuple to the scalar multiplication of itself.
scale(float) - Method in class javajs.util.M3
Multiplies each element of this matrix by a scalar.
scale(float) - Method in class javajs.util.M4
Multiplies each element of this matrix by a scalar.
scale(float) - Method in class javajs.util.T3
Sets the value of this tuple to the scalar multiplication of itself.
scale3d - Variable in class org.jmol.jvxl.data.JvxlData
 
scale3d - Variable in class org.jmol.jvxl.readers.Parameters
 
scale3d - Static variable in class org.jmol.script.T
 
scale3d - Variable in class org.jmol.shape.Mesh
 
scale3D - Variable in class org.jmol.viewer.TransformManager
 
scale4(float) - Method in class javajs.util.T4
Sets the value of this tuple to the scalar multiplication of itself.
scaleAdd(double, T3d, T3d) - Method in class javajs.util.T3d
Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
scaleAdd(int, T3i, T3i) - Method in class javajs.util.T3i
Sets the value of this tuple to the scalar multiplication of tuple t1 plus tuple t2 (this = s*t1 + t2).
scaleAdd(Matrix, double) - Method in class javajs.util.Matrix
X = A + B*scale
scaleAdd2(double, T3d, T3d) - Method in class javajs.util.T3d
Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
scaleAdd2(float, T3, T3) - Method in class javajs.util.T3
Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
scaleangstromsperinch - Static variable in class org.jmol.script.T
 
scaleAxes(float[]) - Method in class org.jmol.shapespecial.Ellipsoid
 
scaleBox(P3[], float) - Static method in class org.jmol.util.BoxInfo
 
SCALEBY - Enum constant in enum class jspecview.common.ScriptToken
 
scaleColor - Variable in class jspecview.common.PanelData
 
SCALECOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
ScaleData - Class in jspecview.common
Stores information about scale and range that JSVPanel needs to to display a graph with a single plot.
ScaleData(Coordinate[], int, int, boolean, boolean) - Constructor for class jspecview.common.ScaleData
Calculates values that JSVPanel needs in order to render a graph, (eg.
scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
 
scaleFractionalVibs() - Method in class org.jmol.adapter.smarter.XtalSymmetry
magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes.
scaleObject - Variable in class org.jmol.shape.Echo
 
scalePixelsPerAngstrom - Variable in class org.jmol.export.___Exporter
 
scalePixelsPerMicron - Variable in class org.jmol.modelset.Text
 
scalePixelsPerMicron - Variable in class org.jmol.render.MeshRenderer
 
scaleSelectedBy(double) - Method in class jspecview.common.PanelData
 
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.CsfReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.AdfReader
Perform implementation-specific scaling.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.AmsReader
Perform implementation-specific scaling.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.DgridReader
Perform implementation-specific scaling.
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.AmsReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.DgridReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
 
scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
scaleSpectrum(int, double) - Method in class jspecview.common.ViewData
 
scaleT(T3) - Method in class javajs.util.T3
{x*p.x, y*p.y, z*p.z) used for three-way scaling
scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
 
scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
 
scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
 
scaleVectorsToMax(float) - Method in class org.jmol.modelset.AtomCollection
Scales vibrations and associated vectors such that the maximum length is the given value
scaleVibration(float) - Method in interface org.jmol.api.JmolModulationSet
 
scaleVibration(float) - Method in class org.jmol.util.ModulationSet
 
scaleYBy(double) - Method in class jspecview.common.PanelData
 
scalingFactor - Variable in class jspecview.common.PanelData
 
scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
 
scene - Static variable in class org.jmol.script.T
 
SCENE_TAG - Static variable in class org.jmol.viewer.OutputManagerAwt
 
SCENE_TAG - Static variable in class org.jmol.viewer.OutputManagerJS
 
schemes - Variable in class org.jmol.util.ColorEncoder
 
scm - Variable in class org.jmol.viewer.Viewer
 
score - Variable in class org.jmol.util.ContactPair
 
scrCoords - Variable in class org.jmol.renderspecial.DotsRenderer
 
SCREEN - Enum constant in enum class org.jmol.atomdata.RadiusData.EnumType
 
screenDotCount - Variable in class org.jmol.renderspecial.DotsRenderer
 
screenHeight - Variable in class org.jmol.export.___Exporter
 
screenLevel - Variable in class org.jmol.renderspecial.DotsRenderer
 
screenLocation(Location) - Static method in class com.sparshui.common.Location
 
screenPixelCount - Variable in class org.jmol.viewer.TransformManager
 
screens - Variable in class org.jmol.render.MeshRenderer
 
screenSize - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
screenWidth - Variable in class org.jmol.export.___Exporter
 
screenx - Static variable in class org.jmol.script.T
 
screenxyz - Static variable in class org.jmol.script.T
 
screeny - Static variable in class org.jmol.script.T
 
screenz - Static variable in class org.jmol.script.T
 
script - Variable in class org.jmol.jvxl.readers.Parameters
 
script - Variable in class org.jmol.modelset.Text
 
script - Variable in class org.jmol.script.ScriptContext
 
script - Variable in class org.jmol.script.ScriptCompiler
 
script - Static variable in class org.jmol.script.T
 
script - Variable in class org.jmol.thread.TimeoutThread
 
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
script(String) - Method in class jspecview.appletjs.JSVApplet
Deprecated.
script(String) - Method in class jspecview.appletjs.JSVAppletPro
JSVAppletPro uses "script()" for executing a real script, not a parameter initialization.
script(String) - Method in interface org.jmol.api.JmolAppletInterface
 
script(String) - Method in class org.jmol.api.JmolViewer
 
script(String) - Method in class org.jmol.util.GenericApplet
 
script(String) - Method in class org.jmol.viewer.Viewer
 
SCRIPT - Enum constant in enum class jspecview.common.ScriptToken
 
SCRIPT - Enum constant in enum class org.jmol.c.CBK
 
SCRIPT_COMPLETED - Static variable in class org.jmol.viewer.JC
 
SCRIPT_CONSOLE - Static variable in class org.jmol.viewer.JC
 
SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JC
 
SCRIPT_EXT - Static variable in class org.jmol.viewer.JC
 
SCRIPT_GUI - Static variable in class org.jmol.viewer.JC
 
SCRIPT_ISEDITOR - Static variable in class org.jmol.viewer.JC
 
SCRIPT_NOENDCHECK - Static variable in class org.jmol.viewer.JC
 
SCRIPT_ONLY - Static variable in interface org.jmol.api.JmolScriptManager
 
SCRIPT_QUIET - Static variable in class org.jmol.viewer.JC
 
SCRIPT_START - Static variable in class org.jmol.viewer.JC
 
SCRIPT_STEP - Static variable in class org.jmol.viewer.JC
 
SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
scriptCallback(String) - Method in class org.molecularplayground.MPJmolApp
 
scriptCheck(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptCheck(String) - Method in class org.jmol.api.JmolViewer
 
scriptCheck(String) - Method in class org.jmol.util.GenericApplet
 
scriptCheck(String) - Method in class org.jmol.viewer.Viewer
 
scriptCheckRet(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
scriptCheckRet(String, boolean) - Method in class org.jmol.script.ScriptManager
 
scriptCommand - Static variable in class org.jmol.script.T
 
scriptCommand - Variable in class org.jmol.shape.Mesh
 
ScriptCompiler - Class in org.jmol.script
 
ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
 
scriptCompleted(StatusManager, String, String) - Method in class org.jmol.viewer.ChimeMessenger
called when a script exits.
scriptCompleted(StatusManager, String, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
 
ScriptContext - Class in org.jmol.script
 
scriptEcho(String) - Method in class org.jmol.viewer.Viewer
 
scriptEditor - Variable in class org.jmol.console.JmolConsole
 
ScriptEditor - Class in org.jmol.console
 
ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
 
ScriptEditorAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
 
scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
 
ScriptError - Class in org.jmol.script
Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
ScriptError() - Constructor for class org.jmol.script.ScriptError
 
ScriptEval - Class in org.jmol.script
 
ScriptEval() - Constructor for class org.jmol.script.ScriptEval
 
ScriptException - Exception Class in org.jmol.script
 
ScriptExt - Class in org.jmol.scriptext
 
ScriptExt() - Constructor for class org.jmol.scriptext.ScriptExt
 
scriptFileName - Variable in class org.jmol.script.ScriptContext
 
scriptFileName - Variable in class org.jmol.script.ScriptEval
 
ScriptFunction - Class in org.jmol.script
 
ScriptFunction() - Constructor for class org.jmol.script.ScriptFunction
 
ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
 
ScriptInterface - Interface in jspecview.api
 
ScriptInterruption - Exception Class in org.jmol.script
 
ScriptInterruption(ScriptEval, String, int) - Constructor for exception class org.jmol.script.ScriptInterruption
 
scriptLevel - Variable in class org.jmol.script.ScriptEval
 
ScriptManager - Class in org.jmol.script
 
ScriptManager() - Constructor for class org.jmol.script.ScriptManager
 
ScriptMathProcessor - Class in org.jmol.script
Reverse Polish Notation Engine for IF, SET, and @{...} Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f -- Bob Hanson 2/16/2007
scriptNoWait(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptNoWait(String) - Method in class org.jmol.util.GenericApplet
 
ScriptParallelProcessor - Class in org.jmol.script
 
ScriptParallelProcessor() - Constructor for class org.jmol.script.ScriptParallelProcessor
parallel operations
ScriptParam - Class in org.jmol.script
The ScriptParam class holds methods used to parse parameters in Jmol scripts.
ScriptParam() - Constructor for class org.jmol.script.ScriptParam
 
ScriptProcessRunnable - Class in org.jmol.script
 
ScriptProcessRunnable(ScriptParallelProcessor, ScriptProcess, Object, ShapeManager) - Constructor for class org.jmol.script.ScriptProcessRunnable
 
scriptqueue - Static variable in class org.jmol.script.T
 
scriptQueue - Variable in class jspecview.common.JSViewer
 
scriptQueue - Variable in class org.jmol.script.ScriptManager
 
ScriptQueueThread - Class in org.jmol.script
 
ScriptQueueThread(ScriptManager, Viewer, boolean, int) - Constructor for class org.jmol.script.ScriptQueueThread
 
scriptreportinglevel - Static variable in class org.jmol.script.T
 
scriptStatus(String) - Method in class org.jmol.viewer.Viewer
scriptCallback is the primary way to monitor script status.
scriptStatusMsg(String, String) - Method in class org.jmol.viewer.Viewer
 
ScriptToken - Enum Class in jspecview.common
ScriptToken takes care of script command processing
ScriptTokenizer - Class in jspecview.common
 
ScriptTokenizer(String, boolean) - Constructor for class jspecview.common.ScriptTokenizer
 
scriptWait(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWait(String) - Method in class org.jmol.api.JmolViewer
 
scriptWait(String) - Method in class org.jmol.util.GenericApplet
 
scriptWait(String) - Method in class org.jmol.viewer.Viewer
 
scriptWait(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWait(String, String) - Method in class org.jmol.util.GenericApplet
 
scriptWaitOutput(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWaitOutput(String) - Method in class org.jmol.util.GenericApplet
 
scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
 
scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
 
ScriptWindowAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
 
sD - Variable in class org.jmol.util.Point3fi
screen diameter
search - Static variable in class org.jmol.script.T
 
SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
 
seek(long) - Method in interface javajs.api.GenericBinaryDocument
 
seek(long) - Method in class javajs.util.BinaryDocument
 
SEESAW - Static variable in class org.jmol.smiles.SmilesStereo
 
select - Static variable in class org.jmol.script.T
 
select(BS, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
 
SELECT - Enum constant in enum class jspecview.common.ScriptToken
 
SELECT - Enum constant in enum class org.jmol.c.CBK
 
selectAll() - Method in class org.jmol.api.JmolViewer
 
selectAll() - Method in class org.jmol.viewer.Viewer
 
selectAll(boolean) - Method in class jspecview.dialog.ViewsDialog
 
selectallmodels - Static variable in class org.jmol.script.T
 
selectBonds(BS) - Method in class org.jmol.viewer.Viewer
 
selectDisplayed(BS) - Method in class org.jmol.modelset.Trajectory
Remove trajectories that are not currently displayed from the visible frames bitset.
selected - Static variable in class org.jmol.script.T
 
selectedfloat - Static variable in class org.jmol.script.T
 
selectedGroupCount - Variable in class org.jmol.modelset.Chain
Calculated just prior to coloring by group so that the range is appropriate for each chain.
selectedIndex - Variable in class org.jmol.modelset.Group
for coloring by group
selectedPanel - Variable in class jspecview.common.JSViewer
 
selectedPolyOnly - Variable in class org.jmol.render.MeshRenderer
 
selectedRow - Variable in class jspecview.java.AwtDialog
 
selectedRow - Variable in class jspecview.js2d.JsDialog
 
selectedTrajectory - Variable in class org.jmol.modelset.Model
 
selectedTreeNode(JSVTreeNode) - Method in class jspecview.common.JSViewer
 
selectFrameNode(JSVPanel) - Method in class jspecview.common.JSViewer
 
selectFromEntireSet(int) - Method in class jspecview.common.PanelData
sets bsSelected to the specified pointer from "select 3.1*1"
selecthetero - Static variable in class org.jmol.script.T
 
selecthydrogen - Static variable in class org.jmol.script.T
 
selection - Static variable in class org.jmol.script.T
 
selectionChanged(BS) - Method in interface org.jmol.api.JmolSelectionListener
Called when the selected atoms change
selectionhalos - Static variable in class org.jmol.script.T
 
SelectionManager - Class in org.jmol.viewer
 
selectPanel(JSVPanel, Lst<PanelNode>) - Method in class jspecview.common.JSViewer
 
selectPeakByFileIndex(String, String, String) - Method in class jspecview.common.PanelData
 
selectPeakByFileIndex(String, String, String) - Method in class jspecview.common.Spectrum
 
selectPeakByFilePathTypeModel(String, String, String) - Method in class jspecview.common.Spectrum
 
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
selectSpectrum(String, String, String, boolean) - Method in class jspecview.common.PanelData
 
selectStatus(BS, boolean, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
"SELECT" starting with comma triggers the SELECT callback from a SELECT command.
selectTableRow(int) - Method in interface jspecview.api.PlatformDialog
 
selectTableRow(int) - Method in class jspecview.dialog.JSVDialog
 
selectTableRow(int) - Method in class jspecview.java.AwtDialog
 
selectTableRow(int) - Method in class jspecview.js2d.JsDialog
 
semicolon - Static variable in class org.jmol.script.T
 
sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
sendConsoleEcho(String) - Method in class org.jmol.console.GenericConsole
 
sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
sendConsoleMessage(String) - Method in class org.jmol.console.GenericConsole
 
sendConsoleMessage(String) - Method in class org.jmol.viewer.Viewer
 
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
sendMessage(Map<String, Object>, String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
sendPanelChange() - Method in class jspecview.common.JSViewer
 
sendToJmol(int, String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
from JmolPanel and SYNC command
sendToJmol(int, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
send the message - not for replies.
seqcode - Variable in class org.jmol.modelset.Group
 
seqcode - Static variable in class org.jmol.script.T
 
seqid - Static variable in class org.jmol.script.T
 
sequence - Static variable in class org.jmol.script.T
 
sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
 
serialize() - Method in interface com.sparshui.common.Event
Serializes this event for transmission over the network.
serialize() - Method in class com.sparshui.common.messages.events.DragEvent
Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.FlickEvent
Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.RelativeDragEvent
Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.RotateEvent
Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.SpinEvent
Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.TouchEvent
Constructs the data packet with this event data.
serialize() - Method in class com.sparshui.common.messages.events.ZoomEvent
Constructs the data packet with this event data.
serializeDisplaySchemes(Writer) - Method in class jspecview.application.DisplaySchemesProcessor
Serializes the display schemes to the given writer
serverCycle() - Method in class org.molecularplayground.MPJmolApp
 
serverCycle() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
serverCycle() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
 
ServerToClientProtocol - Class in com.sparshui.server
Represents the server to client connection.
ServerToClientProtocol(Socket) - Constructor for class com.sparshui.server.ServerToClientProtocol
Constructs a new connection to the client.
service - Variable in class org.molecularplayground.MPJmolApp
 
SERVICE - Enum constant in enum class org.jmol.c.CBK
 
SERVICE_LOST - Static variable in class com.sparshui.common.messages.events.EventType
 
SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
 
set - Static variable in class org.jmol.script.T
 
set(double, double) - Method in class jspecview.common.Coordinate
Constructor
set(double, double, double) - Method in class javajs.util.T3d
Sets the value of this tuple to the specified xyz coordinates.
set(float, float, float) - Method in class javajs.util.T3
Sets the value of this tuple to the specified xyz coordinates.
set(float, float, float) - Method in interface org.jmol.util.Node
 
set(int) - Method in class javajs.util.BS
Sets the bit at the specified index to true.
set(int) - Method in class javajs.util.Eigen
 
set(int, int) - Method in class org.jmol.awtjs.swing.Dimension
 
set(int, int, char, int, int, char, int, int) - Method in class org.jmol.adapter.smarter.Structure
 
set(int, int, int) - Method in class javajs.util.T3i
Sets the value of this tuple to to the specified x, y, and z coordinates.
set(int, Map<String, Integer>, RadiusData, String, String, String, TickInfo, boolean, boolean, Boolean, boolean, int, short, Text, float, BS) - Method in class org.jmol.modelset.MeasurementData
 
set(int, BS, int[]) - Method in class org.jmol.minimize.MMConstraint
 
set(InputStream, String[], String) - Method in interface jspecview.api.JSVZipReader
 
set(InputStream, String[], String) - Method in class jspecview.common.JSVZipFileSequentialReader
 
set(Object, PrintLayout, boolean) - Method in interface jspecview.api.JSVPrintDialog
 
set(Object, PrintLayout, boolean) - Method in class jspecview.java.AwtPrintDialog
Initialises a modal PrintLayoutDialog with a default title of "Print Layout".
set(String) - Method in class org.jmol.viewer.binding.JmolBinding
 
set(String, int) - Method in interface org.jmol.api.JmolParallelProcessor
 
set(String, int) - Method in class org.jmol.script.ScriptFunction
 
set(GenericLineReader, BufferedReader, boolean) - Method in interface javajs.api.GenericCifDataParser
 
set(GenericLineReader, BufferedReader, boolean) - Method in class javajs.util.CifDataParser
A Chemical Information File data parser.
set(Quat) - Method in class javajs.util.Quat
 
set(JSViewer) - Method in interface jspecview.api.JSVFileDropper
 
set(JSViewer) - Method in interface jspecview.api.JSVFileHelper
 
set(JSViewer) - Method in class jspecview.dialog.DialogManager
 
set(JSViewer) - Method in class jspecview.java.AwtFileDropper
 
set(JSViewer) - Method in class jspecview.java.AwtFileHelper
 
set(JSViewer) - Method in class jspecview.js2d.JsFileHelper
 
set(PanelData, ScriptToken, String) - Method in class jspecview.common.ColorParameters
 
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
set(JmolJDXMOLReader, String, Map<String, Object>) - Method in interface org.jmol.api.JmolJDXMOLParser
 
set(JmolJDXMOLReader, String, Map<String, Object>) - Method in class org.jmol.jsv.JDXMOLParser
 
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.CircleRenderer
 
set(JmolRendererInterface, GData) - Method in interface org.jmol.g3d.G3DRenderer
 
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.HermiteRenderer
 
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.TriangleRenderer
 
set(SymmetryInterface, Atom, Atom[], BS, float) - Method in class org.jmol.symmetry.UnitCellIterator
 
set(AtomDataServer, int, short[]) - Method in interface org.jmol.api.JmolEnvCalc
 
set(AtomDataServer, int, short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
set(ModelSet) - Method in class org.jmol.modelset.MeasurementPending
 
set(ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
 
set(ModelSet, int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelset.Model
 
set(MeshSlicer) - Method in class org.jmol.util.MeshCapper
 
set(FileManager) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
 
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
 
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.io.FilesReader
 
set(TransformManager, Viewer) - Method in interface org.jmol.api.JmolNavigatorInterface
 
set(TransformManager, Viewer) - Method in class org.jmol.navigate.Navigator
 
set(Viewer) - Method in class org.jmol.adapter.readers.quantum.NBOParser
 
set(Viewer) - Method in interface org.jmol.api.JmolDataManager
 
set(Viewer) - Method in class org.jmol.quantum.MepCalculation
 
set(Viewer) - Method in class org.jmol.viewer.ChimeMessenger
 
set(Viewer) - Method in class org.jmol.viewer.DataManager
 
set(Viewer) - Method in interface org.jmol.viewer.JmolChimeMessenger
 
set(Viewer, BS) - Method in class org.jmol.symmetry.CIPData
Actual constructor.
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CDXMLWriter
 
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CIFWriter
 
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CMLWriter
 
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PDBWriter
 
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PWMATWriter
 
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.XSFWriter
 
set(Viewer, OC, Object[]) - Method in interface org.jmol.api.JmolWriter
 
set(Viewer, ModelSet) - Method in class org.jmol.modelsetbio.BioModelSet
 
set(Viewer, ShapeManager) - Method in interface org.jmol.api.JmolRepaintManager
 
set(Viewer, ShapeManager) - Method in class org.jmol.render.RepaintManager
 
set2(int, boolean) - Method in class org.jmol.smiles.SmilesBond
 
set2(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.Monomer
 
set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
set2DCrossHairsLinked(GraphSet, double, double, boolean) - Method in class jspecview.common.PanelData
 
set33(int, int, float) - Method in class javajs.util.M34
 
set3dContourVector(Lst<Object>, int[][], T3[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.
set4(float, float, float, float) - Method in class javajs.util.A4
Sets the value of this axis angle to the specified x,y,z,angle.
set4(float, float, float, float) - Method in class javajs.util.T4
Sets the value of this tuple to the specified xyzw coordinates.
setA(double[]) - Method in class javajs.util.T3d
Sets the value of this tuple from the 3 values specified in the array.
setA(double, double, Spectrum, String, boolean, boolean, int, int) - Method in class jspecview.common.Annotation
 
setA(float[]) - Method in class javajs.util.M3
Sets the values in this Matrix3f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
setA(float[]) - Method in class javajs.util.M4
Sets the values in this Matrix4f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
setA(float[]) - Method in class javajs.util.T3
Sets the value of this tuple from the 3 values specified in the array.
setAA(A4) - Method in class javajs.util.A4
Sets the value of this axis angle to the value of axis angle t1.
setAA(A4) - Method in class javajs.util.M3
Sets the value of this matrix to the matrix conversion of the single precision axis and angle argument.
setAA(A4) - Method in class javajs.util.Quat
 
setAA33(A4) - Method in class javajs.util.M34
 
setAbc(String, float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
set cell vectors by string.
setABC(int) - Method in class org.jmol.util.MeshSurface
 
setAbcFromParams(float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
 
setAbstractButtonLabels(Map<String, Object>, Map<String, String>) - Static method in class org.jmol.console.GenericConsole
 
setACDAssignments(String, String, int, Lst<String[]>, String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
setACDAssignments(String, String, int, Lst<String[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
 
setActionCommand(String) - Method in interface org.jmol.api.SC
 
setActionCommand(String) - Method in class org.jmol.awt.AwtSwingComponent
 
setActionCommand(String) - Method in class org.jmol.awtjs.swing.JComponent
 
setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
Changes the activation state for a logging level.
setActiveMenu(String) - Method in class org.jmol.modelkit.ModelKitPopup
Set the active menu and request a repaint.
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
 
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.P2nReader
 
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PdbReader
adaptable via subclassing
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PqrReader
 
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
setAlignment(int) - Method in class org.jmol.modelset.Text
 
setAlignmentLCR(String) - Method in class org.jmol.modelset.Text
 
setAll(int) - Static method in class org.jmol.util.BSUtil
 
setAll(P3, M3, P3, float, float, float, float, float, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
 
setAllConformation(BS) - Method in class org.jmol.modelsetbio.BioModelSet
 
setAllowJSThreads(boolean) - Method in class org.jmol.script.ScriptEval
 
setAllProteinType(BS, STR) - Method in class org.jmol.modelsetbio.BioModelSet
called from state STRUCTURE command
setAllStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.BioModelSet
 
setAmbientOcclusion(int) - Method in class org.jmol.util.GData
 
setAmbientPercent(int) - Method in class org.jmol.util.GData
fractional distance from black for ambient color
setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
 
setAnimation(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
 
setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
 
setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.AnimationManager
 
setAnimDisplay(BS) - Method in class org.jmol.viewer.Viewer
 
setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAPa(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
 
setAPm(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
 
setApplicationProperties(boolean) - Method in class jspecview.application.JSpecView
 
setArrays(Atom[], BS, Bond[], int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setAsBallRotation(float, float, float) - Method in class javajs.util.M3
3D ball rotation from dx dy in-plane mouse motion adapted from Andrew Hanson Computer Graphics beyond the Third Dimension: Geometry, Orientation Control, and Rendering for Graphics in Dimensions Greater than Three Course Notes for SIGGRAPH ’98 http://www.cse.ohio-state.edu/~hwshen/888_su02/hanson_note.pdf
setAsBallRotation(M4, float, float, float, float) - Method in class org.jmol.viewer.TransformManager4D
4D ball rotation from nominal dx, dy, dz motion.
setAsXRotation(float) - Method in class javajs.util.M3
Sets the value of this matrix to a rotation matrix about the x axis by the passed angle.
setAsXYRotation(float) - Method in class javajs.util.M4
Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
setAsXZRotation(float) - Method in class javajs.util.M4
Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
setAsYRotation(float) - Method in class javajs.util.M3
Sets the value of this matrix to a rotation matrix about the y axis by the passed angle.
setAsYZRotation(float) - Method in class javajs.util.M4
Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.
setAsZRotation(float) - Method in class javajs.util.M3
Sets the value of this matrix to a rotation matrix about the z axis by the passed angle.
setAtom(int, int, P3, float, BS, int, short, int, boolean) - Method in class org.jmol.modelset.Atom
 
setAtom(Atom, int, int, int, float, float, float) - Method in class org.jmol.adapter.readers.simple.InputReader
 
setAtom(Atom, int, String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
setAtomBits(BS) - Method in class org.jmol.modelset.Chain
 
setAtomBits(BS) - Method in class org.jmol.modelset.Group
note that we may pick up additional bits here that were added later
setAtomBits(BS) - Method in interface org.jmol.modelset.Structure
 
setAtomBits(BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
setAtomBits(BS) - Method in class org.jmol.modelsetbio.ProteinStructure
 
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Chain
 
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Group
Setting and clearing
setAtomBitsAndClear(BS, BS) - Method in interface org.jmol.modelset.Structure
 
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.ProteinStructure
 
setAtomChooser() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setAtomChooser() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setAtomClickability() - Method in class org.jmol.shape.AtomShape
 
setAtomClickability() - Method in class org.jmol.shape.Balls
 
setAtomClickability() - Method in class org.jmol.shape.Labels
 
setAtomClickability() - Method in class org.jmol.shape.Shape
 
setAtomClickability() - Method in class org.jmol.shape.Sticks
 
setAtomClickability() - Method in class org.jmol.shapebio.Backbone
 
setAtomClickability() - Method in class org.jmol.shapebio.BioShape
 
setAtomClickability() - Method in class org.jmol.shapebio.BioShapeCollection
 
setAtomClickability() - Method in class org.jmol.shapespecial.Dots
 
setAtomClickability() - Method in class org.jmol.shapespecial.Ellipsoids
 
setAtomColoring(int, int) - Method in class jme.JMEmol
 
setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoord2(BS, int, Object) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoords(BS, int, Object) - Method in class org.jmol.modelset.ModelSet
 
setAtomCoords(BS, int, Object) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordScaled(Atom, String[], int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.modelset.ModelSet
 
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordTokens(Atom, String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
 
setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
 
setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the atomic mass of the atom.
setAtomIndexes(int, int) - Method in class org.jmol.util.Tensor
 
setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
 
setAtomMapAnyCase() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomName(int, String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setAtomNamesAndNumbers(int, int, AtomCollection, boolean) - Method in class org.jmol.modelset.ModelSet
 
setAtomNumber(int, int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setAtomProp(String, Object, BS) - Method in class org.jmol.script.ScriptEval
 
setAtomProperties(double, double, int, int) - Method in class jme.JMEmol
 
setAtomProperties(String, Object, int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
 
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
 
setAtoms(Node[], int, BS) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
 
setAtomsCoordRelative(BS, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the partial atomic charges based on asc auxiliary info
setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetFrequency(int, String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energies
setAtomSetModelPropertyForSet(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the a property for the an AtomSet
setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the name for the current AtomSet
setAtomSetNumber(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomsForSmiles(Viewer, String) - Method in class org.jmol.symmetry.CIPDataSmiles
 
setAtomTensors(int, Lst<Object>) - Method in class org.jmol.modelset.AtomCollection
 
setAtropisomerOptions() - Method in class org.jmol.modelset.Bond
 
setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
 
setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
 
setAutoscrolls(boolean) - Method in interface org.jmol.api.SC
 
setAutoscrolls(boolean) - Method in class org.jmol.awt.AwtSwingComponent
 
setAutoscrolls(boolean) - Method in class org.jmol.awtjs.swing.JComponent
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
 
setB(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
 
setBackground(GenericColor) - Method in class org.jmol.awtjs.swing.Component
 
setBackgroundArgb(int) - Method in class org.jmol.util.GData
sets background color to the specified argb value
setBackgroundColor(GenericColor) - Method in interface jspecview.api.JSVPanel
 
setBackgroundColor(GenericColor) - Method in class jspecview.java.AwtPanel
 
setBackgroundColor(GenericColor) - Method in class jspecview.js2d.JsPanel
 
setBackgroundImage(Object) - Method in class org.jmol.util.GData
 
setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
 
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
 
setBannerLabel(String) - Method in class org.molecularplayground.MPJmolApp
 
setBaseModels(BS) - Method in class org.jmol.modelset.Trajectory
set bits for all base models only
setBbcage(float) - Method in class org.jmol.util.BoxInfo
 
setBBox(T3, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setBFactor(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setBigEndian(boolean) - Method in interface javajs.api.GenericBinaryDocumentReader
 
setBigEndian(boolean) - Method in class javajs.util.BinaryDocument
 
setBigEndian(boolean) - Method in class javajs.util.OC
 
setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
 
setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
 
setBioColix(short) - Method in class org.jmol.renderbio.BackboneRenderer
 
setBioColix(short) - Method in class org.jmol.renderbio.CartoonRenderer
 
setBioColix(short) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
setBioColix(short) - Method in class org.jmol.renderbio.RibbonsRenderer
 
setBioColix(short) - Method in class org.jmol.renderbio.RocketsRenderer
 
setBioColix(short) - Method in class org.jmol.renderbio.StrandsRenderer
 
setBioColix(short) - Method in class org.jmol.renderbio.TraceRenderer
 
setBits(int, int) - Method in class javajs.util.BS
Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to true.
setBitTo(int, boolean) - Method in class javajs.util.BS
Sets the bit at the specified index to the specified value.
setBlockID(double) - Method in class jspecview.source.JDXDataObject
 
setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
 
setBondArray() - Method in class org.jmol.smiles.SmilesAtom
 
setBondingRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setBondMeasure(int, MeasurementPending) - Method in class org.jmol.modelkit.ModelKit
 
setBondProperties(int, int, int, int) - Method in class jme.JMEmol
 
setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
 
setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
 
setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
 
setBoolean(ScriptToken, boolean) - Method in class jspecview.common.PanelData
 
setBoolean(ScriptToken, boolean) - Method in class jspecview.common.Parameters
 
setBoolean(ScriptToken, ItemEvent) - Method in class jspecview.application.ApplicationMenu
 
setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
 
setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptParam
 
setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setBooleanPropertyTok(String, int, boolean) - Method in class org.jmol.viewer.Viewer
 
setBooleans(Parameters, ScriptToken) - Method in class jspecview.common.PanelData
 
setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.util.BoxInfo
 
setBoundBoxFromOABC(T3[]) - Method in class org.jmol.util.BoxInfo
 
setBoundingBox(P3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setBoundingBox(P3[]) - Method in class org.jmol.util.MeshSurface
 
setBox(float, float, P3, V3, V3, P3, float) - Method in class org.jmol.modelsetbio.Sheet
 
setBox(P3, P3) - Method in class org.jmol.util.MeshSurface
 
setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.modelset.Text
 
setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.modelset.Text
 
setBSAtomsForSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Add a full set of atoms to BSAtoms if they are not already indicated there.
setBsHidden(BS) - Method in class org.jmol.modelset.AtomCollection
 
setButton(String) - Method in class org.jmol.console.GenericConsole
 
setButton(String) - Method in class org.jmol.console.JmolConsole
 
setButton(String) - Method in class org.jmol.consolejs.AppletConsole
 
setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setBytes(byte[]) - Method in class javajs.util.OC
 
setC(short) - Method in interface org.jmol.api.JmolRendererInterface
sets current color from colix color index
setC(short) - Method in class org.jmol.export.Export3D
sets current color from colix color index
setC(short) - Method in class org.jmol.g3d.Graphics3D
sets current color from colix color index
setC(short) - Method in class org.jmol.util.GData
 
setCA(double, double, Spectrum, String, GenericColor, boolean, boolean, int, int) - Method in class jspecview.common.ColoredAnnotation
 
setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.ModulationSet
get updated value for offset vector and for occupancy
setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.Vibration
 
setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
setCallback(String, Object) - Method in interface org.jmol.api.JmolAppletInterface
 
setCallback(String, Object) - Method in class org.jmol.util.GenericApplet
set a callback either as a function or a function name from JavaScript
setCallback(ScriptToken, String) - Method in class jspecview.application.MainFrame
 
setCallbackFunction(String, Object) - Method in class org.jmol.viewer.StatusManager
Set a JmolScript or JavaScript or Java callback.
setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
 
setCallbackFunction(String, String) - Method in class org.jmol.console.GenericConsole
 
setCallbackFunction(String, String) - Method in class org.jmol.util.GenericApplet
From StatusManager
setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setCamera(float, float) - Method in class org.jmol.viewer.TransformManager
 
setCameraDepthPercent(float, boolean) - Method in class org.jmol.viewer.TransformManager
either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
setCanvasImage(Object, int, int) - Method in interface javajs.api.js.J2SObjectInterface
 
setCel(boolean) - Method in class org.jmol.util.GData
 
setCellSelectionEnabled(boolean) - Method in interface jspecview.api.PlatformDialog
 
setCellSelectionEnabled(boolean) - Method in class jspecview.java.AwtDialog
 
setCellSelectionEnabled(boolean) - Method in class jspecview.js2d.JsDialog
 
setCellSelectionEnabled(boolean) - Method in class org.jmol.awtjs.swing.JTable
 
setCelPower(int) - Method in class org.jmol.util.GData
 
setCenter(Location) - Method in class com.sparshui.common.messages.events.RotateEvent
 
setCenter(Location) - Method in class com.sparshui.common.messages.events.ZoomEvent
 
setCenter(P3) - Method in class org.jmol.shapespecial.Ellipsoid
 
setCenter(T3, float) - Method in interface org.jmol.api.AtomIndexIterator
 
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
setCenter(T3, float) - Method in class org.jmol.symmetry.UnitCellIterator
 
setCenter2(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
setCenterAt(int, P3) - Method in class org.jmol.viewer.TransformManager
 
setCenterBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
 
setCenterSelected() - Method in class org.jmol.api.JmolViewer
 
setCenterSelected() - Method in class org.jmol.viewer.Viewer
 
setCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cell
setCGO(Lst<Object>) - Method in class org.jmol.viewer.Viewer
 
setChainID(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the charge of the atom.
setChemicalShiftReference(String, float) - Method in interface org.jmol.api.JmolNMRInterface
 
setChemicalShiftReference(String, float) - Method in class org.jmol.quantum.NMRCalculation
 
setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
setCIPChirality(int) - Method in class org.jmol.modelset.Atom
 
setCIPChirality(int) - Method in class org.jmol.modelset.Bond
Not implemented.
setCIPChirality(int) - Method in class org.jmol.smiles.SmilesAtom
 
setCIPChirality(int) - Method in class org.jmol.util.Edge
 
setCIPChirality(int) - Method in interface org.jmol.util.Node
 
setCIPChirality(int) - Method in interface org.jmol.util.SimpleNode
 
setCIR(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
 
setClickable(int) - Method in class org.jmol.modelset.Atom
 
setClipboard(Object) - Static method in class jspecview.java.AwtClipboard
Transfers text or image into the clipboard.
setClipboard(Object) - Static method in class org.jmol.awt.AwtClipboard
Transfers text or image into the clipboard.
setColix(short) - Method in class org.jmol.render.MeshRenderer
 
setColix(short) - Method in class org.jmol.renderbio.BackboneRenderer
 
setColix(short) - Method in class org.jmol.renderbio.CartoonRenderer
 
setColix(short) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
setColix(short) - Method in class org.jmol.renderbio.RibbonsRenderer
 
setColix(short) - Method in class org.jmol.renderbio.RocketsRenderer
 
setColix(short) - Method in class org.jmol.renderbio.StrandsRenderer
 
setColix(short) - Method in class org.jmol.renderbio.TraceRenderer
 
setColix(short) - Method in class org.jmol.util.MeshSurface
 
setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
 
setColixBack(short) - Method in class org.jmol.util.MeshSurface
 
setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setColor(float[], boolean) - Method in class javajs.export.PDFCreator
 
setColor(int) - Method in class org.jmol.util.GData
 
setColor(ScriptToken, GenericColor) - Method in class jspecview.common.ColorParameters
Sets the color of an element
setColor(ScriptToken, GenericColor) - Method in class jspecview.common.PanelData
 
setColorBackground(String) - Method in class org.jmol.api.JmolViewer
 
setColorBackground(String) - Method in class org.jmol.viewer.Viewer
 
setColorFromString(ScriptToken, String) - Method in class jspecview.common.ColorParameters
 
setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.common.PanelData
 
setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.java.AwtPanel
 
setColorOrFont(ColorParameters, ScriptToken) - Method in class jspecview.js2d.JsPanel
 
setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
 
setColumn3(int, float, float, float) - Method in class javajs.util.M3
Sets the specified column of this matrix3d to the three values provided.
setColumn33(int, float[]) - Method in class javajs.util.M34
 
setColumn4(int, float, float, float, float) - Method in class javajs.util.M4
Sets the specified column of this matrix4f to the four values provided.
setColumnA(int, float[]) - Method in class javajs.util.M3
Sets the specified column of this matrix3d to the four values provided.
setColumnA(int, float[]) - Method in class javajs.util.M4
Sets the specified column of this matrix4f to the four values provided.
setColumnComparator(Class, Comparator) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
setColumnV(int, T3) - Method in class javajs.util.M3
Sets the specified column of this matrix3d to the vector provided.
setComboSelected(int) - Method in class jspecview.dialog.JSVDialog
 
setCommandHooks() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setComment(String) - Method in class com.jcraft.jzlib.GZIPHeader
 
setCompiler() - Method in interface org.jmol.api.JmolScriptEvaluator
 
setCompiler() - Method in class org.jmol.script.ScriptEval
 
setConformation(BS) - Method in class org.jmol.modelset.ModelSet
 
setConformation(BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
 
setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
setConsoleFontScale(int) - Method in class org.jmol.viewer.Viewer
 
setConstraint(SymmetryInterface, int, int) - Method in class org.jmol.modelkit.ModelKit
This constraint will be set for the site only.
setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
 
setContactBitSets(BS, BS, boolean, float, RadiusData, boolean) - Method in class org.jmol.scriptext.MathExt
 
setContext() - Method in class jspecview.export.AMLExporter
 
setContext() - Method in class jspecview.export.CMLExporter
 
setContinuous(boolean) - Method in class jspecview.source.JDXDataObject
Sets value to true if spectrum is continuous
setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setContourVector(Lst<Object>, int, BS, float, short, int, SB) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
setConvertedSpectrum(Spectrum) - Method in class jspecview.common.Spectrum
 
setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setCorrelationTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
set the correlation time to be used in the NOE calculation
setCorrelationTimeTauPS(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
set the correlation time to be used in the NOE calculation
setCorrelationTimeTauPS(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
setCount(int) - Method in class org.jmol.modelset.Measurement
 
setCount(int) - Method in class org.jmol.modelset.MeasurementPending
 
setCountM(int) - Method in class org.jmol.modelset.Measurement
 
setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
setCRC(long) - Method in class com.jcraft.jzlib.GZIPHeader
 
setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelSet
 
setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
 
setCurrentAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the number for the current AtomSet
setCurrentCage(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentColor(String, Color) - Method in class jspecview.application.PreferencesDialog
 
setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelID(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndexClear(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for the AtomSet
setCurrentSubSpectrum(int) - Method in class jspecview.common.Spectrum
 
setCursor(int) - Method in interface jspecview.api.ScriptInterface
 
setCursor(int) - Method in class jspecview.app.JSVApp
 
setCursor(int) - Method in class jspecview.application.JSpecView
 
setCursor(int) - Method in class org.jmol.viewer.Viewer
 
setCursor(int, Object) - Method in class jspecview.java.AwtPlatform
 
setCursor(int, Object) - Method in class jspecview.js2d.JsPlatform
 
setCursor(int, Object) - Method in interface org.jmol.api.GenericPlatform
 
setCursor(int, Object) - Method in class org.jmol.awt.Platform
 
setCursor(int, Object) - Method in class org.jmol.awtjs2d.Platform
 
setCursor(JSmolAppletObject, int) - Method in interface org.jmol.api.js.JmolToJSmolInterface
 
setCursorObject(Object) - Method in class jspecview.application.MainFrame
 
setCursorWait(boolean) - Method in class org.jmol.script.ScriptError
 
setCutoff(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
sets the cutoff distance beyond which atom interactions are not considered
setCutoffAng(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
sets the cutoff distance beyond which atom interactions are not considered
setCutoffAng(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
sets the cutoff distance beyond which atom interactions are not considered
setData(byte[], int) - Method in class javajs.img.PngEncoder
 
setData(Object) - Method in class javajs.util.ArrayDataReader
 
setData(Object) - Method in class javajs.util.DataReader
 
setData(Object) - Method in class javajs.util.ListDataReader
 
setData(Object) - Method in class javajs.util.StringDataReader
 
setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
A general-purpose data storage method.
setData(String, Object[], int, int, int, int, int, int) - Method in interface org.jmol.api.JmolDataManager
 
setData(String, Object[], int, int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
This method needs to be redone using a class instead of Object[]
setData(AnnotationData) - Method in class jspecview.dialog.JSVDialog
 
setDataClass(String) - Method in class jspecview.source.JDXHeader
Sets the data class
setDataDistanceToPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
 
setDataType(String) - Method in class jspecview.source.JDXHeader
Sets the data type
setDate(String) - Method in class jspecview.source.JDXHeader
Sets the date the file was created
setDebugging() - Method in interface org.jmol.api.JmolScriptEvaluator
 
setDebugging() - Method in class org.jmol.script.ScriptEval
 
setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
 
setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
 
setDefaultLattice(P3) - Method in class org.jmol.viewer.Viewer
 
setDefaultPrintOptions(PrintLayout) - Method in class jspecview.common.PanelData
 
setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
 
setDepth(int) - Method in class org.jmol.util.GData
clipping from the front and the back
setDescription(String) - Method in class jspecview.java.AwtDialogFileFilter
Sets the description for the JSpecViewFileFilter
setDialog(Component) - Method in interface org.jmol.awtjs.swing.SwingController
The HTML for this dialog has been generated.
setDialogLocation(Point) - Method in class org.jmol.dialog.FileChooser
 
setDialogSize(Dimension) - Method in class org.jmol.dialog.FileChooser
 
setDictionary(byte[], int) - Method in class com.jcraft.jzlib.Deflater
 
setDictionary(byte[], int) - Method in class com.jcraft.jzlib.Inflater
 
setDiffusePercent(int) - Method in class org.jmol.util.GData
df in I = df * (N dot L) + sf * (R dot V)^p
setDihedrals(float[], BS[], float) - Method in class org.jmol.modelset.ModelSet
 
setDihedrals(float[], BS[], float) - Method in class org.jmol.viewer.Viewer
 
setDirLastExported(String) - Method in interface jspecview.api.JSVFileHelper
 
setDirLastExported(String) - Method in class jspecview.java.AwtFileHelper
 
setDirLastExported(String) - Method in class jspecview.js2d.JsFileHelper
 
setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setDisplay(Object) - Method in interface javajs.api.JSInterface
 
setDisplay(Object) - Method in class jspecview.appletjs.JSVApplet
 
setDisplay(Object) - Method in class jspecview.common.JSViewer
 
setDisplay(Object) - Method in class org.jmol.util.GenericApplet
 
setDisplay(Object) - Method in class org.jmol.viewer.Viewer
 
setDocStream(GenericZipTools, BufferedInputStream) - Method in class javajs.util.CompoundDocument
 
setDocumentBase(JSViewer, URL) - Static method in class jspecview.common.JSVFileManager
 
setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
 
setDragAtomIndex(int) - Method in class org.jmol.viewer.ActionManager
 
setDropTargetListener(boolean, JSViewer) - Method in interface jspecview.api.AppletFrame
 
setDropTargetListener(boolean, JSViewer) - Method in class jspecview.appletjs.JSVApplet
 
setDx(float) - Method in class com.sparshui.common.messages.events.DragEvent
 
setDy(float) - Method in class com.sparshui.common.messages.events.DragEvent
 
setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
 
setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
 
setElement(int, int, float) - Method in class javajs.util.M3
Sets the specified element of this matrix3d to the value provided.
setElement(int, int, float) - Method in class javajs.util.M4
Sets the specified element of this matrix4f to the value provided.
setElement(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setElementAndIsotope(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
allow 13C, 15N, 2H, etc.
setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
 
setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
 
setElementColors(ColorParameters) - Method in class jspecview.common.ColorParameters
 
setEllipsoidAF(float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setEnabled(boolean) - Method in interface jspecview.api.JSVViewPanel
 
setEnabled(boolean) - Method in class jspecview.js2d.JsMainPanel
 
setEnabled(boolean) - Method in class jspecview.js2d.JsPanel
 
setEnabled(boolean) - Method in interface org.jmol.api.JmolAbstractButton
 
setEnabled(boolean) - Method in interface org.jmol.api.SC
 
setEnabled(boolean) - Method in class org.jmol.awt.AwtSwingComponent
 
setEnabled(boolean) - Method in class org.jmol.awtjs.swing.Component
 
setEnabled(boolean, boolean) - Method in class jspecview.popup.JSVGenericPopup
 
setEnabled(Object, boolean) - Method in interface jspecview.api.PlatformDialog
 
setEnabled(Object, boolean) - Method in class jspecview.java.AwtDialog
 
setEnabled(Object, boolean) - Method in class jspecview.js2d.JsDialog
 
setEnabled(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
setEnergy(float) - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
 
setErrorLog(String) - Method in class jspecview.source.JDXSource
Sets the error log for this source
setErrorMessage(String) - Method in class org.jmol.script.ScriptError
 
setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
 
setEval(JmolScriptEvaluator) - Method in class org.jmol.thread.JmolThread
JavaScript only -- -- scriptDelay, moveTo, spin -- save context for restoration later -- move program counter forward one command
setException(ScriptException, String, String) - Method in class org.jmol.script.ScriptEval
 
setExpCouple(String, int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
setExpDist(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of explicit hydrogen atoms bonded with this atom.
setExpNoe(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setExportXAxisDirection(boolean) - Method in class jspecview.common.Spectrum
 
setF(String, float) - Method in class org.jmol.viewer.GlobalSettings
 
setFancyArrowHead(int) - Method in class org.jmol.renderbio.BioMeshRenderer
 
setFancyConic(int, int) - Method in class org.jmol.renderbio.BioMeshRenderer
 
setFancyRibbon(int) - Method in class org.jmol.renderbio.BioMeshRenderer
 
setFields() - Method in class jspecview.dialog.JSVDialog
 
setFileChooser(ExportType) - Method in interface jspecview.api.JSVFileHelper
 
setFileChooser(ExportType) - Method in class jspecview.java.AwtFileHelper
 
setFileChooser(ExportType) - Method in class jspecview.js2d.JsFileHelper
 
setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
Set fullPathName, fileName, and nameAsGiven
setFilename(String) - Method in class org.jmol.console.ScriptEditor
 
setFilePath(String) - Method in interface jspecview.api.JSVAppletInterface
 
setFilePath(String) - Method in class jspecview.app.JSVApp
 
setFilePath(String) - Method in class jspecview.appletjs.JSVApplet
 
setFilePath(String) - Method in class jspecview.application.MainFrame
 
setFilePath(String) - Method in class jspecview.source.JDXDataObject
 
setFilePath(String) - Method in class jspecview.source.JDXSource
 
setFileType(String) - Method in class org.jmol.viewer.FileManager
 
setFillColor(GenericColor) - Method in class jspecview.common.Spectrum
 
setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFilterAtomTypeStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in interface org.jmol.api.SymmetryInterface
 
setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in class org.jmol.symmetry.Symmetry
 
setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
 
setFloatProperty(String, float) - Method in class org.jmol.script.ScriptParam
 
setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
 
setFocus() - Method in class org.jmol.viewer.Viewer
 
setFocus(boolean) - Method in interface jspecview.api.PlatformDialog
 
setFocus(boolean) - Method in class jspecview.dialog.JSVDialog
 
setFocus(boolean) - Method in class jspecview.java.AwtDialog
 
setFocus(boolean) - Method in class jspecview.js2d.JsDialog
 
setFocusable(boolean) - Method in interface jspecview.api.JSVViewPanel
 
setFocusable(boolean) - Method in class jspecview.js2d.JsMainPanel
 
setFocusable(boolean) - Method in class jspecview.js2d.JsPanel
 
setFont(Object, int, int, float, boolean) - Method in class jspecview.common.PanelData
 
setFont(Object, Font) - Method in class jspecview.common.PDFWriter
 
setFont(Object, Font) - Method in class jspecview.java.AwtG2D
 
setFont(Object, Font) - Method in class jspecview.js2d.JsG2D
 
setFont(Object, Font) - Method in interface org.jmol.api.GenericGraphics
 
setFont(Object, Font) - Method in class org.jmol.awt.AwtG2D
 
setFont(Object, Font) - Method in class org.jmol.awtjs2d.JsG2D
 
setFont(String, float) - Method in class javajs.export.PDFCreator
 
setFont(Font) - Method in class org.jmol.g3d.Graphics3D
 
setFont(Font) - Method in class org.jmol.util.GData
 
setFont(Font, boolean) - Method in class org.jmol.modelset.Text
 
setFontBold(String, float) - Method in class org.jmol.util.GData
 
setFontFromFid(int) - Method in class org.jmol.modelset.Text
 
setFontName(ScriptToken, String) - Method in class jspecview.common.PanelData
 
setFontScale(float) - Method in class org.jmol.modelset.Text
 
setFontScale(int) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
setFor(JSVPanel, ColorParameters, boolean) - Method in class jspecview.common.ColorParameters
 
setFormalCharge(int) - Method in class org.jmol.modelset.Atom
 
setFormalCharges(BS, int) - Method in class org.jmol.modelset.AtomCollection
 
setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
 
setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFractionalCoordPt(P3, P3, boolean) - Method in class org.jmol.modelset.Atom
 
setFrame(int) - Method in class org.jmol.viewer.AnimationManager
 
setFrame(JFrame) - Method in class jme.JME
 
setFrameAndTreeNode(int) - Method in class jspecview.common.JSViewer
 
setFrameCount(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
 
setFrameDelayMs(long) - Method in class org.jmol.viewer.Viewer
 
setFrameDelayMs(long, BS) - Method in class org.jmol.modelset.ModelSet
 
setFrameDeltaCouple(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
 
setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
 
setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setFrameDeltaNoe(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
 
setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setFrameModelInfo(String, Object) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
setFrameNumberChangeViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
 
setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
 
setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
 
setFrameOffsets(BS, boolean) - Method in class org.jmol.viewer.Viewer
 
setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
 
setFrameTitle(String) - Method in class jspecview.common.PanelNode
 
setFrameTitle(BS, Object) - Method in class org.jmol.modelset.ModelSet
 
setFrameTitleObj(Object) - Method in class org.jmol.viewer.Viewer
 
setFrameVisible(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
 
setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setFromAsymmetricTensor(double[][], String, String) - Method in class org.jmol.util.Tensor
Standard constructor for QM tensors
setFromAxes(V3[]) - Method in class org.jmol.util.Tensor
Standard constructor for ellipsoids based on axes
setFromBits(int, BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setFromEigenVectors(T3[], float[], String, String, Tensor) - Method in class org.jmol.util.Tensor
Standard constructor for charge and iso.
setFromMD(MeasurementData, boolean) - Method in class org.jmol.modelset.Measurement
 
setFromThermalEquation(double[], String) - Method in class org.jmol.util.Tensor
standard constructor for thermal ellipsoids convention beta (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setGraphicsColor(Object, GenericColor) - Method in class jspecview.common.PDFWriter
 
setGraphicsColor(Object, GenericColor) - Method in class jspecview.java.AwtG2D
 
setGraphicsColor(Object, GenericColor) - Method in class jspecview.js2d.JsG2D
 
setGraphicsColor(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
 
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
 
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
 
setGraphSetKey(String) - Method in interface jspecview.api.AnnotationData
 
setGraphSetKey(String) - Method in class jspecview.common.MeasurementData
 
setGraphSetKey(String) - Method in class jspecview.dialog.JSVDialog
 
setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
controls greyscale rendering
setGroup(Group) - Method in class com.sparshui.server.TouchPoint
Set the group for this touch point.
setGroup(Chain, String, int, int, int) - Method in class org.jmol.modelset.Group
 
setGroup1(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setGroup1(ModelSet, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
setGroup1(ModelSet, int) - Method in class org.jmol.dssx.AnnotationParser
 
setGroup1(ModelSet, int) - Method in class org.jmol.dssx.DSSR1
 
setGroupID(String) - Method in class org.jmol.modelset.Group
 
setGroupID(String) - Method in class org.jmol.modelsetbio.Monomer
 
setGroupLists(int) - Method in class org.jmol.modelsetbio.BioResolver
 
setHasUnitCell() - Method in class org.jmol.modelkit.ModelKit
 
setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.BioResolver
 
setHeaderTable(Lst<String[]>) - Method in class jspecview.source.JDXHeader
Sets the headerTable for this Source or spectrum
setHighlightColor(GenericColor) - Method in class jspecview.common.PanelData
 
setHighlightedPeak(PeakInfo) - Method in class jspecview.common.Spectrum
 
setHistory(String) - Method in class org.jmol.viewer.Viewer
 
setHorizAlignment(int, int) - Static method in class org.jmol.viewer.JC
 
setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
 
setHoverLabel(String, String) - Method in class org.jmol.modelkit.ModelKit
 
setHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
Finalizes the hydrogen count hydrogens in a SmilesMolecule.
setHydrogenCount(int) - Method in class jspecview.source.JDXDataObject
 
setHZtoPPM(boolean) - Method in class jspecview.source.JDXDataObject
Sets the value to true if the spectrum should be displayed with abscissa unit of Part Per Million (PPM) instead of Hertz (HZ)
setIcon(Object) - Method in interface org.jmol.api.SC
 
setIcon(Object) - Method in class org.jmol.awt.AwtSwingComponent
 
setIcon(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
 
setId(String) - Method in class jspecview.common.Spectrum
 
setID(String) - Method in class jspecview.source.JDXSource
 
setIdentity() - Method in class javajs.util.M4
Sets this Matrix4f to identity.
setImage(Object) - Method in interface org.jmol.api.GenericImageDialog
 
setImage(Object) - Method in class org.jmol.console.ImageDialog
 
setImage(Object) - Method in class org.jmol.modelset.Text
 
setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Sets the output image dimensions.
setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
 
setImageInfo(int, int, String) - Method in class org.jmol.dialog.Dialog
 
setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of implicit hydrogen atoms bonded with this atom.
setIncreasing(boolean) - Method in class jspecview.source.JDXDataObject
Sets value to true if spectrum is increasing
setIndex(int) - Method in interface jspecview.api.JSVTreeNode
 
setIndex(int) - Method in class jspecview.application.AwtTreeNode
 
setIndex(int) - Method in class jspecview.tree.SimpleTreeNode
 
setIndex(int) - Method in class org.jmol.smiles.SmilesAtom
Constructs a SmilesAtom.
setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Sets the indexes to the atomSetIndex values of each leaf of the node.
setInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelSet
 
setInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setInlineData(String) - Method in class jspecview.source.JDXDataObject
 
setInlineData(String) - Method in class jspecview.source.JDXSource
 
setInMotion(boolean) - Method in class org.jmol.api.JmolViewer
 
setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
 
setInsertedCommand(String) - Method in class org.jmol.viewer.Viewer
 
setInt(double, double, Spectrum, double, double, double) - Method in class jspecview.common.Integral
 
setInt(int) - Method in class org.jmol.util.Rgb16
 
setIntegrationRatios(String) - Method in class jspecview.common.PanelData
DEPRECATED Sets the integration ratios that will be displayed
setIntLocation(int[]) - Method in interface jspecview.api.PlatformDialog
 
setIntLocation(int[]) - Method in class jspecview.java.AwtDialog
 
setIntLocation(int[]) - Method in class jspecview.js2d.JsDialog
 
setIntoFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setIntoFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
 
setIntProperty(String, int) - Method in class org.jmol.script.ScriptParam
 
setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
 
setIntPropertyTok(String, int, int) - Method in class org.jmol.viewer.Viewer
 
setInverseNormixes() - Static method in class org.jmol.util.Normix
 
setInvoker(Object) - Method in class org.jmol.awtjs.swing.JPopupMenu
 
setIRmode(String) - Method in class jspecview.common.JSViewer
 
setIRMode(Spectrum.IRMode, String) - Method in class jspecview.common.PanelData
 
setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
 
setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
 
setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelSet
 
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in interface org.jmol.atomdata.AtomDataServer
 
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.modelset.ModelSet
 
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.viewer.Viewer
 
setJcampdx(String) - Method in class jspecview.source.JDXHeader
Sets the JCAMP-DX version number
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
 
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
 
setJmolDataFrame(String, int, int) - Method in class org.jmol.modelset.ModelSet
 
setJmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setJmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setJmolSize(Dimension) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
 
setJSOptions(Map<String, Object>) - Method in class org.jmol.util.GenericApplet
 
setJSpecView(String, boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
setLabel(int, String) - Method in class jme.JMEmol
 
setLabel(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
 
setLabel(Object, BS) - Method in class org.jmol.viewer.ShapeManager
 
setLabel(String) - Method in class org.openscience.jmol.app.jsonkiosk.BannerFrame
 
setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setLabels() - Method in class org.jmol.console.GenericConsole
 
setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
setLabelString(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
 
setLastColix(int, boolean) - Method in class org.jmol.util.Shader
 
setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
set symmetry lattice type using Hall rotations
setLattice(int) - Method in class org.jmol.symmetry.Symmetry
 
setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
Shelx and Wien2k readers
setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setLeadAtomIndex() - Method in class org.jmol.modelsetbio.Monomer
 
setLeftComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
 
setLegend(JSVDialog) - Method in class jspecview.common.PanelNode
 
setLength(int) - Method in class javajs.util.SB
 
setLengths() - Method in class org.jmol.shapespecial.Ellipsoid
 
setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
 
setLighting(int) - Method in class org.jmol.shape.Mesh
 
setLine(String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
setLine(String) - Method in class org.jmol.jsv.JDXMOLParser
 
setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
setLineWidth(float) - Method in class javajs.export.PDFCreator
 
setlinkedXMove(GraphSet, double, boolean) - Method in class jspecview.common.PanelData
 
setLoader(ModelLoader) - Method in class org.jmol.modelsetbio.BioResolver
 
setLoadFormat(boolean, String, char, boolean) - Method in class org.jmol.viewer.Viewer
Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first.
setLoading(String, String) - Method in class jspecview.application.MainFrame
 
setLoadNote() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setLoadParameters(Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
 
setLocalPath(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog.
setLocation(int[]) - Method in class org.jmol.awtjs.swing.JDialog
 
setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
Replaces the current logger implementation by a new one.
setLogLevel(int) - Static method in class org.jmol.util.Logger
Activates all logging levels up through a given level.
setLongDate(String) - Method in class jspecview.source.JDXHeader
Sets the long date of when the file was created
setlrefSingle(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setM(double[][]) - Method in interface javajs.api.EigenInterface
 
setM(double[][]) - Method in class javajs.util.Eigen
 
setM(M3) - Method in class javajs.util.A4
Sets the value of this axis-angle to the rotational component of the passed matrix.
setM(ModelSet, Measurement, float, short, String, int) - Method in class org.jmol.modelset.Measurement
 
setM1(double, double, Spectrum) - Method in class jspecview.common.Measurement
 
setM3(M34) - Method in class javajs.util.M3
Sets the value of this matrix to the double value of the Matrix3f argument.
setM33(M34) - Method in class javajs.util.M34
Sets the value of this matrix to the double value of the Matrix3f argument.
setM4(M4) - Method in class javajs.util.M4
Sets the value of this matrix to a copy of the passed matrix m1.
setMad(short) - Method in class org.jmol.modelset.Bond
 
setMadAtom(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
 
setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setMainFrame(MainFrame) - Method in class jspecview.application.JSpecView
 
setManager(Object, Viewer, Object) - Method in class org.jmol.minimize.MinimizationThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.script.CommandWatcherThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.AnimationThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.JmolThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.MoveToThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.SpinThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.VibrationThread
 
setMapBitSet(Map<String, BS>, int, int, String) - Static method in class org.jmol.util.BSUtil
 
setMappingPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
 
setMarBond(short) - Method in class org.jmol.api.JmolViewer
 
setMarBond(short) - Method in class org.jmol.viewer.Viewer
 
setMargin(float) - Method in class org.jmol.util.BoxInfo
 
setMatchingAtom(Node, int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of a matching atom in a molecule.
setMaxSize(int) - Method in class org.jmol.util.CommandHistory
Resets maximum size of command queue.
setMeasurementText(Measurement) - Method in class jspecview.source.JDXDataObject
 
setMenu(String, boolean) - Method in class org.jmol.api.JmolViewer
 
setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setMenu(ModelKitPopup) - Method in class org.jmol.modelkit.ModelKit
 
setMenuEnables(PanelNode) - Method in class jspecview.application.ApplicationMenu
 
setMenuEnables(PanelNode, boolean) - Method in class jspecview.application.MainFrame
 
setMenuItem(JMenuItem, char, String, int, int, EventListener) - Static method in class jspecview.application.ApplicationMenu
 
setMenuKeys(String, String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setMenuKeys(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
opportunity to adjust menus for a custom application
setMenus(JMenu, JMenu, JMenu, ActionListener) - Static method in class jspecview.application.ApplicationMenu
 
setMenuState() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setMeshColor() - Method in class org.jmol.shape.MeshCollection
 
setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEval
 
setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
 
setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
 
setMinimumIntegral(double) - Method in class jspecview.common.IntegralData
 
setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
 
setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.JScrollPane
 
setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
 
setMinMax0(P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
setMinMax0(P3, P3) - Method in interface org.jmol.adapter.smarter.MSInterface
 
setMinMaxLatticeParameters(int, P3i, P3i, int) - Static method in class org.jmol.util.SimpleUnitCell
 
setMixingTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
sets the mixing time for the NOE experiment
setMixingTimeSec(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
sets the mixing time for the NOE experiment
setMixingTimeSec(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
sets the mixing time for the NOE experiment
setMKState(int) - Method in class org.jmol.modelkit.ModelKit
 
setMnemonic(char) - Method in interface org.jmol.api.JmolAbstractButton
 
setMnemonic(char) - Method in class org.jmol.console.JmolLabel
 
setMO(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
setMod(String, P3, P3, int, Lst<Modulation>, M3, Matrix[], SymmetryInterface, int, int, Vibration, boolean) - Method in class org.jmol.util.ModulationSet
A collection of modulations for a specific atom.
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
setModDim(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
setModel(int) - Method in interface org.jmol.api.JmolJSpecView
 
setModel(int) - Method in class org.jmol.jsv.JSpecView
 
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceField
 
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
 
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.symmetry.UnitCellIterator
 
setModelCage(int, SymmetryInterface) - Method in class org.jmol.modelset.ModelSet
This is the model-specific cage created by a UNITCELL or MODELKIT UNITCELL command.
setModelCagePts(int, T3[], String) - Method in class org.jmol.modelset.ModelSet
 
setModelFields() - Method in class org.jmol.minimize.forcefield.ForceField
 
setModelIndex(int) - Method in class org.jmol.modelset.StateScript
 
setModelIndex(short) - Method in class org.jmol.modelset.Measurement
 
setModelInfoForSet(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for an AtomSet
setModelkitPropertySafely(String, Object) - Method in class org.jmol.viewer.Viewer
Set a ModelKit property, but only if the modelkit exists already.
setModelPDB(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setModelSet(ModelSet) - Method in class org.jmol.modelset.MeasurementData
 
setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
 
setModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
 
setModelSet(ModelSet) - Method in class org.jmol.viewer.Viewer
 
setModelVisibility() - Method in class org.jmol.viewer.Viewer
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Bbcage
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Halos
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.MeshCollection
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Shape
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.TextShape
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapecgo.CGO
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Dipoles
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Draw
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Ellipsoids
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Polyhedra
 
setModeMouse(int) - Method in class org.jmol.viewer.ActionManager
only NONE (-1) is implemented; it just stops the hoverWatcher thread so that the vwr references are all removed
setModifiedTime(long) - Method in class com.jcraft.jzlib.GZIPHeader
 
setModifyKeys(Map<String, String>) - Method in class org.jmol.util.JSONWriter
 
setModTQ(T3, boolean, T3, boolean, float) - Method in interface org.jmol.api.JmolModulationSet
 
setModTQ(T3, boolean, T3, boolean, float) - Method in class org.jmol.util.ModulationSet
Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
setModulation(boolean, XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.readers.cif.MSRdr
Both the Jana reader and the CIF reader will call this to set the modulation for a given model.
setModulation(boolean, XtalSymmetry.FileSymmetry) - Method in interface org.jmol.adapter.smarter.MSInterface
 
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.modelset.ModelSet
Sets the modulation for all atoms in bs.
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.viewer.Viewer
 
setMol(boolean) - Method in class jme.JME
 
setMol(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setMoment() - Method in interface org.jmol.api.JmolModulationSet
 
setMoment() - Method in class org.jmol.util.ModulationSet
 
setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
setMorphCount(int) - Method in class org.jmol.viewer.AnimationManager
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.AmsReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
setMotion(int, boolean) - Method in class org.jmol.viewer.ActionManager
 
setMotionFixed(BS) - Method in class org.jmol.viewer.Viewer
 
setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.Viewer
 
setMouseMode() - Method in class org.jmol.viewer.ActionManager
 
setMovableX(int) - Method in class org.jmol.modelset.Text
 
setMovableXPercent(int) - Method in class org.jmol.modelset.Text
 
setMovableY(int) - Method in class org.jmol.modelset.Text
 
setMovableYPercent(int) - Method in class org.jmol.modelset.Text
 
setMovableZPercent(int) - Method in class org.jmol.modelset.Text
 
setMovie(Map<String, Object>) - Method in class org.jmol.viewer.AnimationManager
support for PyMOL movies and anim FRAMES [....] currently no support for scripted movies
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
setMustResume() - Method in class org.jmol.script.ScriptContext
 
setMV(M3, T3) - Method in class javajs.util.M4
Initializes a Matrix4f from the rotation matrix and translation.
setName(String) - Method in class com.jcraft.jzlib.GZIPHeader
 
setName(String) - Method in class jspecview.common.Parameters
 
setName(String) - Method in interface org.jmol.api.SC
 
setName(String) - Method in class org.jmol.awt.AwtSwingComponent
 
setName(String) - Method in class org.jmol.awtjs.swing.Component
 
setName(String) - Method in class org.jmol.script.SV
 
setNavFps(int) - Method in class org.jmol.viewer.TransformManager
 
setNavigatePt(P3) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
setNavigationDepthPercent(float) - Method in interface org.jmol.api.JmolNavigatorInterface
 
setNavigationDepthPercent(float) - Method in class org.jmol.navigate.Navigator
 
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be invalid input: '<'0 or >100)
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.Viewer
 
setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
 
setNavigationOffsetRelative() - Method in interface org.jmol.api.JmolNavigatorInterface
 
setNavigationOffsetRelative() - Method in class org.jmol.navigate.Navigator
 
setNavigationOffsetRelative() - Method in class org.jmol.viewer.TransformManager
 
setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
 
setNboLabels(String[], int, Lst<Map<String, Object>>, int, String) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
setNewRotationCenter(P3) - Method in class org.jmol.viewer.Viewer
 
setNewWindowParametersForExport() - Method in class org.jmol.util.GData
 
setNextPeak(Coordinate, int) - Method in class jspecview.common.Spectrum
 
setNMRfreq(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
set the NMR frequency for the NOE simulation
setNMRfreqMHz(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
set the NMR frequency for the NOE simulation
setNMRfreqMHz(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
set the NMR frequency for the NOE simulation
setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setNode(PanelNode) - Method in class jspecview.common.JSViewer
 
setNoeExprefValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setNoeNPrefIndices(int[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
 
setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
setNoesy(boolean) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
sets the experiemnt type to NOESY or ROESY
setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
 
setNormixes(V3[]) - Method in class org.jmol.shape.Mesh
 
setNth(int) - Method in class org.jmol.minimize.forcefield.ForceField
 
setNucleusAndFreq(String, boolean) - Method in class jspecview.source.JDXDataObject
 
setNullValue(String) - Method in class javajs.util.CifDataParser
Set the string value of what is returned for "." and "?"
setNumDim(int) - Method in class jspecview.source.JDXDataObject
 
setO(String, Object) - Method in class org.jmol.viewer.GlobalSettings
 
setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectMad10(int, String, int) - Method in class org.jmol.script.ScriptEval
 
setObjectMad10(int, String, int) - Method in class org.jmol.viewer.Viewer
input here is a JC.SHAPE_xxxx identifier
setObjectProp(String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectProperty() - Method in class org.jmol.script.ScriptEval
 
setObjectPropSafe(String, int) - Method in interface org.jmol.api.JmolScriptEvaluator
 
setObjectPropSafe(String, int) - Method in class org.jmol.script.ScriptEval
called by Viewer in setting up a PyMOL scene.
setObjectVisibility(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setObservedFreq(double) - Method in class jspecview.source.JDXDataObject
Sets the Observed Frequency (for NMR Spectra)
setObservedNucleus(String) - Method in class jspecview.source.JDXDataObject
 
setOccupancy(double[], double, double) - Method in class org.jmol.util.ModulationSet
get the occupancy, first from the reader, then from renderer
setOccupancy(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
 
setOffset(int) - Method in class org.jmol.modelset.Text
 
setOffset(int) - Method in class org.jmol.symmetry.Symmetry
 
setOffsetPt(P3) - Method in class org.jmol.shapespecial.Dipole
 
setOffsetPt(T3) - Method in interface org.jmol.api.SymmetryInterface
 
setOffsetPt(T3) - Method in class org.jmol.symmetry.Symmetry
 
setOpacity255(int) - Method in interface javajs.api.GenericColor
 
setOpacity255(int) - Method in class jspecview.java.AwtColor
 
setOpacity255(int) - Method in class org.jmol.awt.AwtColor
 
setOpacity255(int) - Method in class org.jmol.awtjs.swing.Color
 
setOptions(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
setOrder(int) - Method in class org.jmol.modelset.Bond
 
setOrigin(String) - Method in class jspecview.source.JDXHeader
Sets the origin of the JCAMP-DX spectrum
setOS(int) - Method in class com.jcraft.jzlib.GZIPHeader
 
setOutputChannel(GenericBinaryDocument, OC) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.shapesurface.Isosurface
 
setOutputChannel(GenericOutputChannel) - Method in interface javajs.api.GenericBinaryDocument
 
setOutputChannel(GenericOutputChannel) - Method in class javajs.util.BinaryDocument
 
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.JvxlReader
 
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setOutputStream(OutputStream) - Method in class javajs.export.PDFCreator
 
setOwner(String) - Method in class jspecview.source.JDXHeader
Sets the owner
setP(T3) - Method in class javajs.util.T3
 
setP(PanelData, ScriptToken, String) - Method in class jspecview.common.Parameters
 
setPanel(JPanel) - Method in class org.openscience.jmol.app.jsonkiosk.KioskFrame
 
setPanelVisible(boolean) - Method in interface jspecview.api.AppletFrame
 
setPanelVisible(boolean) - Method in class jspecview.appletjs.JSVApplet
 
setParallel() - Method in class org.jmol.viewer.ShapeManager
 
setParallel(boolean) - Method in class org.jmol.viewer.Viewer
 
setparam - Static variable in class org.jmol.script.T
 
setParameters(Spectrum) - Method in class jspecview.export.AMLExporter
 
setParameters(Spectrum) - Method in class jspecview.export.CMLExporter
 
setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
setParams(Object[], int[], BS) - Method in class org.jmol.shapebio.BioShape
 
setParams(String, JSViewer, Spectrum) - Method in class jspecview.dialog.JSVDialog
required initializer; from JSViewer
setParams(Map<String, Object>) - Method in class javajs.img.GifEncoder
we allow for animated GIF by being able to re-enter the code with different parameters held in params
setParams(Map<String, Object>) - Method in class javajs.img.ImageEncoder
 
setParams(Map<String, Object>) - Method in class javajs.img.Jpg64Encoder
 
setParams(Map<String, Object>) - Method in class javajs.img.JpgEncoder
 
setParams(Map<String, Object>) - Method in class javajs.img.PdfEncoder
 
setParams(Map<String, Object>) - Method in class javajs.img.PngEncoder
 
setParams(Map<String, Object>) - Method in class javajs.img.PpmEncoder
 
setParams(BytePoster, String, boolean, OutputStream) - Method in class javajs.util.OC
Set up an output channel.
setParent(Object) - Method in class org.jmol.awtjs.swing.Component
 
setPartialCharge(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setPass2(boolean) - Method in class org.jmol.util.GData
 
setPath(JSVTreePath) - Method in interface jspecview.api.JSVTree
 
setPath(JSVTreePath) - Method in class jspecview.application.AwtTree
 
setPath(JSVTreePath) - Method in class jspecview.tree.SimpleTree
 
setPdbConectBonding(int, int, BS) - Method in class org.jmol.modelset.ModelSet
 
SETPEAK - Enum constant in enum class jspecview.common.ScriptToken
 
setPeakList(Lst<PeakInfo>, String, String) - Method in class jspecview.common.Spectrum
 
setPeakList(Parameters, int, ScaleData) - Method in class jspecview.common.PeakData
 
setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
 
setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
 
setPhongExponent(int) - Method in class org.jmol.util.GData
p in I = df * (N dot L) + sf * (R dot V)^p
setPicked(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
 
setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
 
setPixelRange(int, int) - Method in class jspecview.common.PeakInfo
 
setPlaneParameters(P4) - Method in class org.jmol.jvxl.data.VolumeData
 
setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
Raw file data planes are passed to us here from VolumeFileReader
setPlanes(float[][]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
Planes to use for holding raw file data.
setPlotColors(GenericColor[]) - Method in class jspecview.common.PanelData
 
setPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setPointer(int, int) - Static method in class org.jmol.viewer.JC
 
setPointGroup(Viewer, SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setPointGroup(Viewer, SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in class org.jmol.symmetry.Symmetry
 
setPoints(int) - Method in class org.jmol.shape.Axes
 
setPoints(ModelSet, int[], Point3fi[], TickInfo) - Method in class org.jmol.modelset.Measurement
 
setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
 
setPopulationDisplay(PopulationDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
 
setPopupMenu(boolean, boolean) - Method in class jspecview.common.JSViewer
 
setPosition(float, float, boolean, float[]) - Method in class org.jmol.modelset.Text
 
setPrecision() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
Called by PWMAT ALWAYS and CIFReader as well if a double-precision value for alpha is found.
setPrecision(float) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
setPrecision(float) - Method in class org.jmol.util.SimpleUnitCell
 
setPreferredScrollableViewportSize(Dimension) - Method in class org.jmol.awtjs.swing.JTable
 
setPreferredSize(int, int) - Method in interface jspecview.api.PlatformDialog
 
setPreferredSize(int, int) - Method in class jspecview.java.AwtDialog
 
setPreferredSize(int, int) - Method in class jspecview.js2d.JsDialog
 
setPreferredSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
 
setPreferredWidth(int) - Method in interface org.jmol.awtjs.swing.TableColumn
 
setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
 
setPreviewOptions(boolean) - Method in class org.jmol.dialog.FilePreview
 
setPrimitive(int) - Method in class org.jmol.smiles.SmilesBond
 
setPrint(PrintLayout, String) - Method in class jspecview.common.PanelData
 
setProcessingMenu(JComponent) - Method in class jspecview.application.ApplicationMenu
 
setProp(String, Object, BS) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setPropAS(String, Object, BS) - Method in class org.jmol.shape.AtomShape
 
setPropBSC(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setProperties(Object) - Method in class org.jmol.shape.Shape
 
setProperties(Properties) - Method in class jspecview.app.JSVAppPro
 
setProperties(Properties) - Method in class jspecview.application.JSpecView
 
setProperties(Properties) - Method in interface org.jmol.api.JSVInterface
 
setProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
 
setProperty(String, Object) - Method in class org.jmol.modelkit.ModelKit
Modify the state by setting a property.
setProperty(String, Object, BS) - Method in class org.jmol.shape.Axes
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Balls
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Bbcage
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Echo
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Frank
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Halos
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Hover
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Labels
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Measures
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Shape
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Stars
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Sticks
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Uccage
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Backbone
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShape
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Trace
 
setProperty(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dots
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Ellipsoids
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Polyhedra
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Vectors
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Contact
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.MolecularOrbital
 
setProperty(String, String) - Method in class jspecview.common.JSViewer
 
setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorRangeData(float[], BS) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
setPropFLS(String, Object) - Method in class org.jmol.shape.FontLineShape
 
setPropI(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
 
setPropMC(String, Object, BS) - Method in class org.jmol.shape.MeshCollection
 
setPropS(String, Object, BS) - Method in class org.jmol.shape.Shape
 
setPropTS(String, Object, BS) - Method in class org.jmol.shape.TextShape
 
setProteinStructureType(STR, int) - Method in class org.jmol.modelset.Group
 
setProteinStructureType(STR, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setProteinType(BS, STR) - Method in class org.jmol.modelset.ModelSet
 
setProteinType(STR, BS) - Method in class org.jmol.viewer.Viewer
 
setPt2(double, double) - Method in class jspecview.common.Measurement
 
setPt2(Spectrum, boolean) - Method in class jspecview.common.Measurement
 
setRadius(float) - Method in class org.jmol.modelset.Atom
 
setRandom(boolean) - Method in class javajs.util.BinaryDocument
 
setRange(float, float, boolean) - Method in class org.jmol.util.ColorEncoder
 
setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setRastAB(int, int, int, int) - Method in class org.jmol.g3d.PrecisionRenderer
 
setRastABFloat(float, float, float, float) - Method in class org.jmol.g3d.PrecisionRenderer
 
setReader(CifReader) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
filter "TOPOS_TYPES=hb" will only load hydrogen bonds; options include v, vw, and hb
setRecentMenu(Lst<String>) - Method in class jspecview.application.ApplicationMenu
 
setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setRef(Quat) - Method in class javajs.util.Quat
 
setRequiredFile(String, String) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
setRequiredFile(String, String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setRequiredFile(String, String) - Method in class org.jmol.shapesurface.Isosurface
 
setResno(int) - Method in class org.jmol.modelset.Group
 
setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
 
setRhoStar(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
 
setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
 
setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setRightComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
 
setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingData(int, boolean, int) - Method in class org.jmol.smiles.SmilesSearch.SmilesTarget
 
setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingsClickable() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingsVisible(boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setRotation(M3) - Method in class org.jmol.viewer.TransformManager
 
setRotationMatrix(M3) - Method in class org.jmol.g3d.Graphics3D
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
 
setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelSet
 
setRotationScale(M3) - Method in class javajs.util.M4
Replaces the upper 3x3 matrix values of this matrix with the values in the matrix m1.
setRotationX(float) - Method in class com.sparshui.common.messages.events.SpinEvent
 
setRotationY(float) - Method in class com.sparshui.common.messages.events.SpinEvent
 
setRotationZ(float) - Method in class com.sparshui.common.messages.events.SpinEvent
 
setRow(int, float, float, float) - Method in class javajs.util.M3
Sets the specified row of this matrix3d to the three values provided.
setRow33(int, float[]) - Method in class javajs.util.M34
 
setRowA(int, float[]) - Method in class javajs.util.M3
Sets the specified row of this matrix3d to the four values provided.
setRowA(int, float[]) - Method in class javajs.util.M4
Sets the specified row of this matrix4f to the four values provided.
setRowSelectionAllowed(boolean) - Method in class org.jmol.awtjs.swing.JTable
 
setRowSelectionInterval(int, int) - Method in class org.jmol.awtjs.swing.JTable
 
setRowV(int, T3) - Method in class javajs.util.M3
Sets the specified row of this matrix3d to the Vector provided.
setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
 
setRule6Full(boolean) - Method in class org.jmol.symmetry.CIPData
 
setScale() - Method in class org.jmol.viewer.ShapeManager
 
setScale(float) - Method in class javajs.util.M3
Sets this Matrix3f to a scalar * Identity.
setScale(float) - Method in class org.jmol.modelset.Text
 
setScale(float, boolean) - Method in class org.jmol.shapespecial.Ellipsoid
 
setScale(int, int, int, boolean) - Method in class jspecview.common.ViewData
 
setScalePixelsPerMicron(float) - Method in class org.jmol.modelset.Text
 
setScreenDimension(int, int) - Method in interface javajs.api.JSInterface
 
setScreenDimension(int, int) - Method in class jspecview.appletjs.JSVApplet
 
setScreenDimension(int, int) - Method in class jspecview.common.JSViewer
 
setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
 
setScreenDimension(int, int) - Method in class org.jmol.util.GenericApplet
 
setScreenDimension(int, int) - Method in class org.jmol.viewer.Viewer
 
setScript(String) - Method in class org.jmol.modelset.Text
 
setScriptArguments(Object, boolean) - Method in class org.jmol.script.ScriptParam
 
setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
 
setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
 
setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
 
setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
 
setSelected(boolean) - Method in interface org.jmol.api.SC
 
setSelected(boolean) - Method in class org.jmol.awt.AwtSwingComponent
 
setSelected(boolean) - Method in class org.jmol.awtjs.swing.AbstractButton
 
setSelected(Object, boolean) - Method in interface jspecview.api.PlatformDialog
 
setSelected(Object, boolean) - Method in class jspecview.java.AwtDialog
 
setSelected(Object, boolean) - Method in class jspecview.js2d.JsDialog
 
setSelected(String, boolean) - Method in class jspecview.popup.JSVGenericPopup
 
setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
setSelected(Component) - Method in interface org.jmol.awtjs.swing.SwingController
Convey to the HTML object that this check box's selection has been changed.
setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
 
setSelectedAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
 
setSelectedIndex(int) - Method in class org.jmol.awtjs.swing.JComboBox
 
setSelectedIndex(Object, int) - Method in interface jspecview.api.PlatformDialog
 
setSelectedIndex(Object, int) - Method in class jspecview.java.AwtDialog
 
setSelectedIndex(Object, int) - Method in class jspecview.js2d.JsDialog
 
setSelectedIndex(Component) - Method in interface org.jmol.awtjs.swing.SwingController
Convey to the HTML object that this combo box's selected item has been changed.
setSelectedIntegral(double) - Method in class jspecview.common.PanelData
 
setSelectedIntegral(Measurement, double) - Method in class jspecview.common.IntegralData
 
setSelectedPanel(JSVPanel) - Method in class jspecview.application.MainFrame
 
setSelectedPanel(ScriptInterface, JSVPanel) - Method in interface jspecview.api.JSVTree
 
setSelectedPanel(ScriptInterface, JSVPanel) - Method in class jspecview.application.AwtTree
 
setSelectedPanel(ScriptInterface, JSVPanel) - Method in class jspecview.tree.SimpleTree
 
setSelectedPanel(JSViewer, JSVPanel, Lst<PanelNode>) - Method in interface jspecview.api.JSVMainPanel
 
setSelectedPanel(JSViewer, JSVPanel, Lst<PanelNode>) - Method in class jspecview.java.AwtMainPanel
 
setSelectedPanel(JSViewer, JSVPanel, Lst<PanelNode>) - Method in class jspecview.js2d.JsMainPanel
 
setSelectedPeak(PeakInfo) - Method in class jspecview.common.Spectrum
 
setSelectionHalos(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
 
setSelectionHalosEnabled(boolean) - Method in class org.jmol.viewer.Viewer
 
setSelections(boolean, boolean, boolean, JSVPanel) - Method in class jspecview.application.ApplicationMenu
 
setSelectionSet(BS) - Method in class org.jmol.api.JmolViewer
 
setSelectionSet(BS) - Method in class org.jmol.viewer.Viewer
 
setSelectionSubset(BS) - Method in class org.jmol.viewer.SelectionManager
 
setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
 
setShapeId(int, int, boolean) - Method in class org.jmol.scriptext.ScriptExt
 
setShapeNameParameter(int) - Method in class org.jmol.script.ScriptEval
 
setShapeProperties(int, Object[]...) - Method in class org.jmol.viewer.ShapeManager
 
setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEval
 
setShapeProperty(int, String, Object) - Method in class org.jmol.scriptext.ScriptExt
 
setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
 
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.script.ScriptEval
 
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.viewer.ShapeManager
 
setShapeSize(int, int, BS) - Method in class org.jmol.viewer.Viewer
 
setShapeSizeBs(int, int, BS) - Method in class org.jmol.script.ScriptEval
 
setShapeSizeBs(int, int, RadiusData, BS) - Method in class org.jmol.viewer.ShapeManager
 
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shape.Shape
 
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.Backbone
 
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setShapeTranslucency(int, String, String, float, BS) - Method in class org.jmol.script.ScriptEval
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
 
setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowWithin(Lst<P3>, float, boolean) - Method in class org.jmol.shape.Mesh
 
setSigma(String, Matrix) - Method in class org.jmol.symmetry.SymmetryOperation
 
setSimpleCage(SymmetryInterface) - Method in class org.jmol.modelset.Model
 
setSimulated(String) - Method in class jspecview.common.Spectrum
 
setSite(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setSize(int, BS) - Method in class org.jmol.shape.AtomShape
 
setSize(int, BS) - Method in class org.jmol.shape.Balls
 
setSize(int, BS) - Method in class org.jmol.shape.Measures
 
setSize(int, BS) - Method in class org.jmol.shape.Shape
 
setSize(int, BS) - Method in class org.jmol.shape.Sticks
sets the size of a bond, or sets the selectedBonds set
setSize(int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
 
setSize2(int, BS) - Method in class org.jmol.shape.AtomShape
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.AtomShape
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Balls
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Shape
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shapespecial.Dots
 
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shape.AtomShape
 
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shapespecial.Vectors
 
setSlab(int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
setSlab(int) - Method in class org.jmol.export.Export3D
 
setSlab(int) - Method in class org.jmol.util.GData
clipping from the front and the back
setSlabAndZShade(int, int, int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.util.GData
 
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
set internal slab or depth from screen-based slab or depth
setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
 
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.AdfReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.AmsReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.DgridReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
after the vectors intinfo and floatinfo are completed, we
setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
after the vectors intinfo and floatinfo are completed, we
setSmilesString(String) - Method in class org.jmol.viewer.Viewer
 
setSolutionColor(String) - Method in class jspecview.common.PanelData
 
setSortingStatus(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
setSourceEnabled(boolean) - Method in class jspecview.application.ApplicationMenu
 
setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroup(int, SymmetryInterface, BS) - Method in class org.jmol.modelset.ModelSet
Set up all the model-related fields in association with a new space group.
setSpaceGroupName(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSpaceGroupName(String) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroupName(String) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroupTo(Object) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroupTo(Object) - Method in class org.jmol.symmetry.Symmetry
 
setSpecForIRMode(Spectrum) - Method in class jspecview.common.PanelData
 
setSpecShift(double) - Method in interface jspecview.api.AnnotationData
 
setSpecShift(double) - Method in class jspecview.common.IntegralData
 
setSpecShift(double) - Method in class jspecview.common.MeasurementData
 
setSpecShift(double) - Method in class jspecview.dialog.JSVDialog
 
setSpectrum(int, boolean) - Method in class jspecview.common.PanelData
 
setSpectrumNumber(int) - Method in interface jspecview.api.JSVAppletInterface
Sets the spectrum to the specified block number
setSpectrumNumber(int) - Method in class jspecview.app.JSVApp
Sets the spectrum to the specified block number
setSpectrumNumber(int) - Method in class jspecview.appletjs.JSVApplet
 
setSpectrumNumber(int) - Method in class jspecview.application.MainFrame
 
setSpectrumPeaks(int, String, String) - Method in class jspecview.source.JDXReader
 
setSpectrumPeaks(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
setSpectrumPeaks(int, String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
setSpecular(boolean) - Method in class org.jmol.util.GData
 
setSpecularExponent(int) - Method in class org.jmol.util.GData
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
setSpecularPercent(int) - Method in class org.jmol.util.GData
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
setSpecularPower(int) - Method in class org.jmol.util.GData
fractional distance to white for specular dot
setSphereMatrix(T3, float, float, float, A4, M4) - Method in class org.jmol.export.__CartesianExporter
 
setSpin(String, int) - Method in class org.jmol.viewer.Viewer
 
setSpinOff() - Method in class org.jmol.viewer.TransformManager
 
setSpinOn() - Method in class org.jmol.viewer.TransformManager
 
setSpinVectors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setSplitPane(boolean) - Method in class jspecview.application.MainFrame
 
setState(boolean) - Method in interface jspecview.api.AnnotationData
 
setState(boolean) - Method in class jspecview.common.MeasurementData
 
setState(boolean) - Method in class jspecview.dialog.JSVDialog
 
setState(int) - Method in class com.sparshui.server.TouchPoint
 
setStatement(T[], int) - Method in class org.jmol.script.ScriptEval
provides support for @x and @{....} in statements.
setStateScriptVersion(Viewer, String) - Static method in class org.jmol.script.ScriptManager
 
setStatic(int, int) - Method in interface org.jmol.api.JmolScriptEvaluator
 
setStatic(int, int) - Method in class org.jmol.script.ScriptEval
set a static variable, with checking for range
setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
 
SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
setStatusAtomMoved(boolean, BS) - Method in class org.jmol.viewer.Viewer
 
setStatusAtomPicked(int, String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
 
setStatusDragDropped(int, int, int, String, String[]) - Method in interface javajs.api.JSInterface
 
setStatusDragDropped(int, int, int, String, String[]) - Method in class jspecview.appletjs.JSVApplet
 
setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.util.GenericApplet
 
setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.viewer.Viewer
Allows a handler to set Jmol variable doDrop=false to cancel and also set the file type directly (Java) via the Jmol variable dropFileType (Java or JavaScript) if desired.
setStatusListener(JmolStatusListener) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
 
setStatusPicked(int, T3, Map<String, Object>) - Method in class org.jmol.shape.MeshCollection
 
setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
resizeCallback is called whenever the applet gets a resize notification from the browser jmolSetCallback("resizeCallback", "myResizeCallback") function myResizeCallback(width, height) {}
setStatusSelect(BS) - Method in class org.jmol.viewer.Viewer
Make the SelectCallback call and reset the hasSelected value to false.
setStatusStructureModified(int, int, int, String, int, BS) - Method in class org.jmol.viewer.StatusManager
 
setStereo(boolean, Object) - Method in class org.jmol.viewer.Viewer
 
setStereoGraphics(boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
setStereoGraphics(boolean) - Method in class org.jmol.util.GenericApplet
 
setStereoMode(int[], STER, float) - Method in class org.jmol.viewer.Viewer
 
setStrandCount() - Method in class org.jmol.renderbio.StrandsRenderer
 
setStream(BufferedInputStream, boolean) - Method in interface javajs.api.GenericBinaryDocument
 
setStream(BufferedInputStream, boolean) - Method in class javajs.util.BinaryDocument
 
setStream(OutputStream) - Method in class org.jmol.util.JSONWriter
 
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
setStreamData(DataInputStream, boolean) - Method in interface javajs.api.GenericBinaryDocument
 
setStreamData(DataInputStream, boolean) - Method in class javajs.util.BinaryDocument
 
setString(String) - Method in class javajs.util.CifDataParser
sets global str and line to be parsed from the beginning \1 ....
setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
 
setStringProperty(String, String) - Method in class org.jmol.script.ScriptParam
 
setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
 
setStrokeBold(Object, boolean) - Method in class jspecview.common.PDFWriter
 
setStrokeBold(Object, boolean) - Method in class jspecview.java.AwtG2D
 
setStrokeBold(Object, boolean) - Method in class jspecview.js2d.JsG2D
 
setStrokeBold(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
 
setStrokeBold(Object, boolean) - Method in class org.jmol.awt.AwtG2D
 
setStrokeBold(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
 
setStrucNo(int) - Method in class org.jmol.modelset.Group
 
setStrucNo(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setStrucNo(int) - Method in class org.jmol.modelsetbio.Monomer
 
setStructure(String, Translator) - Method in class org.jmol.popup.PopupResource
 
setStructureBS(int, int, STR, BS, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
bits in the bitset determines the type
setStructureIndexes() - Method in class org.jmol.modelset.ModelSet
 
setStructureList(float[], STR) - Method in class org.jmol.viewer.GlobalSettings
 
setStructureList(float[], STR) - Method in class org.jmol.viewer.Viewer
 
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelset.ModelSet
 
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.AminoPolymer
 
setSubstituent(String) - Method in class jme.JME
 
setSurfaceInfo(P4, P3, int, String) - Method in class org.jmol.jvxl.data.JvxlData
 
setSurfaceInfoFromBitSet(BS, P4) - Method in class org.jmol.jvxl.data.JvxlData
 
setSurfaceInfoFromBitSetPts(BS, P4, P3) - Method in class org.jmol.jvxl.data.JvxlData
 
setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
Sets the symbol of the atm.
setSymmetry(XtalSymmetry.FileSymmetry) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSymmetryInfoFromFile(ModelSet, int, float[]) - Method in class org.jmol.symmetry.Symmetry
Set space group and unit cell from the auxiliary info generated by XtalSymmetry specific to a given model.
setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSymop(int, boolean) - Method in class org.jmol.modelset.Atom
 
setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
 
setSyncFlush(boolean) - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
setT(T3) - Method in class javajs.util.T3
Sets the value of this tuple to the value of the Tuple3f argument.
setT(T3d) - Method in class javajs.util.T3d
Sets the value of this tuple to the value of the Tuple3d argument.
setT(T3i) - Method in class javajs.util.T3i
Sets the value of this tuple to the value of tuple t1.
setTA(T3, float) - Method in class javajs.util.Quat
q = (cos(theta/2), sin(theta/2) * n)
settable - Static variable in class org.jmol.script.T
 
setTableHeader(JTableHeader) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
setTableModel(TableModel) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
setTableSelectionEnabled(boolean) - Method in class jspecview.dialog.JSVDialog
 
setTainted(boolean) - Method in class org.jmol.viewer.Viewer
 
setTaintedAll() - Method in class jspecview.common.PanelData
 
setTaintedAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
 
setTemplate(String, String) - Method in class jme.JME
 
setTempVertex(T3, T3, T3) - Static method in class org.jmol.export.___Exporter
 
setTensor(Tensor) - Method in class org.jmol.shapespecial.Ellipsoid
 
setTensors() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setText(Object, String) - Method in interface jspecview.api.PlatformDialog
 
setText(Object, String) - Method in class jspecview.java.AwtDialog
 
setText(Object, String) - Method in class jspecview.js2d.JsDialog
 
setText(String) - Method in class jme.JME
 
setText(String) - Method in interface org.jmol.api.JmolAbstractButton
 
setText(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
 
setText(String) - Method in interface org.jmol.api.SC
 
setText(String) - Method in class org.jmol.awt.AwtSwingComponent
 
setText(String) - Method in class org.jmol.awtjs.swing.Component
 
setText(String) - Method in interface org.jmol.awtjs.swing.SwingController
Convey to the HTML object that this component's text has been changed.
setText(String) - Method in interface org.jmol.console.GenericTextArea
 
setText(String) - Method in class org.jmol.modelset.Text
 
setText(String, String) - Method in class org.jmol.popup.GenericPopup
 
setTextPosition(int) - Method in class org.jmol.util.GData
 
setThreshold(double) - Method in class jspecview.dialog.JSVDialog
 
setTime(String) - Method in class jspecview.source.JDXHeader
Sets the time the file was created
setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
 
setTimeout(Viewer, Map<String, Object>, String, int, String) - Static method in class org.jmol.thread.TimeoutThread
 
setTitle() - Method in class org.jmol.console.GenericConsole
 
setTitle() - Method in class org.jmol.console.JmolConsole
 
setTitle() - Method in class org.jmol.consolejs.AppletConsole
 
setTitle(Object) - Method in class org.jmol.shape.MeshCollection
 
setTitle(Object) - Method in class org.jmol.shapespecial.Draw
 
setTitle(String) - Method in interface jspecview.api.JSVViewPanel
 
setTitle(String) - Method in interface jspecview.api.PlatformDialog
 
setTitle(String) - Method in class jspecview.java.AwtMainPanel
 
setTitle(String) - Method in class jspecview.java.AwtPanel
 
setTitle(String) - Method in class jspecview.js2d.JsMainPanel
 
setTitle(String) - Method in class jspecview.js2d.JsPanel
 
setTitle(String) - Method in class jspecview.source.JDXHeader
Sets the title of the spectrum
setTitle(String) - Method in interface org.jmol.api.js.JSConsole
 
setTitle(String) - Method in class org.jmol.awtjs.swing.JDialog
 
setToAA(A4) - Method in class javajs.util.M4
Sets the rotational component (upper 3x3) of this matrix to a rotation given by an axis angle
setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
 
setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
 
setToM3(M34) - Method in class javajs.util.M4
Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are initialized as if this were an identity matrix (ie, affine matrix with no translational component).
setToolTipText(String) - Method in interface jspecview.api.JSVPanel
 
setToolTipText(String) - Method in class jspecview.common.PanelData
 
setToolTipText(String) - Method in class jspecview.js2d.JsPanel
 
setToolTipText(String) - Method in interface org.jmol.api.JmolAbstractButton
 
setTopoAtom(int, int, String, int, int) - Method in class org.jmol.smiles.SmilesAtom
 
setTopoCoordinates(SmilesAtom, SmilesAtom, SmilesAtom, Node[], boolean) - Method in class org.jmol.smiles.SmilesStereo
 
setTorsionData(T3, T3, T3, T3, VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
calculate temporary points
setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
 
setTrajectoryBs(BS) - Method in class org.jmol.modelset.ModelSet
 
setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setTranslation(T3) - Method in class javajs.util.M4
Modifies the translational components of this matrix to the values of the Vector3f argument; the other values of this matrix are not modified.
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
 
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
 
setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
 
setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setTranslucent(float, boolean) - Method in class org.jmol.modelset.Text
 
setTranslucentVertices(BS) - Method in class org.jmol.util.MeshSurface
Must create bsTransPolygons, polygonTranslucencies, and new triangle set for partially translucent polygons
setTransparentCursor(Object) - Method in class jspecview.java.AwtPlatform
 
setTransparentCursor(Object) - Method in class jspecview.js2d.JsPlatform
 
setTransparentCursor(Object) - Method in interface org.jmol.api.GenericPlatform
 
setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
 
setTransparentCursor(Object) - Method in class org.jmol.awtjs2d.Platform
 
setTreeNode(JSVTreeNode) - Method in class jspecview.common.PanelNode
 
setTurn() - Method in class org.jmol.shapebio.Rockets
 
setType(int) - Method in class org.jmol.util.Vibration
 
setType(String) - Method in class javajs.util.OC
 
setType(String) - Method in class org.jmol.util.Tensor
Note that type may be null here to skip type initialization and allow later setting of type; this should be used with care.
setType(Annotation.AType) - Method in class jspecview.dialog.JSVDialog
 
setU(Atom, int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setUndoMax(int) - Method in class org.jmol.viewer.StateManager
 
setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnitCell(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCell(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
setUnitCellAtomIndex(int) - Method in class org.jmol.viewer.AnimationManager
 
setUnitCellFromParams(float[], boolean, float) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCellFromParams(float[], boolean, float) - Method in class org.jmol.symmetry.Symmetry
 
setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnits(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
 
setup(int, float[], P3[], BS) - Method in class org.jmol.quantum.MepCalculation
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.cif.BCIFReader
binary must set up initially
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.cif.MMTFReader
standard set up
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setup(JSViewer, Spectrum, OC, int, int) - Method in class jspecview.export.AMLExporter
 
setup(JSViewer, Spectrum, OC, int, int) - Method in class jspecview.export.CMLExporter
 
setup(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
 
setupAC() - Method in class org.jmol.modelset.AtomCollection
 
setupArrays() - Method in class org.jmol.modelset.Model
 
setupASCR(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setupBC() - Method in class org.jmol.modelset.BondCollection
 
setupCalculation(Map<String, Object>, boolean, VolumeData, BS, T3[], Atom[], int, int[][], float[], float[], boolean, float[][], T3[]) - Method in class org.jmol.quantum.MOCalculation
 
setupCalculation(VolumeData, BS, BS, BS[], T3[], int, boolean, T3[], float[], int) - Method in class org.jmol.quantum.NciCalculation
 
setupConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setupConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setupCoordinates(float[], float[], BS, T3[], Atom[], T3[], boolean) - Method in class org.jmol.quantum.QuantumCalculation
 
setupDisplay() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setupDisplay() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setupDnD() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setupDnD() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setupLabels(Map<String, String>) - Method in class org.jmol.console.GenericConsole
 
setupLabels0(Map<String, String>) - Method in class org.jmol.console.GenericConsole
 
setupLabels0(Map<String, String>) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setupPS(AlphaPolymer, STR, int, int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
setupRR(BioShape, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
 
setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
setupUI(boolean) - Method in class org.jmol.dialog.Dialog
 
setupUIManager() - Static method in class org.jmol.dialog.Dialog
Setup the UIManager (for i18n)
setUseNumberLocalization(boolean) - Static method in class javajs.util.DF
 
setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
 
setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
 
setUserVariable(String, SV) - Method in class org.jmol.viewer.GlobalSettings
 
setUserYFactor(double) - Method in class jspecview.common.Spectrum
Set by JSViewer
setVA(V3, float) - Method in class javajs.util.A4
Sets the value of this AxisAngle4f to the specified axis and angle.
setValence(int) - Method in class org.jmol.modelset.Atom
 
setValence(int) - Method in class org.jmol.smiles.SmilesAtom
 
setValue(double) - Method in class jspecview.common.Measurement
 
setValueAt(Object, int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
 
setValues(LabelToken[], Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
 
setVariable(int, int, String, boolean) - Method in class org.jmol.script.ScriptEval
 
setVarName(String) - Method in class jspecview.source.JDXDataObject
From ##VARNAME
setVectorAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVectorScale(float) - Method in class org.jmol.api.JmolViewer
 
setVectorScale(float) - Method in class org.jmol.viewer.Viewer
 
setVertexAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
 
setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
sets the period of vibration -- period > 0: sets the period and turns vibration on -- period invalid input: '<' 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)
setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
 
setVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
 
setViewer(JFrame, Viewer, Container) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
setViewer(PlatformViewer, Object) - Method in class jspecview.java.AwtPlatform
 
setViewer(PlatformViewer, Object) - Method in class jspecview.js2d.JsPlatform
 
setViewer(PlatformViewer, Object) - Method in interface org.jmol.api.GenericPlatform
 
setViewer(PlatformViewer, Object) - Method in class org.jmol.awt.Platform
 
setViewer(PlatformViewer, Object) - Method in class org.jmol.awtjs2d.Platform
 
setViewer(Viewer) - Method in class org.jmol.adapter.writers.MOLWriter
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolJSpecView
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolNMRInterface
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolPropertyManager
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptEvaluator
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptManager
 
setViewer(Viewer) - Method in class org.jmol.console.GenericConsole
 
setViewer(Viewer) - Method in class org.jmol.jsv.JSpecView
 
setViewer(Viewer) - Method in class org.jmol.modelsetbio.BioResolver
 
setViewer(Viewer) - Method in class org.jmol.quantum.NMRCalculation
 
setViewer(Viewer) - Method in class org.jmol.script.ScriptEval
 
setViewer(Viewer) - Method in class org.jmol.script.ScriptManager
 
setViewer(Viewer) - Method in class org.jmol.viewer.PropertyManager
 
setViewer(Viewer) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
 
setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
 
setViewer(Viewer, String) - Method in class org.jmol.thread.JmolThread
 
setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
 
setViewerG3dShapeID(Viewer, int) - Method in class org.jmol.render.ShapeRenderer
 
setViewTitle(String) - Method in class jspecview.common.PanelData
 
setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
 
setVisibilityInfo() - Method in class org.jmol.shape.Measures
 
setVisible(boolean) - Method in interface jspecview.api.JSVAppletInterface
 
setVisible(boolean) - Method in interface jspecview.api.PlatformDialog
 
setVisible(boolean) - Method in class jspecview.app.JSVApp
 
setVisible(boolean) - Method in class jspecview.appletjs.JSVApplet
 
setVisible(boolean) - Method in class jspecview.dialog.JSVDialog
 
setVisible(boolean) - Method in class jspecview.java.AwtDialog
 
setVisible(boolean) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
setVisible(boolean) - Method in interface org.jmol.api.js.JSConsole
 
setVisible(boolean) - Method in class org.jmol.awtjs.swing.Component
 
setVisible(boolean) - Method in class org.jmol.awtjs.swing.JDialog
 
setVisible(boolean) - Method in class org.jmol.console.AppletConsole
 
setVisible(boolean) - Method in class org.jmol.console.GenericConsole
 
setVisible(boolean) - Method in class org.jmol.console.JmolConsole
 
setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
 
setVisible(boolean) - Method in class org.jmol.consolejs.AppletConsole
 
setVisible(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
setVisible(boolean) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
setVisible(boolean) - Method in interface org.openscience.jmol.app.JmolPlugin
 
setVisible(Component) - Method in interface org.jmol.awtjs.swing.SwingController
Convey to the HTML object that this component's text has been changed.
setVolumeDataV(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelDataAsArray(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
for sparse data mapping, as for a plane
setWhiteSpace(boolean) - Method in class org.jmol.util.JSONWriter
 
setWidthHeight(boolean) - Method in class org.jmol.util.GData
 
setWidthHeightVar() - Method in class org.jmol.viewer.Viewer
 
setWindow(int, int, float) - Method in class org.jmol.modelset.Text
 
setWindowDimensions(float[]) - Method in class org.jmol.viewer.Viewer
 
setWindowParameters(int, int) - Method in class jspecview.common.PDFWriter
 
setWindowParameters(int, int) - Method in class jspecview.java.AwtG2D
 
setWindowParameters(int, int) - Method in class jspecview.js2d.JsG2D
 
setWindowParameters(int, int) - Method in interface org.jmol.api.GenericGraphics
 
setWindowParameters(int, int) - Method in class org.jmol.awt.AwtG2D
 
setWindowParameters(int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
 
setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
 
setWinParams(int, int, boolean) - Method in class org.jmol.util.GData
 
setWriteNullAsString(boolean) - Method in class org.jmol.util.JSONWriter
Set option to write a null as the string "null" or just null itself.
setX(float) - Method in class com.sparshui.common.messages.events.TouchEvent
 
SETX - Enum constant in enum class jspecview.common.ScriptToken
 
setXFactor(double) - Method in class jspecview.source.JDXDataObject
Sets the original xfactor, from JDXReader and XMLReader
setXLabel(String) - Method in class jspecview.source.JDXDataObject
 
setXPointers(Spectrum, double, Spectrum, double) - Method in class jspecview.common.PanelData
 
setXRangeForSubSpectrum(Coordinate[]) - Method in class jspecview.common.ViewData
 
setXRot(float) - Method in class javajs.util.M34
 
setXUnits(String) - Method in class jspecview.source.JDXDataObject
Sets the units for the x axis
setXVal(double) - Method in class jspecview.common.Coordinate
Sets the x value of the coordinate
setXYA(float[], int) - Method in class org.jmol.modelset.Text
 
setXYCoords(Coordinate[]) - Method in class jspecview.source.JDXDataObject
Sets the array of coordinates
setXYZ(P3, boolean) - Method in class org.jmol.modelset.Text
 
setXYZ(T3) - Method in class org.jmol.util.ModulationSet
 
setXYZ(T3) - Method in class org.jmol.util.Vibration
 
setXYZBohr(T3[]) - Method in class org.jmol.quantum.QuantumCalculation
 
setXYZs(int, int, int, int) - Method in class org.jmol.modelset.Text
 
setY(float) - Method in class com.sparshui.common.messages.events.TouchEvent
 
setY2D(double) - Method in class jspecview.source.JDXDataObject
 
setY2DUnits(String) - Method in class jspecview.source.JDXDataObject
 
setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
setYFactor(double) - Method in class jspecview.source.JDXDataObject
Sets the original y factor, from JDXReader and XMLReader
setYLabel(String) - Method in class jspecview.source.JDXDataObject
 
setYRot(float) - Method in class javajs.util.M34
 
setYStackOffsetPercent(int) - Method in class jspecview.common.PanelData
 
setYUnits(String) - Method in class jspecview.source.JDXDataObject
Sets the units for the y axis
setYVal(double) - Method in class jspecview.common.Coordinate
Sets the y value of the coordinate
setYVal2(double) - Method in class jspecview.common.Measurement
 
setZero() - Method in class javajs.util.M3
Sets this matrix to all zeros.
setZero() - Method in class javajs.util.M4
Sets this matrix to all zeros.
setZeroOffset(float) - Method in class org.jmol.shapespecial.Polyhedron
 
setZIndex(int) - Method in class org.jmol.awtjs.swing.JDialog
 
setZoom(double, double, double, double) - Method in class jspecview.common.PanelData
 
setZoomHeight(boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
setZPosition(int, int) - Static method in class org.jmol.viewer.JC
 
setZRot(float) - Method in class javajs.util.M34
 
setZs(int, int) - Method in class org.jmol.modelset.Text
 
sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
sg - Variable in class org.jmol.shapesurface.Isosurface
 
SG_AS_STRING - Static variable in class org.jmol.viewer.JC
 
SG_CHECK_SUPERCELL - Static variable in class org.jmol.viewer.JC
 
SG_FROM_SCRATCH - Static variable in class org.jmol.viewer.JC
 
SG_IS_ASSIGN - Static variable in class org.jmol.viewer.JC
 
sgName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
SHADE_INDEX_LAST - Static variable in class org.jmol.util.Shader
 
SHADE_INDEX_NOISY_LIMIT - Static variable in class org.jmol.util.Shader
 
SHADE_INDEX_NORMAL - Static variable in class org.jmol.util.Shader
 
shader - Variable in class org.jmol.util.GData
 
Shader - Class in org.jmol.util
All functions.
Shader() - Constructor for class org.jmol.util.Shader
 
shape - Variable in class org.jmol.render.ShapeRenderer
 
shape - Static variable in class org.jmol.script.T
 
Shape - Class in org.jmol.shape
Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover
Shape() - Constructor for class org.jmol.shape.Shape
 
SHAPE_AXES - Static variable in class org.jmol.viewer.JC
 
SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JC
 
SHAPE_BALLS - Static variable in class org.jmol.viewer.JC
 
SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JC
 
SHAPE_CARTOON - Static variable in class org.jmol.viewer.JC
 
SHAPE_CGO - Static variable in class org.jmol.viewer.JC
 
SHAPE_CONTACT - Static variable in class org.jmol.viewer.JC
 
SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JC
 
SHAPE_DOTS - Static variable in class org.jmol.viewer.JC
 
SHAPE_DRAW - Static variable in class org.jmol.viewer.JC
 
SHAPE_ECHO - Static variable in class org.jmol.viewer.JC
 
SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JC
 
SHAPE_FRANK - Static variable in class org.jmol.viewer.JC
 
SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_HALOS - Static variable in class org.jmol.viewer.JC
 
SHAPE_HOVER - Static variable in class org.jmol.viewer.JC
 
SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JC
 
SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_LABELS - Static variable in class org.jmol.viewer.JC
 
SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_MEASURES - Static variable in class org.jmol.viewer.JC
 
SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_MO - Static variable in class org.jmol.viewer.JC
 
SHAPE_NBO - Static variable in class org.jmol.viewer.JC
 
SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JC
 
SHAPE_PMESH - Static variable in class org.jmol.viewer.JC
 
SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JC
 
SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JC
 
SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JC
 
SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STARS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STICKS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STRANDS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STRUTS - Static variable in class org.jmol.viewer.JC
 
SHAPE_TRACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JC
 
SHAPE_VECTORS - Static variable in class org.jmol.viewer.JC
 
shapeClassBases - Static variable in class org.jmol.viewer.JC
 
shapeCommand - Static variable in class org.jmol.script.T
 
shapeID - Variable in class org.jmol.render.ShapeRenderer
 
shapeID - Variable in class org.jmol.shape.Shape
 
shapely - Static variable in class org.jmol.script.T
 
SHAPELY - Enum constant in enum class org.jmol.c.PAL
 
SHAPELY - Static variable in class org.jmol.util.ColorEncoder
 
ShapeManager - Class in org.jmol.viewer
 
ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
 
ShapeRenderer - Class in org.jmol.render
 
ShapeRenderer() - Constructor for class org.jmol.render.ShapeRenderer
 
shapes - Variable in class org.jmol.viewer.ShapeManager
 
shapeTokenIndex(int) - Static method in class org.jmol.viewer.JC
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
 
sheet - Static variable in class org.jmol.script.T
 
Sheet - Class in org.jmol.modelsetbio
 
SHEET - Enum constant in enum class org.jmol.c.STR
 
sheetsmoothing - Static variable in class org.jmol.script.T
 
sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
 
shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
ShelxReader - Class in org.jmol.adapter.readers.xtal
A reader for SHELX output (RES) files.
ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
 
SHIFT - Static variable in class org.jmol.viewer.binding.Binding
 
SHIFT_MASK - Static variable in class org.jmol.awtjs.Event
 
shiftBits(BS, BS, boolean, int) - Static method in class org.jmol.util.BSUtil
this one slides bits to higher positions based on a pattern.
shiftPressed - Variable in class jspecview.common.PanelData
 
shiftSpectrum(int, double, double) - Method in class jspecview.common.PanelData
shifts xyCoords for a spectrum by the specified amount
shiftToXY(double, double) - Method in class jme.JMEmol
shift to an origin and return a dimension
shiftX(Coordinate[], double) - Static method in class jspecview.common.Coordinate
 
SHIFTX - Enum constant in enum class jspecview.common.ScriptToken
 
shiftY(int, int, int, int) - Method in class jspecview.common.IntegralData
 
shm - Variable in class org.jmol.viewer.Viewer
 
shouldApplySpectrumDisplaySettingsNow() - Method in class jspecview.application.PreferencesDialog
 
shouldDisplayXAxisIncreasing() - Method in class jspecview.source.JDXDataObject
Determines if the plot should be displayed decreasing by default
show - Static variable in class org.jmol.script.T
 
show(int, int, boolean) - Method in class org.jmol.popup.GenericPopup
 
show(String[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
show(String[]) - Method in class org.jmol.console.ScriptEditor
 
show(Component, int, int) - Method in class org.jmol.awtjs.swing.JPopupMenu
 
showAnnotation(Annotation.AType, Boolean) - Method in class jspecview.common.PanelData
 
showAtomNumbers - Variable in class jme.JME
 
showAtomNumbers() - Method in class jme.JME
 
showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Show an atom set from the indexes array
showAuxiliaryInfo(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
showaxes - Static variable in class org.jmol.script.T
 
showboundbox - Static variable in class org.jmol.script.T
 
showConsole(boolean) - Method in class org.jmol.viewer.Viewer
 
showContourLines - Variable in class org.jmol.shape.Mesh
 
showDialog(Annotation.AType) - Method in class jspecview.common.PanelData
 
showEditor(String[]) - Method in class org.jmol.viewer.Viewer
 
SHOWERRORS - Enum constant in enum class jspecview.common.ScriptToken
 
showFileOpenDialog(Object, Object[]) - Method in interface jspecview.api.JSVFileHelper
 
showFileOpenDialog(Object, Object[]) - Method in class jspecview.java.AwtFileHelper
 
showFileOpenDialog(Object, Object[]) - Method in class jspecview.js2d.JsFileHelper
 
showfrank - Static variable in class org.jmol.script.T
 
showFrankMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
showFrankMenu() - Method in class org.jmol.popup.JmolPopup
 
showGrid - Variable in class jspecview.common.PrintLayout
whether or not the grid should be printed
showHash(SB, String) - Method in class org.jmol.viewer.ChimeMessenger
#xxxx command output
showHash(SB, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
 
showhiddenselectionhalos - Static variable in class org.jmol.script.T
 
showhydrogens - Static variable in class org.jmol.script.T
 
showHydrogens - Variable in class jme.JME
 
showInfo(JSAppletObject, boolean) - Method in interface javajs.api.js.J2SObjectInterface
 
SHOWINTEGRATION - Enum constant in enum class jspecview.common.ScriptToken
 
SHOWKEY - Enum constant in enum class jspecview.common.ScriptToken
 
showkeystrokes - Static variable in class org.jmol.script.T
 
showmeasurements - Static variable in class org.jmol.script.T
 
SHOWMEASUREMENTS - Enum constant in enum class jspecview.common.ScriptToken
 
showMenu(int, int) - Method in interface jspecview.api.JSVPanel
 
showMenu(int, int) - Method in class jspecview.common.JSViewer
 
showMenu(int, int) - Method in class jspecview.java.AwtPanel
 
showMenu(int, int) - Method in class jspecview.js2d.JsPanel
 
showMenu(int, int) - Method in class org.jmol.modelkit.ModelKit
 
SHOWMENU - Enum constant in enum class jspecview.common.ScriptToken
 
showMessage(Object, String, String) - Method in class jspecview.dialog.DialogManager
 
showMessage(Object, String, String) - Method in class jspecview.java.AwtDialogManager
 
showMessage(Object, String, String) - Method in class jspecview.js2d.JsDialogManager
 
showMessage(String) - Method in class jspecview.common.JSViewer
 
showMessage(String, String) - Method in interface jspecview.api.JSVPanel
 
showMessage(String, String) - Method in class jspecview.java.AwtPanel
 
showMessage(String, String) - Method in class jspecview.js2d.JsPanel
 
showMessage(String, String, int) - Method in class jspecview.dialog.JSVDialog
 
showMessageDialog(Object, String, String, int) - Method in class jspecview.dialog.DialogManager
 
showMessageDialog(Object, String, String, int) - Method in class jspecview.java.AwtDialogManager
 
showMessageDialog(Object, String, String, int) - Method in class jspecview.js2d.JsDialogManager
 
showmodvecs - Static variable in class org.jmol.script.T
 
showmultiplebonds - Static variable in class org.jmol.script.T
 
shownavigationpointalways - Static variable in class org.jmol.script.T
 
showNotImplementedOptionPane() - Method in class jspecview.application.MainFrame
Shows a dialog with the message "Not Yet Implemented"
showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
 
SHOWPEAKLIST - Enum constant in enum class jspecview.common.ScriptToken
 
showPoints - Variable in class org.jmol.shape.Mesh
 
showPreferences() - Method in class jspecview.application.MainFrame
 
showProperties(Object, Spectrum) - Method in class jspecview.dialog.DialogManager
 
showProperties(Object, Spectrum) - Method in class jspecview.java.AwtDialogManager
 
showProperties(Object, Spectrum) - Method in class jspecview.js2d.JsDialogManager
Looks a lot like Swing, right? :)
showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Shows the properties in the propertiesPane of the AtomSetChooser window
SHOWPROPERTIES - Enum constant in enum class jspecview.common.ScriptToken
 
showscript - Static variable in class org.jmol.script.T
 
showSource(Object, Spectrum) - Method in class jspecview.dialog.DialogManager
 
SHOWSOURCE - Enum constant in enum class jspecview.common.ScriptToken
 
showSourceErrors(Object, JDXSource) - Method in class jspecview.dialog.DialogManager
 
showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
 
showString(String) - Method in class org.jmol.script.ScriptEval
 
showString(String) - Method in class org.jmol.scriptext.ScriptExt
 
showString(String, boolean) - Method in class org.jmol.viewer.Viewer
 
showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptError
 
showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptEval
 
showTimeout(String) - Method in class org.jmol.viewer.Viewer
 
showTimeout(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
 
showTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
showtiming - Static variable in class org.jmol.script.T
 
showTiming - Variable in class org.jmol.jvxl.readers.Parameters
 
showTiming - Variable in class org.jmol.viewer.GlobalSettings
 
showTitle - Variable in class jspecview.common.PrintLayout
whether or not the title should be printed
showTrace - Variable in class org.jmol.util.Vibration
 
showTriangles - Variable in class org.jmol.shape.Mesh
 
showunitcell - Static variable in class org.jmol.script.T
 
showunitcelldetails - Static variable in class org.jmol.script.T
 
showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
 
showUrl(String) - Method in class org.jmol.api.JmolViewer
 
showUrl(String) - Method in class org.jmol.util.GenericApplet
 
showUrl(String) - Method in class org.jmol.viewer.Viewer
syncCallback traps script synchronization messages and allows for cancellation (by returning "") or modification jmolSetCallback("syncCallback", "mySyncCallback") function mySyncCallback(app, script, appletName) { ...[modify script here]...
showUrl(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
showXScale - Variable in class jspecview.common.PrintLayout
whether or not the X-scale should be printed
showYScale - Variable in class jspecview.common.PrintLayout
whether or not the Y-scale should be printed
si - Variable in class jspecview.application.AwtTree
 
si - Variable in class jspecview.common.JSViewer
 
si - Variable in class jspecview.tree.SimpleTree
 
siCheckCallbacks(String) - Method in interface jspecview.api.ScriptInterface
 
siCheckCallbacks(String) - Method in class jspecview.app.JSVApp
 
siCheckCallbacks(String) - Method in class jspecview.application.JSpecView
 
sidechain - Static variable in class org.jmol.script.T
 
SiestaReader - Class in org.jmol.adapter.readers.xtal
BH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf SIESTA http://www.icmab.es/siesta/
SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
 
siExecHidden(boolean) - Method in interface jspecview.api.ScriptInterface
 
siExecHidden(boolean) - Method in class jspecview.app.JSVApp
 
siExecHidden(boolean) - Method in class jspecview.application.JSpecView
 
siExecScriptComplete(String, boolean) - Method in interface jspecview.api.ScriptInterface
 
siExecScriptComplete(String, boolean) - Method in class jspecview.app.JSVApp
 
siExecScriptComplete(String, boolean) - Method in class jspecview.application.JSpecView
 
siExecSetCallback(ScriptToken, String) - Method in interface jspecview.api.ScriptInterface
 
siExecSetCallback(ScriptToken, String) - Method in class jspecview.app.JSVApp
 
siExecSetCallback(ScriptToken, String) - Method in class jspecview.application.JSpecView
 
siExecTest(String) - Method in interface jspecview.api.ScriptInterface
 
siExecTest(String) - Method in class jspecview.app.JSVApp
 
siExecTest(String) - Method in class jspecview.application.JSpecView
 
siGetNewJSVPanel(Spectrum) - Method in interface jspecview.api.ScriptInterface
 
siGetNewJSVPanel(Spectrum) - Method in class jspecview.app.JSVApp
 
siGetNewJSVPanel(Spectrum) - Method in class jspecview.application.JSpecView
 
siGetNewJSVPanel2(Lst<Spectrum>) - Method in interface jspecview.api.ScriptInterface
 
siGetNewJSVPanel2(Lst<Spectrum>) - Method in class jspecview.app.JSVApp
 
siGetNewJSVPanel2(Lst<Spectrum>) - Method in class jspecview.application.JSpecView
 
sigma - Variable in class org.jmol.jvxl.readers.Parameters
 
sigma - Static variable in class org.jmol.script.T
 
sign - Static variable in class org.jmol.script.T
 
signFactor - Variable in class org.jmol.modelset.TickInfo
 
silent - Static variable in class org.jmol.script.T
 
siLoaded(String) - Method in interface jspecview.api.ScriptInterface
 
siLoaded(String) - Method in class jspecview.app.JSVApp
 
siLoaded(String) - Method in class jspecview.application.JSpecView
 
SILVER - Static variable in class org.jmol.util.C
 
SIMPLE_LINE - Static variable in class org.jmol.shapecgo.CGOMesh
 
simpleCage - Variable in class org.jmol.modelset.Model
 
SimpleEdge - Interface in org.jmol.util
minimal bond interface for SMILES and CIP
simpleEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
 
SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, Lst<P3>, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
 
SimpleMarchingCubesOld() - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
SimpleNode - Interface in org.jmol.util
Just the bare minimum for CIP, and non-BioSMILES
SimpleTree - Class in jspecview.tree
 
SimpleTree(JSViewer) - Constructor for class jspecview.tree.SimpleTree
 
SimpleTreeEnumeration - Class in jspecview.tree
 
SimpleTreeEnumeration(SimpleTreeNode) - Constructor for class jspecview.tree.SimpleTreeEnumeration
 
SimpleTreeModel - Class in jspecview.tree
 
SimpleTreeModel(JSVTreeNode) - Constructor for class jspecview.tree.SimpleTreeModel
 
SimpleTreeNode - Class in jspecview.tree
 
SimpleTreeNode(String, PanelNode) - Constructor for class jspecview.tree.SimpleTreeNode
 
SimpleTreePath - Class in jspecview.tree
 
SimpleTreePath(Object[]) - Constructor for class jspecview.tree.SimpleTreePath
 
SimpleUnitCell - Class in org.jmol.util
general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity
SimpleUnitCell() - Constructor for class org.jmol.util.SimpleUnitCell
 
SIMULATION_PROTOCOL - Static variable in class jspecview.common.JSVFileManager
 
SIMULATION_PROTOCOL - Static variable in class org.jmol.viewer.FileManager
 
sin - Static variable in class org.jmol.script.T
 
sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
 
sinBeta - Variable in class org.jmol.util.SimpleUnitCell
 
siNewWindow(boolean, boolean) - Method in interface jspecview.api.ScriptInterface
 
siNewWindow(boolean, boolean) - Method in class jspecview.app.JSVApp
Shows the applet in a Frame
siNewWindow(boolean, boolean) - Method in class jspecview.application.JSpecView
 
sinGamma - Variable in class org.jmol.util.SimpleUnitCell
 
SINGLE - Static variable in class org.jmol.viewer.binding.Binding
 
SinglePointGesture - Class in org.jmol.multitouch.sparshui
SINGLE_POINT_GESTURE only passes single-touch gestures.
SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
 
siNodeSet(PanelNode) - Method in interface jspecview.api.ScriptInterface
 
siNodeSet(PanelNode) - Method in class jspecview.app.JSVApp
 
siNodeSet(PanelNode) - Method in class jspecview.application.JSpecView
 
siOpenDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String, String) - Method in interface jspecview.api.ScriptInterface
 
siOpenDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String, String) - Method in class jspecview.app.JSVApp
 
siOpenDataOrFile(Object, String, Lst<Spectrum>, String, int, int, boolean, String, String) - Method in class jspecview.application.JSpecView
 
siProcessCommand(String) - Method in interface jspecview.api.ScriptInterface
 
siProcessCommand(String) - Method in class jspecview.app.JSVApp
overloaded in JSVAppletPro
siProcessCommand(String) - Method in class jspecview.app.JSVAppPro
 
siProcessCommand(String) - Method in class jspecview.application.JSpecView
 
siSendPanelChange() - Method in interface jspecview.api.ScriptInterface
 
siSendPanelChange() - Method in class jspecview.app.JSVApp
 
siSendPanelChange() - Method in class jspecview.application.JSpecView
 
siSetCurrentSource(JDXSource) - Method in interface jspecview.api.ScriptInterface
 
siSetCurrentSource(JDXSource) - Method in class jspecview.app.JSVApp
 
siSetCurrentSource(JDXSource) - Method in class jspecview.application.JSpecView
 
siSetLoaded(String, String) - Method in interface jspecview.api.ScriptInterface
 
siSetLoaded(String, String) - Method in class jspecview.app.JSVApp
 
siSetLoaded(String, String) - Method in class jspecview.application.JSpecView
 
siSetMenuEnables(PanelNode, boolean) - Method in interface jspecview.api.ScriptInterface
 
siSetMenuEnables(PanelNode, boolean) - Method in class jspecview.app.JSVApp
 
siSetMenuEnables(PanelNode, boolean) - Method in class jspecview.application.JSpecView
 
siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in interface jspecview.api.ScriptInterface
 
siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in class jspecview.app.JSVApp
 
siSetPropertiesFromPreferences(JSVPanel, boolean) - Method in class jspecview.application.JSpecView
Sets the display properties as specified from the preferences dialog or the properties file
siSetSelectedPanel(JSVPanel) - Method in interface jspecview.api.ScriptInterface
 
siSetSelectedPanel(JSVPanel) - Method in class jspecview.app.JSVApp
 
siSetSelectedPanel(JSVPanel) - Method in class jspecview.application.JSpecView
 
siSourceClosed(JDXSource) - Method in interface jspecview.api.ScriptInterface
 
siSourceClosed(JDXSource) - Method in class jspecview.app.JSVApp
 
siSourceClosed(JDXSource) - Method in class jspecview.application.JSpecView
Closes the JDXSource specified by source
siSyncLoad(String) - Method in interface jspecview.api.ScriptInterface
 
siSyncLoad(String) - Method in class jspecview.app.JSVApp
Loads a new file into the existing applet window
siSyncLoad(String) - Method in class jspecview.application.JSpecView
 
site - Static variable in class org.jmol.script.T
 
siUpdateBoolean(ScriptToken, boolean) - Method in interface jspecview.api.ScriptInterface
 
siUpdateBoolean(ScriptToken, boolean) - Method in class jspecview.app.JSVApp
 
siUpdateBoolean(ScriptToken, boolean) - Method in class jspecview.application.JSpecView
 
siUpdateRecentMenus(String) - Method in interface jspecview.api.ScriptInterface
 
siUpdateRecentMenus(String) - Method in class jspecview.app.JSVApp
 
siUpdateRecentMenus(String) - Method in class jspecview.application.JSpecView
 
siValidateAndRepaint(boolean) - Method in interface jspecview.api.ScriptInterface
 
siValidateAndRepaint(boolean) - Method in class jspecview.app.JSVApp
 
siValidateAndRepaint(boolean) - Method in class jspecview.application.JSpecView
 
sixdots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
size - Static variable in class org.jmol.script.T
 
size() - Method in class javajs.util.BS
Returns the number of bits of space actually in use by this BitSet to represent bit values.
skew() - Method in class org.jmol.util.Tensor
a measure of asymmetry.
skip(long) - Method in class com.jcraft.jzlib.InflaterInputStream
 
skipComments(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
skipComments(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
skipComments(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
skipLoop(boolean) - Method in interface javajs.api.GenericCifDataParser
 
skipLoop(boolean) - Method in class javajs.util.CifDataParser
Skips all associated loop data.
skipLoop(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
 
skipLoopKeyword() - Method in class org.jmol.adapter.readers.cif.CifReader
 
skipNextToken() - Method in interface javajs.api.GenericCifDataParser
 
skipNextToken() - Method in class javajs.util.CifDataParser
 
skipping - Variable in class org.jmol.adapter.readers.cif.CifReader
 
skipTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
 
skipTo(String, String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
skipTo(String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
skipTo(String, String) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
slab - Static variable in class org.jmol.script.T
 
slab - Variable in class org.jmol.util.GData
 
slabbingObject - Variable in class org.jmol.shape.Mesh
 
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSlicer
"slabs" an isosurface into the first Brillouin zone moving points as necessary.
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSurface
 
slabbyatom - Static variable in class org.jmol.script.T
 
slabbymolecule - Static variable in class org.jmol.script.T
 
slabColix - Variable in class org.jmol.util.MeshSurface
 
slabenabled - Static variable in class org.jmol.script.T
 
slabEnabled - Variable in class org.jmol.viewer.TransformManager
 
slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
 
slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
 
slabInternal(P4, boolean) - Method in class org.jmol.viewer.TransformManager
 
slabIsosurface(Lst<Object[]>) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
slabMeshType - Variable in class org.jmol.util.MeshSurface
 
slabOptions - Variable in class org.jmol.util.MeshSurface
 
slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
 
slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSlicer
 
slabPolygonsList(Lst<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
 
slabrange - Static variable in class org.jmol.script.T
 
slabReset() - Method in class org.jmol.viewer.TransformManager
 
slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
slabValue - Variable in class org.jmol.jvxl.data.JvxlData
 
slabValue - Variable in class org.jmol.viewer.TransformManager
 
slabXY - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
slabZ - Variable in class org.jmol.export.___Exporter
 
slaterArray - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
SlaterData - Class in org.jmol.quantum
 
SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
 
slaters - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
sleepTime - Variable in class org.jmol.thread.JmolThread
 
slen - Variable in class org.jmol.script.ScriptParam
 
slen - Variable in class org.jmol.scriptext.ScriptExt
 
slm - Variable in class org.jmol.viewer.Viewer
 
slop - Variable in class org.jmol.adapter.writers.XtlWriter
 
slop - Variable in class org.jmol.util.SimpleUnitCell
initial value is set in subclass UnitCell
SLOP_PARAMS - Static variable in class org.jmol.util.SimpleUnitCell
 
SLOPDP - Static variable in class org.jmol.util.SimpleUnitCell
 
SLOPSP - Static variable in class org.jmol.util.SimpleUnitCell
allowance for rounding in [0,1)
sm - Variable in class org.jmol.modelset.ModelSet
 
sm - Variable in class org.jmol.script.ScriptEval
 
sm - Variable in class org.jmol.viewer.Viewer
 
smallAtomWidthLabel - Variable in class jme.AtomDisplayLabel
 
smallmoleculemaxatoms - Static variable in class org.jmol.script.T
 
smartaromatic - Static variable in class org.jmol.script.T
 
SmarterJmolAdapter - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
 
smarts - Variable in class org.jmol.shapespecial.Polyhedron
 
smiles - Static variable in class org.jmol.script.T
 
smiles - Variable in class org.jmol.shapespecial.Polyhedron
 
smiles() - Method in class jme.JME
 
smiles() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
SMILES_2D - Static variable in class org.jmol.viewer.JC
 
SMILES_AROMATIC_DEFINED - Static variable in class org.jmol.viewer.JC
AROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.
SMILES_AROMATIC_DOUBLE - Static variable in class org.jmol.viewer.JC
AROMATIC_DOUBLE allows a distinction between single and double, as for example is necessary to distinguish between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing)
SMILES_AROMATIC_MMFF94 - Static variable in class org.jmol.viewer.JC
AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.
SMILES_AROMATIC_PLANAR - Static variable in class org.jmol.viewer.JC
AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)
SMILES_AROMATIC_STRICT - Static variable in class org.jmol.viewer.JC
AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds
SMILES_FIRST_MATCH_ONLY - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_ALL_COMPONENTS - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_ATOM_COMMENT - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_BIO - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_BIO_COMMENT - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_BIO_COV_CROSSLINK - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_BIO_HH_CROSSLINK - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_BIO_NOCOMMENTS - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_EXPLICIT_H_ALL - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_EXPLICIT_H2_ONLY - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_NO_BRANCHES - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_POLYHEDRAL - Static variable in class org.jmol.viewer.JC
 
SMILES_GEN_TOPOLOGY - Static variable in class org.jmol.viewer.JC
 
SMILES_GROUP_BY_MODEL - Static variable in class org.jmol.viewer.JC
 
SMILES_IGNORE_ATOM_CLASS - Static variable in class org.jmol.viewer.JC
 
SMILES_IGNORE_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
 
SMILES_INVERT_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
 
SMILES_MAP_UNIQUE - Static variable in class org.jmol.viewer.JC
 
SMILES_NO_AROMATIC - Static variable in class org.jmol.viewer.JC
 
SMILES_TYPE_OPENSMARTS - Static variable in class org.jmol.viewer.JC
 
SMILES_TYPE_OPENSMILES - Static variable in class org.jmol.viewer.JC
 
SMILES_TYPE_SMARTS - Static variable in class org.jmol.viewer.JC
 
SMILES_TYPE_SMILES - Static variable in class org.jmol.viewer.JC
 
smiles2dimageformat - Static variable in class org.jmol.script.T
 
SmilesAromatic - Class in org.jmol.smiles
 
SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
 
SmilesAtom - Class in org.jmol.smiles
This class represents an atom in a SmilesMolecule.
SmilesAtom() - Constructor for class org.jmol.smiles.SmilesAtom
 
SmilesBond - Class in org.jmol.smiles
Bond in a SmilesMolecule
SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
SmilesBond constructor
SmilesExt - Class in org.jmol.scriptext
 
SmilesExt() - Constructor for class org.jmol.scriptext.SmilesExt
 
SmilesGenerator - Class in org.jmol.smiles
Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
 
SmilesMatcher - Class in org.jmol.smiles
Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods
SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
 
SmilesMatcherInterface - Interface in org.jmol.api
 
SmilesMeasure - Class in org.jmol.smiles
 
SmilesParser - Class in org.jmol.smiles
Parses a SMILES string or SMARTS pattern to create a SmilesSearch.
SmilesSearch - Class in org.jmol.smiles
A class to build and carry out a SMILES or SMARTS match
SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
 
SmilesSearch.SmilesTarget - Class in org.jmol.smiles
 
SmilesStereo - Class in org.jmol.smiles
This class relates to stereochemical issues
SmilesTarget() - Constructor for class org.jmol.smiles.SmilesSearch.SmilesTarget
 
smilesurlformat - Static variable in class org.jmol.script.T
 
snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
 
snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
 
solid - Static variable in class org.jmol.script.T
 
solidOnly - Variable in class org.jmol.export.___Exporter
 
solvent - Static variable in class org.jmol.script.T
 
solventprobe - Static variable in class org.jmol.script.T
 
solventproberadius - Static variable in class org.jmol.script.T
 
solvName - Variable in class jspecview.export.AMLExporter
 
solvName - Variable in class jspecview.export.CMLExporter
 
solvRef - Variable in class jspecview.export.AMLExporter
 
solvRef - Variable in class jspecview.export.CMLExporter
 
someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelSet
 
someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelSet
 
someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelSet
 
sort - Static variable in class org.jmol.g3d.Graphics3D
 
sort - Static variable in class org.jmol.script.T
 
Sort(int, String) - Constructor for class org.jmol.script.SV.Sort
 
sortAssemblyModels() - Method in class org.jmol.adapter.readers.cif.MMCifReader
issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ...
sortedItem(Lst<String>, int) - Static method in class javajs.util.AU
 
sortMapArray(String) - Method in class org.jmol.script.SV
 
sortMOs() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.AdfReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.AmsReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.DgridReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
sorts coefficients by atomic number for speed later
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.WebMOReader
sorts coefficients by atomic number for speed later
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.AdfReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.AmsReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.CsfReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrReverse(int) - Method in class org.jmol.script.SV
 
SortSet() - Constructor for class org.jmol.jvxl.data.MeshData.SortSet
 
source - Variable in class jspecview.common.PanelNode
 
source - Variable in class jspecview.source.AnIMLReader
 
SOURCE - Enum constant in enum class jspecview.common.ExportType
 
sourceClosed(JDXSource) - Method in class jspecview.application.MainFrame
 
sourceID - Variable in class jspecview.source.JDXDataObject
 
sourceLabel - Static variable in class jspecview.common.JSViewer
 
SourceReader - Interface in jspecview.api
 
SOUTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
 
SP - Static variable in class org.jmol.quantum.QS
 
spacebeforesquare - Static variable in class org.jmol.script.T
 
spacefill - Static variable in class org.jmol.script.T
 
spacegroup - Static variable in class org.jmol.script.T
 
spaceGroup - Variable in class org.jmol.symmetry.Symmetry
 
SpaceGroup - Class in org.jmol.symmetry
A general class to deal with Hermann-Mauguin or Hall names Bob Hanson 9/2006 references: International Tables for Crystallography Vol.
SpaceGroupFinder - Class in org.jmol.symmetry
A relatively simple space group finder given a unit cell.
SpaceGroupFinder() - Constructor for class org.jmol.symmetry.SpaceGroupFinder
 
span() - Method in class org.jmol.util.Tensor
width of the signal; |e2 - e0|
spardirCache - Variable in class org.jmol.viewer.FileManager
 
SparseArray(String) - Constructor for class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
SparshClient - Interface in com.sparshui.client
The Client interface must be implemented in all clients wishing to connect to the Sparsh-UI gesture server.
SpartanInputReader - Class in org.jmol.adapter.readers.spartan
 
SpartanInputReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanInputReader
 
SpartanReader - Class in org.jmol.adapter.readers.spartan
 
SpartanReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanReader
 
SpartanSmolReader - Class in org.jmol.adapter.readers.spartan
 
SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanSmolReader
 
spartanUtil() - Method in class org.jmol.viewer.FileManager
An isolated class to retrieve Spartan file data from compound documents, zip files, and directories
SpartanUtil - Class in org.jmol.adapter.readers.spartan
A class to isolate Spartan file reading methods from the rest of Jmol.
SpartanUtil() - Constructor for class org.jmol.adapter.readers.spartan.SpartanUtil
 
spec - Variable in class jspecview.common.MeasurementData
 
spec - Variable in class jspecview.dialog.JSVDialog
 
spec_alternate - Static variable in class org.jmol.script.T
 
spec_atom - Static variable in class org.jmol.script.T
 
spec_chain - Static variable in class org.jmol.script.T
 
spec_model - Static variable in class org.jmol.script.T
 
spec_model2 - Static variable in class org.jmol.script.T
 
spec_name_pattern - Static variable in class org.jmol.script.T
 
spec_resid - Static variable in class org.jmol.script.T
 
spec_seqcode - Static variable in class org.jmol.script.T
 
spec_seqcode_range - Static variable in class org.jmol.script.T
 
Special - Variable in class org.jmol.popup.JmolPopup
 
SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.C
 
specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
 
specialAtomNames - Static variable in class org.jmol.modelset.Group
 
specialLabel - Variable in class org.jmol.shape.Hover
 
specialposition - Static variable in class org.jmol.script.T
 
spectra - Variable in class jspecview.common.PanelData
 
spectraTree - Variable in class jspecview.common.JSViewer
 
spectrum - Variable in class jspecview.common.PeakInfo
 
Spectrum - Class in jspecview.common
JDXSpectrum implements the Interface Spectrum for the display of JDX Files.
Spectrum() - Constructor for class jspecview.common.Spectrum
Constructor
SPECTRUM - Enum constant in enum class jspecview.common.ScriptToken
 
Spectrum.IRMode - Enum Class in jspecview.common
 
SPECTRUMNUMBER - Enum constant in enum class jspecview.common.ScriptToken
 
spectypeInitials - Variable in class jspecview.export.AMLExporter
 
spectypeInitials - Variable in class jspecview.export.CMLExporter
 
specular - Static variable in class org.jmol.script.T
 
specularexponent - Static variable in class org.jmol.script.T
 
specularpercent - Static variable in class org.jmol.script.T
 
specularpower - Static variable in class org.jmol.script.T
 
sphere - Static variable in class org.jmol.script.T
 
SPHERE - Static variable in class org.jmol.shapecgo.CGOMesh
 
sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
 
sphereMean(Quat[], float[], float) - Static method in class javajs.util.Quat
 
SphereRenderer - Class in org.jmol.g3d
Implements high performance rendering of shaded spheres.
sphereShadeIndexes - Variable in class org.jmol.util.Shader
 
sphereShapeCache - Variable in class org.jmol.util.Shader
 
spin - Static variable in class org.jmol.script.T
 
SPIN_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
SPIN_EVENT - Static variable in class com.sparshui.GestureType
 
SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
SPIN_GESTURE - Static variable in class com.sparshui.GestureType
 
SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
spine - Static variable in class org.jmol.script.T
 
SpinEvent - Class in com.sparshui.common.messages.events
 
SpinEvent() - Constructor for class com.sparshui.common.messages.events.SpinEvent
 
SpinEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.SpinEvent
Constructs a new SpinEvent from a serialized version - 4 bytes : rotationX - 4 bytes : rotationY - 4 bytes : rotationZ - 12 bytes total
SpinEvent(float, float, float) - Constructor for class com.sparshui.common.messages.events.SpinEvent
 
spinfps - Static variable in class org.jmol.script.T
 
spinFps - Variable in class org.jmol.viewer.TransformManager
 
spinOn - Variable in class org.jmol.viewer.TransformManager
 
spinThread - Variable in class org.jmol.viewer.TransformManager
 
SpinThread - Class in org.jmol.thread
 
SpinThread() - Constructor for class org.jmol.thread.SpinThread
 
spinx - Static variable in class org.jmol.script.T
 
spinX - Variable in class org.jmol.viewer.TransformManager
 
spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
 
spiny - Static variable in class org.jmol.script.T
 
spinY - Variable in class org.jmol.viewer.TransformManager
 
spinz - Static variable in class org.jmol.script.T
 
spinZ - Variable in class org.jmol.viewer.TransformManager
 
splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
Splash - Class in org.openscience.jmol.app.jmolpanel
 
Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
 
splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
 
SplashInterface - Interface in org.openscience.jmol.app
 
split - Static variable in class org.jmol.script.T
 
split(String, String) - Static method in class javajs.util.PT
proper splitting, even for Java 1.3 -- if the text ends in the run, no new line is appended.
splitSpectra() - Method in class jspecview.common.JSViewer
 
splitStack(boolean) - Method in class jspecview.common.PanelData
 
sppm - Variable in class org.jmol.render.LabelsRenderer
 
sprintf(String, String, Object[]) - Static method in class javajs.util.PT
sprintf emulation uses (almost) c++ standard string formats 's' string 'i' or 'd' integer, 'e' double, 'f' float, 'p' point3f 'q' quaternion/plane/axisangle with added "i" (equal to the insipid "d" -- digits?)
sprintf(String, SV) - Static method in class org.jmol.script.SV
 
sqrt - Static variable in class org.jmol.script.T
 
SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesStereo
 
squared - Static variable in class org.jmol.script.T
 
squareEuclideanDist(double, double, double, double) - Static method in class jme.JMEUtil
 
SQZ - Enum constant in enum class jspecview.common.ExportType
 
sr - Variable in class org.jmol.jvxl.data.VolumeData
 
ssbond - Static variable in class org.jmol.script.T
 
ssbondsbackbone - Static variable in class org.jmol.script.T
 
st - Variable in class org.jmol.script.ScriptParam
 
st - Variable in class org.jmol.scriptext.ScriptExt
 
STACKOFFSETY - Enum constant in enum class jspecview.common.ScriptToken
 
STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
 
standardGroupList - Static variable in class org.jmol.modelset.Group
 
standardLevel - Static variable in class org.jmol.util.Geodesic
3 levels, 0 through 3
star - Variable in class jme.JME
 
star - Static variable in class org.jmol.script.T
 
Stars - Class in org.jmol.shape
 
Stars() - Constructor for class org.jmol.shape.Stars
 
StarsRenderer - Class in org.jmol.render
 
StarsRenderer() - Constructor for class org.jmol.render.StarsRenderer
 
start() - Method in class jme.JME
 
start() - Method in class org.jmol.thread.JmolThread
 
start() - Method in class org.jmol.util.PatternMatcher.JSPattern
 
start() - Method in class org.openscience.jmol.app.InputScannerThread
 
start() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
start(JFrame, Viewer, Map<String, Object>) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
 
start(JFrame, Viewer, Map<String, Object>) - Method in interface org.openscience.jmol.app.JmolPlugin
 
start(Viewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
start(Viewer) - Method in class org.jmol.console.AppletConsole
 
start(Viewer) - Method in class org.jmol.consolejs.AppletConsole
 
start(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
START - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
START_ELEMENT - Static variable in class jspecview.source.XMLParser
 
START_END_ELEMENT - Static variable in class jspecview.source.XMLParser
 
startChainID - Variable in class org.jmol.adapter.smarter.Structure
 
startCommandWatcher(boolean) - Method in interface org.jmol.api.JmolScriptManager
 
startCommandWatcher(boolean) - Method in class org.jmol.script.ScriptManager
 
startDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
startGestureServer() - Method in class com.sparshui.server.GestureServer
two independent threads -- one accepting multiple clients, one not.
startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
 
startHoverWatcher(boolean) - Method in interface javajs.api.JSInterface
 
startHoverWatcher(boolean) - Method in class jspecview.appletjs.JSVApplet
 
startHoverWatcher(boolean) - Method in class org.jmol.util.GenericApplet
 
startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
 
startHoverWatcher(boolean) - Method in class org.jmol.viewer.Viewer
 
startIndex - Variable in class jspecview.export.AMLExporter
 
startIndex - Variable in class jspecview.export.CMLExporter
 
STARTINDEX - Enum constant in enum class jspecview.common.ScriptToken
 
startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
startJmol(JmolApp) - Static method in class org.openscience.jmol.app.Jmol
 
startLayout() - Method in interface jspecview.api.PlatformDialog
 
startLayout() - Method in class jspecview.java.AwtDialog
 
startLayout() - Method in class jspecview.js2d.JsDialog
 
startMinimization() - Method in class org.jmol.minimize.Minimizer
 
startNBO(String) - Method in class org.jmol.viewer.Viewer
 
startOpenTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
 
startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startPlugin(String) - Method in class org.jmol.viewer.Viewer
startup -U nbo option
startPos - Variable in class javajs.img.PngEncoder
 
startRecording() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
startService(int, JsonNioClient, Viewer, String, int) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
startService(int, JsonNioClient, Viewer, String, int) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
startSimulator(Object) - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
startSpinningAxis(T3, T3, boolean) - Method in class org.jmol.viewer.Viewer
 
startTime - Variable in class org.jmol.thread.JmolThread
 
startTimer(String) - Static method in class org.jmol.util.Logger
 
startTrace(int) - Method in class org.jmol.util.Vibration
 
startupDim - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startupHeight - Variable in class org.openscience.jmol.app.JmolApp
 
startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startupPinTip - Variable in class jspecview.common.PanelData
 
startupWidth - Variable in class org.openscience.jmol.app.JmolApp
 
startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startViewer(JmolViewer, SplashInterface, boolean) - Method in class org.openscience.jmol.app.JmolApp
 
starwidth - Static variable in class org.jmol.script.T
 
state - Variable in class jspecview.export.AMLExporter
 
state - Variable in class jspecview.export.CMLExporter
 
state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
state - Variable in class org.jmol.jvxl.readers.Parameters
 
state - Static variable in class org.jmol.script.T
 
STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.JC
 
stateButton - Variable in class org.jmol.console.GenericConsole
 
stateChanged(ChangeEvent) - Method in class org.jmol.dialog.Dialog.QualityListener
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
StateCreator - Class in org.jmol.viewer
StateCreator handles all aspects of working with the "state" as generally defined, including -- creating the state script -- general output, including logging -- handling undo/redo -- processing SYNC directives Called by reflection only; all state generation script here, for modularization in JavaScript
StateCreator() - Constructor for class org.jmol.viewer.StateCreator
 
StateManager - Class in org.jmol.viewer
 
statement - Variable in class org.jmol.script.ScriptContext
 
statementAsString(Viewer, T[], int, boolean) - Static method in class org.jmol.script.ScriptEval
 
StateScript - Class in org.jmol.modelset
 
stateScripts - Variable in class org.jmol.modelset.ModelSet
 
stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
 
staticCleanTransform(String) - Method in interface org.jmol.api.SymmetryInterface
 
staticCleanTransform(String) - Method in class org.jmol.symmetry.Symmetry
 
staticConvertOperation(String, M4) - Method in interface org.jmol.api.SymmetryInterface
 
staticConvertOperation(String, M4) - Method in class org.jmol.symmetry.Symmetry
 
staticGetAtomSetCollection(AtomSetCollectionReader) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
staticGetAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
The primary file or string reader -- returns just the reader now
staticGetTransformABC(Object, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
staticGetTransformABC(Object, boolean) - Method in class org.jmol.symmetry.Symmetry
 
staticID - Static variable in class org.jmol.minimize.Minimizer
 
staticToRationalXYZ(P3, String) - Method in interface org.jmol.api.SymmetryInterface
 
staticToRationalXYZ(P3, String) - Method in class org.jmol.symmetry.Symmetry
 
stats() - Method in class org.jmol.bspt.Bspf
 
stats() - Method in class org.jmol.bspt.Bspt
prints some simple stats to stdout
status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
 
STATUS_COORD - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
 
STATUS_TEXT - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
 
STATUS_TIME - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
 
StatusBar - Class in org.openscience.jmol.app.jmolpanel
 
StatusBar(int) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
 
statusForm - Variable in class org.jmol.util.GenericApplet
 
statusList - Variable in class org.jmol.viewer.StatusManager
 
StatusListener - Class in org.openscience.jmol.app.jmolpanel
 
StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusListener
 
StatusManager - Class in org.jmol.viewer
The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
statusreporting - Static variable in class org.jmol.script.T
 
statusText - Variable in class org.jmol.util.GenericApplet
 
statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
statusTextarea - Variable in class org.jmol.util.GenericApplet
 
stddev - Static variable in class org.jmol.script.T
 
stdinchi - Static variable in class org.jmol.script.T
 
stdinchikey - Static variable in class org.jmol.script.T
 
steepestDescentInitialize(int, double, double) - Method in class org.jmol.minimize.forcefield.ForceField
 
steepestDescentTakeNSteps(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
step - Static variable in class org.jmol.script.T
 
stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
stepMinimization() - Method in class org.jmol.minimize.Minimizer
 
stepPausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
 
stepPausedExecution() - Method in class org.jmol.script.ScriptEval
 
steps - Variable in class jspecview.common.ScaleData
The step values for the X and Y scales
steps - Variable in class org.jmol.jvxl.readers.Parameters
 
STER - Enum Class in org.jmol.c
 
stereo - Variable in class jme.JME
 
stereo - Static variable in class org.jmol.script.T
 
stereo - Variable in class org.jmol.smiles.SmilesAtom
 
stereodegrees - Static variable in class org.jmol.script.T
 
stereoTransformation(int[], int[]) - Static method in class jme.JMEUtil
 
Sticks - Class in org.jmol.shape
 
Sticks() - Constructor for class org.jmol.shape.Sticks
 
SticksRenderer - Class in org.jmol.render
 
SticksRenderer() - Constructor for class org.jmol.render.SticksRenderer
 
stm - Variable in class org.jmol.viewer.Viewer
 
stop - Static variable in class org.jmol.script.T
 
stop() - Method in class jme.JME
 
STOP - Static variable in class org.jmol.shapecgo.CGOMesh
 
stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
 
stopMotion() - Method in class org.jmol.viewer.TransformManager
 
stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
stopped - Variable in class org.jmol.thread.JmolThread
 
stopScriptThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
 
stopScriptThreads() - Method in class org.jmol.script.ScriptEval
 
stopThread(boolean) - Method in class org.jmol.viewer.AnimationManager
 
store() - Method in class jspecview.application.DisplaySchemesProcessor
Saves the display schemes to file in XML format
str - Variable in class javajs.util.CifDataParser
working string (buffer)
str - Variable in class jme.AtomDisplayLabel
 
STR - Enum Class in org.jmol.c
 
straightness - Static variable in class org.jmol.script.T
 
STRAIGHTNESS - Enum constant in enum class org.jmol.c.PAL
 
strandcount - Static variable in class org.jmol.script.T
 
strandCount - Variable in class org.jmol.adapter.smarter.Structure
 
strandCount - Variable in class org.jmol.renderbio.StrandsRenderer
 
strandcountformeshribbon - Static variable in class org.jmol.script.T
 
strandcountforstrands - Static variable in class org.jmol.script.T
 
strandID - Variable in class org.jmol.adapter.smarter.Structure
 
strands - Static variable in class org.jmol.script.T
 
Strands - Class in org.jmol.shapebio
 
Strands() - Constructor for class org.jmol.shapebio.Strands
 
strandSeparation - Variable in class org.jmol.renderbio.StrandsRenderer
 
StrandsRenderer - Class in org.jmol.renderbio
 
StrandsRenderer() - Constructor for class org.jmol.renderbio.StrandsRenderer
 
stream - Variable in class javajs.util.BinaryDocument
 
StreamReader(BufferedInputStream, String) - Constructor for class javajs.util.Rdr.StreamReader
 
streamToBytes(InputStream) - Static method in class javajs.util.Rdr
Read an InputStream in its entirety as a byte array, closing the stream.
streamToString(InputStream) - Static method in class javajs.util.Rdr
Read an InputStream in its entirety as a string, closing the stream.
streamToUTF8String(BufferedInputStream) - Static method in class javajs.util.Rdr
Read a UTF-8 stream fully, converting it to a String.
strFormat - Variable in class org.jmol.modelset.Measurement
 
strFormat - Variable in class org.jmol.modelset.MeasurementData
 
string - Static variable in class org.jmol.script.T
 
StringDataReader - Class in javajs.util
 
StringDataReader() - Constructor for class javajs.util.StringDataReader
 
StringDataReader(String) - Constructor for class javajs.util.StringDataReader
 
stringHeight(FontMetrics) - Static method in class jme.JMEUtil
Provide the ideal height of a string consisting of usual upper case characters.
stringParameter(int) - Method in class org.jmol.script.ScriptParam
 
stringParameter(int) - Method in class org.jmol.scriptext.ScriptExt
 
stringParameterSet(int) - Method in class org.jmol.script.ScriptParam
 
strings - Variable in class org.jmol.shape.Labels
 
stringToByteArray(String) - Static method in class com.sparshui.common.utils.Converter
 
stringWidth(String) - Method in class org.jmol.util.Font
 
stripPath(String) - Static method in class org.jmol.viewer.FileManager
 
stripTypePrefix(String) - Static method in class org.jmol.viewer.FileManager
Stip PDB::file://...
strJavaVendor - Static variable in class org.jmol.viewer.Viewer
 
strJavaVersion - Static variable in class org.jmol.viewer.Viewer
 
strListValue(T) - Static method in class org.jmol.script.SV
 
strMenuStructure - Variable in class org.jmol.popup.GenericPopup
 
StrObFreq - Variable in class jspecview.source.AnIMLReader
 
stroke() - Method in class javajs.export.PDFCreator
 
strOSName - Static variable in class org.jmol.viewer.Viewer
 
strparam - Static variable in class org.jmol.script.T
 
strproperty - Static variable in class org.jmol.script.T
 
strSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
strucid - Static variable in class org.jmol.script.T
 
strucno - Static variable in class org.jmol.script.T
 
structure - Variable in class org.jmol.popup.PopupResource
 
structure - Static variable in class org.jmol.script.T
 
Structure - Class in org.jmol.adapter.smarter
 
Structure - Interface in org.jmol.modelset
 
Structure(int, STR, STR, String, String, int, BS[]) - Constructor for class org.jmol.adapter.smarter.Structure
 
STRUCTURE - Enum constant in enum class org.jmol.c.PAL
 
structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structureID - Variable in class org.jmol.adapter.smarter.Structure
 
StructureIterator - Class in org.jmol.adapter.smarter
 
STRUCTUREMODIFIED - Enum constant in enum class org.jmol.c.CBK
 
structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
 
structureTainted - Variable in class org.jmol.modelset.Model
 
structureType - Variable in class org.jmol.adapter.smarter.Structure
 
structureTypes - Variable in class org.jmol.renderbio.BackboneRenderer
 
structureTypes - Variable in class org.jmol.renderbio.CartoonRenderer
 
structureTypes - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
structureTypes - Variable in class org.jmol.renderbio.RibbonsRenderer
 
structureTypes - Variable in class org.jmol.renderbio.RocketsRenderer
 
structureTypes - Variable in class org.jmol.renderbio.StrandsRenderer
 
structureTypes - Variable in class org.jmol.renderbio.TraceRenderer
 
strutdefaultradius - Static variable in class org.jmol.script.T
 
strutlengthmaximum - Static variable in class org.jmol.script.T
 
struts - Static variable in class org.jmol.script.T
 
strutsmultiple - Static variable in class org.jmol.script.T
 
strutspacing - Static variable in class org.jmol.script.T
 
sType - Variable in class com.sparshui.GestureType
 
sType - Variable in class org.jmol.minimize.MinAtom
 
sub - Static variable in class org.jmol.script.T
 
sub(double[], double[], V3d) - Static method in class org.jmol.minimize.Util
 
sub(M3) - Method in class javajs.util.M3
Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
sub(M4) - Method in class javajs.util.M4
Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
sub(Matrix) - Method in class javajs.util.Matrix
subtract two matrices
sub(T3) - Method in class javajs.util.T3
Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).
sub(T3d) - Method in class javajs.util.T3d
Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).
sub2(T3d, T3d) - Method in class javajs.util.T3d
Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).
sub2(T3, T3) - Method in class javajs.util.T3
Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).
sub33(M34) - Method in class javajs.util.M34
 
sublistAt(Lst<Object>, int...) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
subscripts - Variable in class jme.AtomDisplayLabel
 
subset - Static variable in class org.jmol.script.T
 
SubSpecChangeEvent - Class in jspecview.common
 
SubSpecChangeEvent(int, String) - Constructor for class jspecview.common.SubSpecChangeEvent
 
substring(int) - Method in class javajs.util.SB
 
substring2(int, int) - Method in class javajs.util.SB
 
substructure - Static variable in class org.jmol.script.T
 
substructureType - Variable in class org.jmol.adapter.smarter.Structure
 
subsystem - Static variable in class org.jmol.script.T
 
subsystemCode - Variable in class org.jmol.symmetry.SymmetryOperation
 
subzones - Variable in class org.jmol.util.BZone
 
sum - Static variable in class org.jmol.script.T
 
sum2 - Static variable in class org.jmol.script.T
 
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shape.Mesh
 
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
sumVertexNormals2(Mesh, T3[], V3[]) - Static method in class org.jmol.shape.Mesh
 
supercell - Static variable in class org.jmol.script.T
 
superscripts - Variable in class jme.AtomDisplayLabel
 
surface - Static variable in class org.jmol.script.T
 
SURFACE - Enum constant in enum class org.jmol.c.PAL
 
SURFACE_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_RADICAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
surfaceAtoms - Variable in class org.jmol.jvxl.readers.Parameters
 
surfaceAtoms - Variable in class org.jmol.util.MeshSurface
 
surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
surfacedistance - Static variable in class org.jmol.script.T
 
surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
 
SurfaceGenerator - Class in org.jmol.jvxl.readers
 
SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
 
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
SurfaceReader - Class in org.jmol.jvxl.readers
 
surfaceSet - Variable in class org.jmol.util.MeshSurface
 
SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
Class that holds the surface status information that the surface tool needs.
SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SurfaceTool - Class in org.openscience.jmol.app.surfacetool
 
SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
 
SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SurfaceToolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
 
surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SV - Class in org.jmol.script
ScriptVariable class
SV() - Constructor for class org.jmol.script.SV
 
SV.Sort - Class in org.jmol.script
 
sValue(T) - Static method in class org.jmol.script.SV
 
SVG - Enum constant in enum class jspecview.common.ExportType
 
SVGExporter - Class in jspecview.export
class SVGExporter contains static methods to export a Graph as as SVG.
SVGExporter() - Constructor for class jspecview.export.SVGExporter
 
SVGI - Enum constant in enum class jspecview.common.ExportType
 
swap(Object[], int, int) - Static method in class javajs.util.AU
 
swap(T[], int, int) - Static method in class jme.JMEUtil
 
swapBytesI(int) - Method in interface javajs.api.GenericBinaryDocument
 
swapBytesI(int) - Method in class javajs.util.BinaryDocument
 
swapBytesS(short) - Method in interface javajs.api.GenericBinaryDocument
 
swapBytesS(short) - Method in class javajs.util.BinaryDocument
 
swapInt(int[], int, int) - Static method in class javajs.util.AU
 
swapXZ() - Method in class org.jmol.jvxl.readers.JvxlReader
 
swapXZ() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
swapXZ() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
SwingConstants - Class in org.jmol.awtjs.swing
 
SwingConstants() - Constructor for class org.jmol.awtjs.swing.SwingConstants
 
SwingController - Interface in org.jmol.awtjs.swing
SwingController is an interface that org.jmol.awtjs.swing classes will need.
swipeCount - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
swipeCutoff - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
swipeDelayMs - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
swipeFactor - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
swipeStartTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
switchAtoms() - Method in class org.jmol.util.ContactPair
 
switchcmd - Static variable in class org.jmol.script.T
 
sX - Variable in class org.jmol.util.Point3fi
screen X
sY - Variable in class org.jmol.util.Point3fi
screen Y
symbol - Static variable in class org.jmol.script.T
 
symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
symMatrix - Variable in class org.jmol.util.Tensor
 
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
symmetry - Static variable in class org.jmol.script.T
 
Symmetry - Class in org.jmol.symmetry
 
Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
 
SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
SymmetryDesc - Class in org.jmol.symmetry
A class to handle requests for information about space groups and symmetry operations.
SymmetryDesc() - Constructor for class org.jmol.symmetry.SymmetryDesc
 
symmetryhermannmauguin - Static variable in class org.jmol.script.T
 
SymmetryInterface - Interface in org.jmol.api
 
SymmetryOperation - Class in org.jmol.symmetry
 
symop - Static variable in class org.jmol.script.T
 
symopColixes - Variable in class org.jmol.shape.Mesh
 
symopNormixes - Variable in class org.jmol.shape.Mesh
 
symops - Variable in class org.jmol.adapter.readers.cif.CifReader
 
symops - Variable in class org.jmol.shape.Mesh
 
sync - Static variable in class org.jmol.script.T
 
sync() - Method in class com.jcraft.jzlib.Inflater
 
SYNC - Enum constant in enum class org.jmol.c.CBK
 
SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
 
SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
 
SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
 
SYNCCALLBACKFUNCTIONNAME - Enum constant in enum class jspecview.common.ScriptToken
 
syncID - Variable in class jspecview.common.JSViewer
 
SYNCID - Enum constant in enum class jspecview.common.ScriptToken
 
syncingScripts - Variable in class org.jmol.viewer.StatusManager
 
syncmouse - Static variable in class org.jmol.script.T
 
syncPoint() - Method in class com.jcraft.jzlib.Inflater
 
syncscript - Static variable in class org.jmol.script.T
 
syncScript(String) - Method in interface jspecview.api.JSVAppletInterface
precede invalid input: '<'Peaks here with full name of Jmol applet (including syncID)
syncScript(String) - Method in class jspecview.app.JSVApp
 
syncScript(String) - Method in class jspecview.appletjs.JSVApplet
 
syncScript(String) - Method in class jspecview.application.MainFrame
 
syncScript(String) - Method in class jspecview.common.JSViewer
incoming script processing of invalid input: '<'PeakAssignment file="" type="xxx"...> record from Jmol
syncScript(String) - Method in interface org.jmol.api.JmolSyncInterface
 
syncScript(String) - Method in class org.jmol.util.GenericApplet
 
syncScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
 
syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
 
syncScript(Viewer, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
syncSend(String, Object, int) - Method in class org.jmol.viewer.StatusManager
 
syncToJmol(String) - Method in interface jspecview.api.ScriptInterface
 
syncToJmol(String) - Method in class jspecview.app.JSVApp
 
syncToJmol(String) - Method in class jspecview.application.JSpecView
 
syncToJmol(String) - Method in class jspecview.application.MainFrame
 
syncToJmol(String) - Method in interface org.jmol.api.JSVInterface
 
syncToJmol(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
syntaxError(String) - Method in class javajs.util.JSJSONParser
Make a JSONException to signal a syntax error.
sZ - Variable in class org.jmol.util.Point3fi
screen Z

T

t(int) - Static method in class org.jmol.script.T
 
T - Class in org.jmol.script
Script token class.
T() - Constructor for class org.jmol.script.T
 
T_SHAPED - Static variable in class org.jmol.smiles.SmilesStereo
 
T3 - Class in javajs.util
A generic 3 element tuple that is represented by single precision floating point x,y and z coordinates.
T3() - Constructor for class javajs.util.T3
 
T3d - Class in javajs.util
A generic 3 element tuple that is represented by double precision floating point x,y and z coordinates.
T3d() - Constructor for class javajs.util.T3d
Constructs and initializes a Tuple3d to (0,0,0).
T3i - Class in javajs.util
A 3-element tuple represented by signed integer x,y,z coordinates.
T3i() - Constructor for class javajs.util.T3i
Constructs and initializes a Tuple3i to (0,0,0).
T4 - Class in javajs.util
A generic 4 element tuple that is represented by single precision floating point x,y,z and w coordinates.
T4() - Constructor for class javajs.util.T4
Constructs and initializes a Tuple4f to (0,0,0,0).
tableCellAlignLeft - Variable in class jspecview.java.AwtDialog
 
tableCellAlignLeft - Variable in class jspecview.js2d.JsDialog
 
TableCellRenderer - Interface in org.jmol.awtjs.swing
 
TableColumn - Interface in org.jmol.awtjs.swing
 
tableModel - Variable in class org.openscience.jmol.app.janocchio.TableSorter
 
TableSorter - Class in org.openscience.jmol.app.janocchio
 
TableSorter() - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
 
TableSorter(TableModel) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
 
TableSorter(TableModel, JTableHeader) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
 
taConvert(Spectrum, Spectrum.IRMode) - Static method in class jspecview.common.Spectrum
 
TAG_NONE - Static variable in class jspecview.source.XMLParser
 
tagName - Variable in class jspecview.source.AnIMLReader
 
tags - Static variable in class org.jmol.quantum.QS
 
tags2 - Static variable in class org.jmol.quantum.QS
 
TAINT_ATOMNAME - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ATOMNO - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ATOMTYPE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_BONDINGRADIUS - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_CHAIN - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ELEMENT - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_HYDROPHOBICITY - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_RESNO - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_SEQID - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_SITE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
 
taintAtom(int, int) - Method in class org.jmol.modelset.AtomCollection
 
taintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
 
tainted - Variable in class org.jmol.modelset.AtomCollection
 
target - Variable in class org.jmol.modelset.Text
 
targetTime - Variable in class org.jmol.thread.JmolThread
 
TBI_AB - Static variable in class org.jmol.minimize.forcefield.ForceField
 
TBI_BC - Static variable in class org.jmol.minimize.forcefield.ForceField
 
TBI_CD - Static variable in class org.jmol.minimize.forcefield.ForceField
 
TEAL - Static variable in class org.jmol.util.C
 
techname - Variable in class jspecview.source.AnIMLReader
 
temp - Static variable in class org.jmol.adapter.readers.cif.BCIFReader
 
TEMP - Enum constant in enum class org.jmol.c.PAL
 
TEMP - Enum constant in enum class org.jmol.c.VDW
 
TempArray - Class in org.jmol.util
 
TempArray() - Constructor for class org.jmol.util.TempArray
 
temperature - Static variable in class org.jmol.script.T
 
templateAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
tempP1 - Variable in class org.jmol.export.___Exporter
 
tempP2 - Variable in class org.jmol.export.___Exporter
 
tempP3 - Variable in class org.jmol.export.___Exporter
 
tempQ1 - Variable in class org.jmol.export._VrmlExporter
 
tempQ2 - Variable in class org.jmol.export._VrmlExporter
 
tempQ3 - Variable in class org.jmol.export._VrmlExporter
 
tempStatement - Variable in class org.jmol.script.ScriptEval
 
tempV1 - Variable in class org.jmol.export.___Exporter
 
tempV2 - Variable in class org.jmol.export.___Exporter
 
tensor - Static variable in class org.jmol.script.T
 
tensor - Variable in class org.jmol.shapespecial.Ellipsoid
 
Tensor - Class in org.jmol.util
 
Tensor() - Constructor for class org.jmol.util.Tensor
Although this constructor is public, to be a valid tensor, one must invoke one of the "setFrom" methods.
tensors - Variable in class org.jmol.adapter.smarter.Atom
 
tensScale - Static variable in class javajs.util.PT
 
terminateEmptyTag(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
 
terminateTag(SB) - Static method in class org.jmol.adapter.writers.CMLWriter
 
test() - Static method in class javajs.util.Measure
 
test(String) - Static method in class javajs.util.DebugJS
Insert a JavaScript debug statement
Test - Class in org.openscience.jmol.app.webexport
 
TEST - Enum constant in enum class jspecview.common.ScriptToken
 
testAsync - Variable in class org.jmol.viewer.Viewer
 
testflag1 - Static variable in class org.jmol.script.T
 
testflag2 - Static variable in class org.jmol.script.T
 
testflag3 - Static variable in class org.jmol.script.T
 
testflag4 - Static variable in class org.jmol.script.T
 
testFlags - Variable in class org.jmol.jvxl.readers.Parameters
 
testRule6Full - Variable in class org.jmol.symmetry.CIPData
A flag that, if set, returns rr for bicyclo[2.2.2]octane
TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
 
text - Variable in class jspecview.common.Annotation
 
text - Variable in class org.jmol.awtjs.swing.Component
 
text - Variable in class org.jmol.modelset.Measurement
 
text - Variable in class org.jmol.modelset.MeasurementData
 
text - Variable in class org.jmol.modelset.Text
 
text - Variable in class org.jmol.shape.Hover
 
Text - Class in org.jmol.modelset
 
Text() - Constructor for class org.jmol.modelset.Text
 
TEXT_ALIGN_CENTER - Static variable in class org.jmol.viewer.JC
 
TEXT_ALIGN_LEFT - Static variable in class org.jmol.viewer.JC
 
TEXT_ALIGN_NONE - Static variable in class org.jmol.viewer.JC
 
TEXT_ALIGN_RIGHT - Static variable in class org.jmol.viewer.JC
 
textAlign - Variable in class org.jmol.render.LabelsRenderer
 
TextShape - Class in org.jmol.shape
 
TextShape() - Constructor for class org.jmol.shape.TextShape
 
textUnformatted - Variable in class org.jmol.modelset.Text
 
textY - Variable in class org.jmol.util.GData
 
thePlane - Variable in class org.jmol.jvxl.readers.Parameters
 
thePlane - Variable in class org.jmol.render.MeshRenderer
 
theta - Static variable in class org.jmol.script.T
 
theta0 - Variable in class org.jmol.minimize.MinAngle
 
theTok - Variable in class org.jmol.script.ScriptParam
 
theTok - Variable in class org.jmol.script.ScriptCompiler
 
theToken - Variable in class org.jmol.script.ScriptParam
 
theToken - Variable in class org.jmol.script.ScriptCompiler
 
THIS_MODEL_ONLY - Static variable in class org.jmol.viewer.JC
specifically for ECHO and DRAW to have these specific for a given model and only appearing when there is only one model showing (see MODELKIT SET KEY ON)
thisAtom - Variable in class org.jmol.quantum.QuantumCalculation
 
thisBiomolecule - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
thisCommand - Variable in class org.jmol.script.ScriptEval
 
thisContext - Variable in class org.jmol.script.ScriptParam
 
thisContour - Variable in class org.jmol.jvxl.data.JvxlData
 
thisDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
 
thisID - Variable in class org.jmol.modelset.Measurement
 
thisID - Variable in class org.jmol.modelset.MeasurementData
 
thisID - Variable in class org.jmol.shape.Mesh
 
thisID - Variable in class org.jmol.shape.TextShape
 
thisInside - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
thisJsvp - Variable in class jspecview.popup.JSVGenericPopup
 
thisMesh - Variable in class org.jmol.shapesurface.Isosurface
 
thismodel - Static variable in class org.jmol.script.T
 
thisModelOnly - Variable in class org.jmol.modelset.Text
 
thisModelOnly - Variable in class org.jmol.shapespecial.DrawMesh
 
thisPopup - Variable in class org.jmol.popup.GenericPopup
 
thisSet - Variable in class org.jmol.jvxl.data.JvxlData
 
thisValue() - Method in class jspecview.source.XMLParser
for value without surrounding tag
thisWidget - Variable in class jspecview.common.PanelData
 
thisWidth - Variable in class jspecview.common.PanelData
 
thisx - Variable in class org.jmol.popup.GenericPopup
 
thisy - Variable in class org.jmol.popup.GenericPopup
 
throwcmd - Static variable in class org.jmol.script.T
 
tickA - Variable in class org.jmol.render.FontLineShapeRenderer
 
tickAs - Variable in class org.jmol.render.FontLineShapeRenderer
 
tickB - Variable in class org.jmol.render.FontLineShapeRenderer
 
tickBs - Variable in class org.jmol.render.FontLineShapeRenderer
 
tickEdges - Variable in class org.jmol.render.AxesRenderer
 
tickEdges - Variable in class org.jmol.render.BbcageRenderer
 
tickEdges - Variable in class org.jmol.render.UccageRenderer
 
tickInfo - Variable in class org.jmol.modelset.Measurement
 
tickInfo - Variable in class org.jmol.modelset.MeasurementData
 
tickInfo - Variable in class org.jmol.render.FontLineShapeRenderer
 
TickInfo - Class in org.jmol.modelset
 
TickInfo(P3) - Constructor for class org.jmol.modelset.TickInfo
 
tickInfos - Variable in class org.jmol.shape.FontLineShape
 
tickLabelFormats - Variable in class org.jmol.modelset.TickInfo
 
tickParamAsStr(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptParam
 
ticks - Variable in class org.jmol.modelset.TickInfo
 
ticks - Static variable in class org.jmol.script.T
 
time - Variable in class jspecview.export.AMLExporter
 
time - Variable in class jspecview.export.CMLExporter
 
time - Variable in class jspecview.source.JDXHeader
 
time - Variable in class org.jmol.viewer.MouseState
 
timeBegin - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeCount - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeLast - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeout - Static variable in class org.jmol.script.T
 
timeouts - Variable in class org.jmol.viewer.Viewer
 
TimeoutThread - Class in org.jmol.thread
 
TimeoutThread(Viewer, String, int, String) - Constructor for class org.jmol.thread.TimeoutThread
 
times - Static variable in class org.jmol.script.T
 
timestimes - Static variable in class org.jmol.script.T
 
timeTotal - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
TinkerReader - Class in org.jmol.adapter.readers.simple
simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu
TinkerReader() - Constructor for class org.jmol.adapter.readers.simple.TinkerReader
 
title - Variable in class jspecview.common.PanelData
 
title - Variable in class jspecview.common.PrintLayout
 
title - Variable in class jspecview.dialog.JSVDialog
 
title - Variable in class jspecview.export.AMLExporter
 
title - Variable in class jspecview.export.CMLExporter
 
title - Variable in class jspecview.source.JDXHeader
 
title - Variable in class jspecview.source.AnIMLReader
 
title - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
title - Variable in class org.jmol.console.ScriptEditor
 
title - Variable in class org.jmol.jvxl.data.JvxlData
 
title - Variable in class org.jmol.jvxl.readers.Parameters
 
title - Static variable in class org.jmol.script.T
 
title - Variable in class org.jmol.shape.Mesh
 
title - Variable in class org.jmol.shape.MeshCollection
 
TITLEBOLDON - Enum constant in enum class jspecview.common.ScriptToken
 
titleColor - Variable in class jspecview.common.PanelData
 
titleColor - Variable in class org.jmol.shapespecial.DrawMesh
 
TITLECOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
titleDrawn - Variable in class jspecview.common.PanelData
 
titleFontName - Variable in class jspecview.common.ColorParameters
 
TITLEFONTNAME - Enum constant in enum class jspecview.common.ScriptToken
 
titleformat - Static variable in class org.jmol.script.T
 
titleOn - Variable in class jspecview.common.PanelData
 
TITLEON - Enum constant in enum class jspecview.common.ScriptToken
 
TlsDataOnlyReader - Class in org.jmol.adapter.readers.more
 
TlsDataOnlyReader() - Constructor for class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
tm - Variable in class org.jmol.export.___Exporter
 
tm - Variable in class org.jmol.render.ShapeRenderer
 
tm - Variable in class org.jmol.viewer.Viewer
 
tmpEnd - Variable in class jspecview.source.AnIMLReader
 
to - Static variable in class org.jmol.script.T
 
TO_ABS - Enum constant in enum class jspecview.common.Spectrum.IRMode
 
TO_TRANS - Enum constant in enum class jspecview.common.Spectrum.IRMode
 
to3D(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
toArray() - Method in class org.jmol.script.SV
 
TOAU_ANGSTROMS - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_AU - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_BOHR - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_CM - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_CM_1 - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_EV - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_HARTREE - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_KCAL_MOL - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_KJ_MOL - Static variable in class org.qcschema.QCSchemaUnits
 
TOAU_M - Static variable in class org.qcschema.QCSchemaUnits
 
toAxisAngle4f() - Method in class javajs.util.Quat
 
toByteArray() - Method in class javajs.util.OC
 
toBytes(int, int) - Method in class javajs.util.SB
simple byte conversion properly implementing UTF-8.
toCartesian(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
toCartesian(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
 
toCartesian(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
 
toCartesian(T3, boolean) - Method in class org.jmol.viewer.Viewer
absolute or relative to origin of UNITCELL {x y z}
toCartesianUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
 
toCDXML() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
toCSSString(GenericColor) - Static method in class javajs.util.CU
 
toExternalForm(URL) - Method in class javajs.util.AjaxURLStreamHandler
 
toFFGGGfromRGB(int) - Static method in class javajs.util.CU
Return a greyscale rgb value 0-FF using NTSC color lightness algorithm
toFractional(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
toFractional(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
 
toFractional(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
 
toFractional(T3, boolean) - Method in class org.jmol.viewer.Viewer
 
toFractionalM(M4) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
toFractionalM(M4) - Method in class org.jmol.util.SimpleUnitCell
 
toFractionalUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
 
toFromPrimitive(boolean, char, T3[], M3) - Method in interface org.jmol.api.SymmetryInterface
 
toFromPrimitive(boolean, char, T3[], M3) - Method in class org.jmol.symmetry.Symmetry
 
toFront() - Method in class org.jmol.awtjs.swing.JDialog
 
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
TOGGLE - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
TOGGLE - Enum constant in enum class jspecview.common.Spectrum.IRMode
 
toggleCoordinate() - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that toggles the coordinate on a JSVPanel
toggleCoordinate() - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that toggles the coordinate on a JSVPanel
toggleCoordinate() - Method in class jspecview.appletjs.JSVApplet
 
toggleCoordinate() - Method in class jspecview.application.MainFrame
 
toggleGrid() - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that toggles the grid on a JSVPanel
toggleGrid() - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that toggles the grid on a JSVPanel
toggleGrid() - Method in class jspecview.appletjs.JSVApplet
 
toggleGrid() - Method in class jspecview.application.MainFrame
 
toggleInPlace(BS, BS) - Static method in class org.jmol.util.BSUtil
a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
toggleIntegration() - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that toggles the integration graph of a JSVPanel.
toggleIntegration() - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that toggles the integration graph of a JSVPanel.
toggleIntegration() - Method in class jspecview.appletjs.JSVApplet
 
toggleIntegration() - Method in class jspecview.application.MainFrame
 
togglelabel - Static variable in class org.jmol.script.T
 
toggleMode() - Method in class com.sparshui.inputdevice.JmolTouchSimulator
 
toggleMode() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
toggleOverlayKeyMenuItem() - Method in class jspecview.application.ApplicationMenu
 
togglePointsOnly() - Method in interface jspecview.api.JSVAppletInterface
Method that can be called from another applet or from javascript that toggles the flag for points only on a JSVPanel
togglePointsOnly() - Method in class jspecview.app.JSVApp
Method that can be called from another applet or from javascript that toggles the coordinate on a JSVPanel
togglePointsOnly() - Method in class jspecview.appletjs.JSVApplet
 
togglePointsOnly() - Method in class jspecview.application.MainFrame
 
toHTML() - Method in class org.jmol.awtjs.swing.Component
 
toHTML() - Method in class org.jmol.awtjs.swing.JButton
 
toHTML() - Method in class org.jmol.awtjs.swing.JCheckBox
 
toHTML() - Method in class org.jmol.awtjs.swing.JComboBox
 
toHTML() - Method in class org.jmol.awtjs.swing.JContentPane
 
toHTML() - Method in class org.jmol.awtjs.swing.JDialog
 
toHTML() - Method in class org.jmol.awtjs.swing.JEditorPane
 
toHTML() - Method in class org.jmol.awtjs.swing.JLabel
 
toHTML() - Method in class org.jmol.awtjs.swing.JMenu
 
toHTML() - Method in class org.jmol.awtjs.swing.JMenuItem
 
toHTML() - Method in class org.jmol.awtjs.swing.JPanel
 
toHTML() - Method in class org.jmol.awtjs.swing.JPopupMenu
 
toHTML() - Method in class org.jmol.awtjs.swing.JScrollPane
 
toHTML() - Method in class org.jmol.awtjs.swing.JSplitPane
 
toHTML() - Method in class org.jmol.awtjs.swing.JTable
 
toHTML() - Method in class org.jmol.awtjs.swing.JTextField
 
toHTML() - Method in class org.jmol.awtjs.swing.JTextPane
 
toHTML(String) - Method in class org.jmol.awtjs.swing.Cell
 
toHTML(String) - Method in class org.jmol.awtjs.swing.Grid
 
toHTML(SB, String, BS) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
 
toJSON() - Method in interface javajs.api.JSONEncodable
 
toJSON() - Method in class javajs.util.A4
 
toJSON() - Method in class javajs.util.BS
 
toJSON() - Method in class javajs.util.T3
 
toJSON() - Method in class javajs.util.T4
 
toJSON() - Method in class org.jmol.script.SV
 
toJSON(String, Object) - Static method in class javajs.util.PT
 
toJSONBytes(Map<String, Object>) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
Guaranteed to create a clean no-whitespace JSON stream terminated by a single \n.
tok - Variable in class org.jmol.script.T
 
tokAction - Variable in class org.jmol.modelset.MeasurementData
 
tokAt(int) - Method in class org.jmol.script.ScriptCompiler
 
tokAt(int) - Method in class org.jmol.script.ScriptParam
 
tokAt(int) - Method in class org.jmol.scriptext.ScriptExt
 
tokAttr(int, int) - Static method in class org.jmol.script.T
 
tokAttrOr(int, int, int) - Static method in class org.jmol.script.T
 
tokCommand - Variable in class org.jmol.script.ScriptCompiler
 
tokenAll - Static variable in class org.jmol.script.T
 
tokenAnd - Static variable in class org.jmol.script.T
 
tokenAndEquals - Variable in class org.jmol.script.ScriptCompiler
 
tokenAndFALSE - Static variable in class org.jmol.script.T
 
tokenAndSpec - Static variable in class org.jmol.script.T
 
tokenArrayClose - Static variable in class org.jmol.script.T
 
tokenArrayOpen - Static variable in class org.jmol.script.T
 
tokenArraySquare - Static variable in class org.jmol.script.T
 
tokenAttr(T, int) - Static method in class org.jmol.script.ScriptCompiler
 
tokenColon - Static variable in class org.jmol.script.T
 
tokenComma - Static variable in class org.jmol.script.T
 
tokenCommand - Variable in class org.jmol.script.ScriptCompiler
 
tokenConnected - Static variable in class org.jmol.script.T
 
tokenCoordinateBegin - Static variable in class org.jmol.script.T
 
tokenCoordinateEnd - Static variable in class org.jmol.script.T
 
tokenDefineString - Static variable in class org.jmol.script.T
 
tokenDivide - Static variable in class org.jmol.script.T
 
tokenEquals - Static variable in class org.jmol.script.T
 
tokenExpressionBegin - Static variable in class org.jmol.script.T
 
tokenExpressionEnd - Static variable in class org.jmol.script.T
 
tokenIf - Static variable in class org.jmol.script.T
 
tokenize(String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
Take the given string and chop it up into a series of strings on whitespace boundries.
tokenLeftBrace - Static variable in class org.jmol.script.T
 
tokenLeftParen - Static variable in class org.jmol.script.T
 
tokenMinus - Static variable in class org.jmol.script.T
 
tokenMul3 - Static variable in class org.jmol.script.T
 
tokenOff - Static variable in class org.jmol.script.T
 
tokenOn - Static variable in class org.jmol.script.T
 
tokenOpIf - Static variable in class org.jmol.script.T
 
tokenOr - Static variable in class org.jmol.script.T
 
tokenOrTRUE - Static variable in class org.jmol.script.T
 
tokenPlus - Static variable in class org.jmol.script.T
 
tokenRightBrace - Static variable in class org.jmol.script.T
 
tokenRightParen - Static variable in class org.jmol.script.T
 
tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
tokenScript - Static variable in class org.jmol.script.T
 
tokenSet - Static variable in class org.jmol.script.T
 
tokenSetArray - Static variable in class org.jmol.script.T
 
tokenSetCmd - Static variable in class org.jmol.script.T
 
tokenSetProperty - Static variable in class org.jmol.script.T
 
tokenSetVar - Static variable in class org.jmol.script.T
 
tokenSpaceBeforeSquare - Static variable in class org.jmol.script.T
 
tokenSwitch - Static variable in class org.jmol.script.T
 
tokenTimes - Static variable in class org.jmol.script.T
 
toLABnorm(int) - Method in class javajs.img.GifEncoder
 
toMap(byte[]) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
toMOL() - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
toOABC(P3[], T3) - Static method in class org.jmol.util.BoxInfo
Delivers [center a b c] for generation of unit cells from a boundbox
toolbar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
top - Static variable in class org.jmol.script.T
 
topAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
toPeak(int) - Method in class jspecview.common.PanelData
 
topMargin - Static variable in class jspecview.common.PanelData
 
toPNG(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
TopoCifParser - Class in org.jmol.adapter.readers.cif
see https://github.com/COMCIFS/TopoCif Basic idea: We have TLinks, TNodes, and TAtoms TLinks each have two TNodes and may also be associated with bridging TAtom sets.
TopoCifParser() - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser
 
toPoint4f() - Method in class javajs.util.Quat
Quaternions are saved as {q1, q2, q3, q0} While this may seem odd, it is so that for any point4 -- planes, axisangles, and quaternions -- we can use the first three coordinates to determine the relavent axis the fourth then gives us offset to {0,0,0} (plane), rotation angle (axisangle), and cos(theta/2) (quaternion).
toRadians - Static variable in class org.jmol.util.SimpleUnitCell
 
toReadable(String, Object) - Static method in class org.jmol.util.Escape
Used only for getProperty("readable",...)
toRGB(P3) - Method in class javajs.img.GifEncoder
 
toRGB3f(int, float[]) - Static method in class javajs.util.CU
 
toRGBHexString(GenericColor) - Static method in class javajs.util.CU
 
torsion - Static variable in class org.jmol.script.T
 
toStdAmino3(String) - Method in class org.jmol.modelsetbio.BioResolver
 
toString() - Method in class com.sparshui.common.Location
 
toString() - Method in class com.sparshui.common.messages.events.DragEvent
 
toString() - Method in class com.sparshui.common.messages.events.FlickEvent
 
toString() - Method in class com.sparshui.common.messages.events.RotateEvent
 
toString() - Method in class com.sparshui.common.messages.events.SpinEvent
 
toString() - Method in class com.sparshui.common.messages.events.TouchEvent
 
toString() - Method in class com.sparshui.common.messages.events.ZoomEvent
 
toString() - Method in class javajs.util.A4
Returns a string that contains the values of this AxisAngle4f.
toString() - Method in class javajs.util.BArray
 
toString() - Method in class javajs.util.BS
Returns a string representation of this bit set.
toString() - Method in class javajs.util.M3
Returns a string that contains the values of this Matrix3f.
toString() - Method in class javajs.util.M4
Returns a string that contains the values of this Matrix4f.
toString() - Method in class javajs.util.Matrix
 
toString() - Method in class javajs.util.OC
 
toString() - Method in class javajs.util.Quat
Java axisAngle / plane / Point4f format all have the format {x y z w} so we go with that here as well
toString() - Method in class javajs.util.SB
 
toString() - Method in class javajs.util.T3
Returns a string that contains the values of this Tuple3f.
toString() - Method in class javajs.util.T3d
Returns a string that contains the values of this Tuple3d.
toString() - Method in class javajs.util.T3i
Returns a string that contains the values of this Tuple3i.
toString() - Method in class javajs.util.T4
Returns a string that contains the values of this Tuple4f.
toString() - Method in class jspecview.common.Annotation
Overrides Objects toString() method
toString() - Method in class jspecview.common.Coordinate
Overides Objects toString() method
toString() - Method in class jspecview.common.Measurement
Overrides Objects toString() method
toString() - Method in class jspecview.common.PanelNode
 
toString() - Method in class jspecview.common.PeakInfo
 
toString() - Method in class jspecview.common.PeakPickEvent
 
toString() - Method in class jspecview.common.Spectrum
 
toString() - Method in class jspecview.common.SubSpecChangeEvent
 
toString() - Method in class jspecview.java.AwtPanel
 
toString() - Method in class jspecview.js2d.JsPanel
 
toString() - Method in class jspecview.tree.SimpleTreeNode
 
toString() - Method in class org.jmol.adapter.smarter.Bond
 
toString() - Method in class org.jmol.adapter.writers.CIFWriter
 
toString() - Method in class org.jmol.adapter.writers.CMLWriter
 
toString() - Method in class org.jmol.adapter.writers.PDBWriter
 
toString() - Method in class org.jmol.adapter.writers.PWMATWriter
 
toString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
 
toString() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
toString() - Method in class org.jmol.adapter.writers.XSFWriter
 
toString() - Method in class org.jmol.atomdata.RadiusData
 
toString() - Method in class org.jmol.awtjs.swing.Color
 
toString() - Method in class org.jmol.minimize.MinAtom
 
toString() - Method in class org.jmol.minimize.Minimizer
 
toString() - Method in class org.jmol.minimize.MinObject
 
toString() - Method in class org.jmol.modelset.Atom
 
toString() - Method in class org.jmol.modelset.Bond
 
toString() - Method in class org.jmol.modelset.Group
 
toString() - Method in class org.jmol.modelset.Measurement
 
toString() - Method in class org.jmol.modelset.StateScript
 
toString() - Method in class org.jmol.modelset.Text
 
toString() - Method in class org.jmol.modelsetbio.BasePair
 
toString() - Method in class org.jmol.modelsetbio.BioPolymer
 
toString() - Method in class org.jmol.modelsetbio.Monomer
 
toString() - Method in class org.jmol.modelsetbio.ProteinStructure
 
toString() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
 
toString() - Method in class org.jmol.quantum.NMRNoeMatrix
 
toString() - Method in class org.jmol.quantum.SlaterData
 
toString() - Method in class org.jmol.script.ScriptEval
 
toString() - Method in exception class org.jmol.script.ScriptException
 
toString() - Method in class org.jmol.script.ScriptFunction
 
toString() - Method in class org.jmol.script.SV
 
toString() - Method in class org.jmol.script.T
 
toString() - Method in class org.jmol.smiles.SmilesAtom
 
toString() - Method in class org.jmol.smiles.SmilesBond
 
toString() - Method in class org.jmol.smiles.SmilesMeasure
 
toString() - Method in class org.jmol.smiles.SmilesSearch
 
toString() - Method in class org.jmol.symmetry.SpaceGroup
 
toString() - Method in class org.jmol.symmetry.SymmetryOperation
 
toString() - Method in class org.jmol.thread.JmolThread
 
toString() - Method in class org.jmol.thread.TimeoutThread
 
toString() - Method in class org.jmol.util.BoxInfo
 
toString() - Method in class org.jmol.util.ContactPair
 
toString() - Method in class org.jmol.util.Font
 
toString() - Method in class org.jmol.util.Modulation
 
toString() - Method in class org.jmol.util.Rgb16
 
toString() - Method in class org.jmol.util.SimpleUnitCell
 
toString() - Method in class org.jmol.util.Tensor
 
toString() - Method in class org.openscience.jmol.app.janocchio.Measure
 
toString2() - Method in class org.jmol.script.T
 
toStringNormRow() - Method in class org.jmol.quantum.NMRNoeMatrix
 
toSupercell(P3) - Method in interface org.jmol.api.SymmetryInterface
 
toSupercell(P3) - Method in class org.jmol.symmetry.Symmetry
 
toSupercell(P3) - Method in class org.jmol.util.SimpleUnitCell
convenience return only after changing fpt
toTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
 
total_in - Variable in class com.jcraft.jzlib.ZStream
 
total_out - Variable in class com.jcraft.jzlib.ZStream
 
toTrm(String, M4) - Static method in class org.jmol.symmetry.UnitCell
 
TOUCH_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
TOUCH_EVENT - Static variable in class com.sparshui.GestureType
 
TOUCH_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
TOUCH_GESTURE - Static variable in class com.sparshui.GestureType
 
TOUCH_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
TouchData() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
 
TouchDataComparator() - Constructor for class com.sparshui.inputdevice.JmolTouchSimulator.TouchDataComparator
 
TouchEvent - Class in com.sparshui.common.messages.events
 
TouchEvent() - Constructor for class com.sparshui.common.messages.events.TouchEvent
 
TouchEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.TouchEvent
Constructs a new TouchEvent from a serialized version - 4 bytes : id - 4 bytes : x - 4 bytes : y - 4 bytes : state - 8 bytes : time - 24 bytes total
TouchEvent(int, float, float, int) - Constructor for class com.sparshui.common.messages.events.TouchEvent
 
TouchEvent(TouchPoint) - Constructor for class com.sparshui.common.messages.events.TouchEvent
 
TouchHandler() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
TouchPoint - Class in com.sparshui.server
Represents a touch point.
TouchPoint(int, Location, long) - Constructor for class com.sparshui.server.TouchPoint
 
TouchPoint(TouchPoint) - Constructor for class com.sparshui.server.TouchPoint
Copy constructor
TouchState - Class in com.sparshui.common
Defines the types of touches that can ocurr in sparsh-UI: Birth, Move, and Death.
TouchState() - Constructor for class com.sparshui.common.TouchState
 
toUnicode(String) - Method in interface javajs.api.GenericCifDataParser
 
toUnicode(String) - Method in class javajs.util.CifDataParser
Only translating the basic Greek set here, not all the other stuff.
toUnicode(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
There is no need to convert to unicode in CIF 2.0.
toUnitCell(P3, P3) - Method in class org.jmol.viewer.Viewer
Returns the relative to origin without regard to offset created using the UNITCELL command.
toUnitCell(T3, T3) - Method in interface org.jmol.api.SymmetryInterface
 
toUnitCell(T3, T3) - Method in class org.jmol.symmetry.Symmetry
 
toUnitCellRnd(T3, T3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
toUnitCellRnd(T3, T3) - Method in class org.jmol.symmetry.UnitCell
when offset is null, use the current cell, otherwise use the original unit cell
toUnits(float, String, boolean) - Static method in class org.jmol.modelset.Measurement
 
toUserUnits(double) - Method in class org.jmol.minimize.forcefield.ForceField
 
toWebAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ToWebAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
 
toWebActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
tQuiet - Variable in class org.jmol.script.ScriptEval
 
trace - Static variable in class org.jmol.script.T
 
trace() - Method in class javajs.util.Matrix
Matrix trace.
Trace - Class in org.jmol.shapebio
 
Trace() - Constructor for class org.jmol.shapebio.Trace
 
tracealpha - Static variable in class org.jmol.script.T
 
tracePt - Variable in class org.jmol.util.Vibration
 
TraceRenderer - Class in org.jmol.renderbio
 
TraceRenderer() - Constructor for class org.jmol.renderbio.TraceRenderer
 
traceX - Variable in class org.jmol.modelset.Measurement
 
traceY - Variable in class org.jmol.modelset.Measurement
 
trajectory - Variable in class org.jmol.modelset.AtomCollection
 
trajectory - Static variable in class org.jmol.script.T
 
Trajectory - Class in org.jmol.modelset
 
Trajectory() - Constructor for class org.jmol.modelset.Trajectory
 
trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
 
trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
transform - Static variable in class org.jmol.script.T
 
transform(T4) - Method in class javajs.util.M4
Transform the vector vec using this Matrix4f and place the result back into vec.
transform(V3, V3) - Method in class org.jmol.jvxl.data.VolumeData
 
transform2(T3, T3) - Method in class javajs.util.Quat
 
transform2(T4, T4) - Method in class javajs.util.M4
Transform the vector vec using this Matrix4f and place the result into vecOut.
transformAtomsToUnitCell(SymmetryInterface, T3[], String) - Method in class org.jmol.modelkit.ModelKit
Transform the atoms to fractional coordinate, set the unit cell to a new cell, and then transform them back to Cartesians.
transformedVectors - Variable in class org.jmol.render.MeshRenderer
 
transformedVectors - Variable in class org.jmol.util.GData
 
TransformManager - Class in org.jmol.viewer
 
TransformManager() - Constructor for class org.jmol.viewer.TransformManager
 
TransformManager4D - Class in org.jmol.viewer
 
TransformManager4D() - Constructor for class org.jmol.viewer.TransformManager4D
 
transformPoints(Lst<P3>, M4, P3) - Static method in class javajs.util.Measure
 
transformPt(T3) - Method in class org.jmol.viewer.TransformManager
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPt2D(T3) - Method in class org.jmol.viewer.TransformManager
 
transformPt2Df(T3, P3) - Method in class org.jmol.viewer.TransformManager
 
transformPt3f(T3, P3) - Method in class org.jmol.viewer.TransformManager
 
transformPtNoClip(T3, T3) - Method in class org.jmol.viewer.TransformManager
 
transformPtScr(T3, P3i) - Method in class org.jmol.viewer.TransformManager
 
transformPtScrT3(T3, T3) - Method in class org.jmol.viewer.TransformManager
 
transformPtScrT32D(T3, P3) - Method in class org.jmol.viewer.TransformManager
 
transformPtVib(P3, Vibration) - Method in class org.jmol.viewer.TransformManager
 
transformUnitCell(M4) - Method in class org.jmol.symmetry.Symmetry
 
transformXYZ(M4, BS) - Method in class org.jmol.atomdata.AtomData
allow for transformed XYZ
translate - Static variable in class org.jmol.script.T
 
translate(char, float, char, BS) - Method in class org.jmol.viewer.Viewer
 
translate(String) - Method in interface org.jmol.api.Translator
 
translate(String) - Method in class org.jmol.i18n.GT
used in custom menu translation only
translate(String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
translateModel(int, T3) - Method in class org.jmol.modelset.ModelSet
move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE
translateScale(float, float, float) - Method in class javajs.export.PDFCreator
 
translateScale(Object, double, double, double) - Method in class jspecview.common.PDFWriter
 
translateScale(Object, double, double, double) - Method in class jspecview.java.AwtG2D
 
translateScale(Object, double, double, double) - Method in class jspecview.js2d.JsG2D
 
translateScale(Object, double, double, double) - Method in interface org.jmol.api.GenericGraphics
 
translateScale(Object, double, double, double) - Method in class org.jmol.awt.AwtG2D
 
translateScale(Object, double, double, double) - Method in class org.jmol.awtjs2d.JsG2D
 
translateSelected - Static variable in class org.jmol.script.T
 
translateToPercent(char, float) - Method in class org.jmol.viewer.TransformManager
 
translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
 
translation - Static variable in class org.jmol.script.T
 
translations - Variable in class org.jmol.modelset.ModelSet
 
Translator - Interface in org.jmol.api
 
translucency - Variable in class org.jmol.jvxl.data.JvxlData
 
translucencyFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
 
translucencyMask - Variable in class org.jmol.g3d.Graphics3D
 
translucent - Static variable in class org.jmol.script.T
 
TRANSLUCENT_MASK - Static variable in class org.jmol.util.C
 
TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.C
 
TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.C
 
translucentAllowed - Variable in class org.jmol.shape.Shape
 
translucentCoverOnly - Variable in class org.jmol.util.GData
 
translucentLevel - Variable in class org.jmol.shape.Shape
 
TRANSPARENT - Static variable in class org.jmol.util.C
 
transpose() - Method in class javajs.util.M3
Sets the value of this matrix to its transpose.
transpose() - Method in class javajs.util.M4
Sets the value of this matrix to its transpose.
transpose() - Method in class javajs.util.Matrix
Matrix transpose.
transpose33() - Method in class javajs.util.M34
 
transposeM(M3) - Method in class javajs.util.M3
Sets the value of this matrix to the transpose of the argument matrix
treeNode - Variable in class jspecview.common.PanelNode
 
TriangleData - Class in org.jmol.util
An adaptation of Marching Cubes that allows for indicating edges on triangles.
TriangleData() - Constructor for class org.jmol.util.TriangleData
 
triangleHeight(double, double, double) - Static method in class jme.JMEUtil
Compute the height of a triangle knowing the length of each side.
TriangleRenderer - Class in org.jmol.g3d
renders triangles
TriangleRenderer() - Constructor for class org.jmol.g3d.TriangleRenderer
 
triangles - Static variable in class org.jmol.script.T
 
triangles - Variable in class org.jmol.shapespecial.Polyhedron
 
triangleTable2 - Static variable in class org.jmol.util.TriangleData
The new triangle table developed specifically for Jmol.
triangulateFaces(int[][], P3[], int[][]) - Method in class org.jmol.util.MeshCapper
generic entry for a set of faces
triangulatePolygon(P3[], int) - Method in class org.jmol.util.MeshCapper
generic entry for a polygon
Triangulator - Class in org.jmol.util
 
Triangulator() - Constructor for class org.jmol.util.Triangulator
 
TRICOLOR_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
trigger(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
 
triggerTimeout(String) - Method in class org.jmol.viewer.Viewer
 
TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
 
TRIGONAL_PYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
 
trim - Static variable in class org.jmol.script.T
 
trim(String, String) - Static method in class javajs.util.PT
 
trimGUI(String) - Method in class org.jmol.console.GenericConsole
 
trimQuotes(String) - Static method in class javajs.util.PT
 
trycmd - Static variable in class org.jmol.script.T
 
tryPt - Variable in class org.jmol.viewer.Viewer
 
TURN - Enum constant in enum class org.jmol.c.STR
 
tv(int, int, Object) - Static method in class org.jmol.script.T
 
twelfthify(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
 
twelfthify(P3) - Method in class org.jmol.util.SimpleUnitCell
 
twelfthsOf(float) - Method in class org.jmol.util.SimpleUnitCell
 
twistedsheets - Static variable in class org.jmol.script.T
 
twistedSheets - Variable in class org.jmol.modelsetbio.BioPolymer
 
twoDEditorAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
TwoDEditorAction(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction
 
twoDEditorActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
twodots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
twoPI - Static variable in class org.jmol.util.Vibration
 
TwoPointGesture - Class in org.jmol.multitouch.sparshui
TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
TwoPointGesture() - Constructor for class org.jmol.multitouch.sparshui.TwoPointGesture
 
Txt - Class in org.jmol.util
 
Txt() - Constructor for class org.jmol.util.Txt
 
txt1 - Variable in class jspecview.dialog.JSVDialog
 
txt2 - Variable in class jspecview.dialog.JSVDialog
 
txt3 - Variable in class jspecview.dialog.JSVDialog
 
type - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
 
type - Variable in class jspecview.dialog.JSVDialog
 
type - Variable in class jspecview.source.JDXSource
 
type - Variable in class org.jmol.minimize.MinObject
 
type - Variable in class org.jmol.minimize.MMConstraint
 
type - Variable in class org.jmol.modelset.TickInfo
 
type - Variable in class org.jmol.modelsetbio.BioPolymer
 
type - Static variable in class org.jmol.script.T
 
type - Variable in class org.jmol.util.Tensor
 
TYPE - Enum constant in enum class org.jmol.c.PAL
 
TYPE_ADP - Static variable in class org.jmol.util.Tensor
 
TYPE_AMINO - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_ANGLE - Static variable in class org.jmol.minimize.MMConstraint
 
TYPE_ANY - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_ATROPISOMER - Static variable in class org.jmol.util.Edge
 
TYPE_ATROPISOMER_REV - Static variable in class org.jmol.util.Edge
 
TYPE_BIO_CROSSLINK - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_BIO_SEQUENCE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_BLOCK - Static variable in class jspecview.source.JDXSource
 
TYPE_BUTTON - Static variable in class org.jmol.awtjs.swing.JMenuItem
 
TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_CHARGE - Static variable in class org.jmol.util.Tensor
 
TYPE_CHECKBOX - Static variable in class org.jmol.awtjs.swing.JMenuItem
 
TYPE_CSA - Static variable in class org.jmol.util.Tensor
 
TYPE_DIHEDRAL - Static variable in class org.jmol.minimize.MMConstraint
 
TYPE_DISP_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_DISP_LEGENDRE - Static variable in class org.jmol.util.Modulation
 
TYPE_DISP_SAWTOOTH - Static variable in class org.jmol.util.Modulation
 
TYPE_DISTANCE - Static variable in class org.jmol.minimize.MMConstraint
 
TYPE_EFG - Static variable in class org.jmol.util.Tensor
 
TYPE_ISC - Static variable in class org.jmol.util.Tensor
 
TYPE_ISO - Static variable in class org.jmol.util.Tensor
 
TYPE_MENU - Static variable in class org.jmol.awtjs.swing.JMenuItem
 
TYPE_MS - Static variable in class org.jmol.util.Tensor
 
TYPE_NOBONDING - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_NTUPLE - Static variable in class jspecview.source.JDXSource
 
TYPE_NUCLEIC - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_OCC_CRENEL - Static variable in class org.jmol.util.Modulation
 
TYPE_OCC_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_OTHER - Static variable in class org.jmol.util.Tensor
 
TYPE_QUADRUPOLE - Static variable in class org.jmol.util.Tensor
 
TYPE_RADIO - Static variable in class org.jmol.awtjs.swing.JMenuItem
 
TYPE_RAMAN - Static variable in class org.jmol.util.Tensor
 
TYPE_RING - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_SEPARATOR - Static variable in class org.jmol.awtjs.swing.JMenuItem
 
TYPE_SIMPLE - Static variable in class jspecview.source.JDXSource
 
TYPE_SPIN - Static variable in class org.jmol.util.Vibration
 
TYPE_SPIN_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_SPIN_SAWTOOTH - Static variable in class org.jmol.util.Modulation
 
TYPE_TLS_R - Static variable in class org.jmol.util.Tensor
 
TYPE_TLS_U - Static variable in class org.jmol.util.Tensor
 
TYPE_U_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_U_LEGENDRE - Static variable in class org.jmol.util.Modulation
 
TYPE_UNKNOWN - Static variable in class jspecview.source.JDXSource
 
TYPE_UNKNOWN - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_VIBRATION - Static variable in class org.jmol.util.Vibration
 
TYPE_VIEW - Static variable in class jspecview.source.JDXSource
 
TYPE_WYCKOFF - Static variable in class org.jmol.util.Vibration
 
typeName - Variable in class org.jmol.script.ScriptFunction
 
TYPES - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
 
typeSymbol - Variable in class org.jmol.adapter.smarter.Atom
 

U

U_LIST - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
uABsM(String) - Static method in class org.jmol.util.Escape
 
UC_TOLERANCE2 - Static variable in class org.jmol.viewer.JC
 
Uccage - Class in org.jmol.shape
 
Uccage() - Constructor for class org.jmol.shape.Uccage
 
UccageRenderer - Class in org.jmol.render
 
UccageRenderer() - Constructor for class org.jmol.render.UccageRenderer
 
uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
 
ucItems - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
uguideAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
UguideAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
 
unaryMinus - Static variable in class org.jmol.script.T
 
unbind - Static variable in class org.jmol.script.T
 
unbindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
 
unBindAction(String, String) - Method in class org.jmol.viewer.Viewer
 
unbindJmolAction(int) - Method in class org.jmol.viewer.binding.Binding
 
unbindMouseAction(int) - Method in class org.jmol.viewer.binding.Binding
 
unbindName(int, String) - Method in class org.jmol.viewer.binding.Binding
 
unbindUserAction(String) - Method in class org.jmol.viewer.binding.Binding
 
undeleteAtom(int) - Method in class org.jmol.modelset.ModelLoader
called from org.jmol.modelsetbio.resolver when adding hydrogens.
undo - Static variable in class org.jmol.script.T
 
undoauto - Static variable in class org.jmol.script.T
 
undomax - Static variable in class org.jmol.script.T
 
undomove - Static variable in class org.jmol.script.T
 
undoMoveAction(int, int) - Method in class org.jmol.viewer.Viewer
 
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
unescape(String) - Static method in class javajs.util.BS
 
unescapeMatrix(String) - Static method in class org.jmol.util.Escape
 
unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.SV
 
unescapeString(String, int, int) - Static method in class org.jmol.script.ScriptCompiler
 
unescapeStringArray(String) - Static method in class org.jmol.util.Escape
 
unescapeUnicode(String) - Static method in class org.jmol.util.Escape
 
uniqueID - Variable in class org.jmol.adapter.smarter.Bond
 
unitAxisVectors - Static variable in class org.jmol.viewer.JC
 
unitcell - Static variable in class org.jmol.script.T
 
unitCell - Variable in class org.jmol.shape.Mesh
 
unitCell - Variable in class org.jmol.symmetry.Symmetry
 
UnitCell - Class in org.jmol.symmetry
a class pseudoprivate to the org.jmol.symmetry and org.jmol.applet.smarter.FileSymmetry to be accessed generally only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.
unitcellcolor - Static variable in class org.jmol.script.T
 
unitCellEquals(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
unitCellEquals(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
UnitCellIterator - Class in org.jmol.symmetry
 
UnitCellIterator() - Constructor for class org.jmol.symmetry.UnitCellIterator
 
unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
unitCellParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
unitCellParams - Variable in class org.jmol.util.SimpleUnitCell
 
unitCells - Variable in class org.jmol.modelset.ModelSet
 
unitCubePoints - Static variable in class org.jmol.util.BoxInfo
 
unitFactor - Variable in class org.jmol.quantum.QuantumCalculation
 
UNITID_ATOM - Static variable in class org.jmol.viewer.JC
 
UNITID_INSCODE - Static variable in class org.jmol.viewer.JC
 
UNITID_MODEL - Static variable in class org.jmol.viewer.JC
 
UNITID_RESIDUE - Static variable in class org.jmol.viewer.JC
 
UNITID_TRIM - Static variable in class org.jmol.viewer.JC
 
unitize(T3) - Method in interface org.jmol.api.SymmetryInterface
 
unitize(T3) - Method in class org.jmol.symmetry.Symmetry
 
unitizeDim(int, T3) - Method in class org.jmol.util.SimpleUnitCell
Used for just about everything; via UnitCell including SpaceGroup.getSiteMultiplicity, Symmetry.getInvariantSymops, Symmetry.removeDuplicates, Symmetry.unitize, Symmetry.toUnitCell, SymmetryDesc.getTransform.
unitizeDimRnd(int, T3, float) - Static method in class org.jmol.util.SimpleUnitCell
Only used for getting equivalent points and checking for duplicates.
unitizeX(float, float) - Static method in class org.jmol.util.SimpleUnitCell
 
unitizeXRnd(float, float) - Static method in class org.jmol.util.SimpleUnitCell
Slightly higher precision -- only used for cmdAssignSpaceGroup checking for duplicates
units - Variable in class jspecview.common.MeasurementData
 
units - Variable in class org.jmol.minimize.Minimizer
 
units - Variable in class org.jmol.modelset.Measurement
 
units - Variable in class org.jmol.modelset.MeasurementData
 
UNITS_ANGSTROMS - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_AU - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_BOHR - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_CM - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_CM_1 - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_EV - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_FRACTIONAL - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_HARTREE - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_KCAL_MOL - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_KJ_MOL - Static variable in class org.qcschema.QCSchemaUnits
 
UNITS_M - Static variable in class org.qcschema.QCSchemaUnits
 
unitsColor - Variable in class jspecview.common.PanelData
 
UNITSCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
unitx - Static variable in class org.jmol.script.T
 
unitxyz - Static variable in class org.jmol.script.T
 
unity - Static variable in class org.jmol.script.T
 
unitz - Static variable in class org.jmol.script.T
 
UNK - Enum constant in enum class jspecview.common.ExportType
 
UNKNOWN - Enum constant in enum class jspecview.common.ScriptToken
 
UNKNOWN - Enum constant in enum class org.jmol.c.HB
 
UNKNOWN - Enum constant in enum class org.jmol.c.PAL
 
UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.C
 
unpack(byte[], int, int) - Static method in class javajs.util.MessagePackReader
mmtf type 14 and 15 Unpack an array of int8 or int16 to int32.
unpack16Deltaf(byte[], int, float) - Static method in class javajs.util.MessagePackReader
mmtf type 10 Decode an array of int16 using run-length decoding of a difference array.
unpackf(byte[], int, int, float) - Static method in class javajs.util.MessagePackReader
mmtf type 12 and 13 Unpack an array of int8 or int16 to int32 and divide to give a float32.
unquoted(String) - Method in class javajs.util.CifDataParser
In CIF 2.0, this method turns a String into an Integer or Float In CIF 1.0 (here) just return the unchanged value.
unquoted(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
Handle unquoted value as Integer or Float if we can.
unscaleToScreen(float, float) - Method in class org.jmol.viewer.TransformManager
 
unsetProperty(String) - Method in class org.jmol.viewer.Viewer
 
unTaintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
 
untransformedPoint - Variable in class org.jmol.viewer.TransformManager
 
unTransformPoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
 
unwrapCdata(String) - Static method in class org.jmol.jvxl.readers.XmlReader
 
uP(String) - Static method in class org.jmol.util.Escape
 
UP - Static variable in class org.jmol.viewer.binding.Binding
 
update() - Method in interface javajs.api.JSInterface
 
update() - Method in class jspecview.appletjs.JSVApplet
 
update() - Method in class org.jmol.util.GenericApplet
 
update(byte[], int, int) - Method in class com.jcraft.jzlib.Adler32
 
update(byte[], int, int) - Method in interface com.jcraft.jzlib.Checksum
 
update(byte[], int, int) - Method in class com.jcraft.jzlib.CRC32
 
update(double, double, double) - Method in class jspecview.common.IntegralData
minY is ignored
update(Location, long, int) - Method in class com.sparshui.server.TouchPoint
Update this touch point with a new location and state.
update(TouchPoint) - Method in class com.sparshui.server.Group
Update the given touch point that belongs to this group.
update(Graphics) - Method in class jme.JME
 
update(Graphics) - Method in class jspecview.java.AwtPanel
 
update(String) - Method in class org.jmol.viewer.ChimeMessenger
called upon script exit and file opening
update(String) - Method in interface org.jmol.viewer.JmolChimeMessenger
 
update(LineEvent) - Method in class org.jmol.util.JmolAudio
 
update(Coordinate, double, int) - Method in class jspecview.dialog.JSVDialog
 
update(Parameters) - Method in class jspecview.common.IntegralData
 
UPDATE - Enum constant in enum class jspecview.common.IntegralData.IntMode
 
UPDATE_ALL - Static variable in class org.jmol.popup.JmolPopup
 
UPDATE_CONFIG - Static variable in class org.jmol.popup.JmolPopup
 
UPDATE_NEVER - Static variable in class jspecview.popup.JSVGenericPopup
 
UPDATE_NEVER - Static variable in class org.jmol.popup.JmolPopup
 
UPDATE_SHOW - Static variable in class org.jmol.popup.JmolPopup
 
updateAboutSubmenu() - Method in class org.jmol.popup.JmolPopup
 
updateAllXtalMenuOptions() - Method in class org.jmol.modelkit.ModelKitPopup
 
updateAtomXYZ(boolean) - Method in class org.jmol.minimize.Minimizer
 
updateAwtMenus(String) - Method in class org.jmol.awt.AwtJmolPopup
 
updateAwtMenus(String) - Method in class org.jmol.awt.AwtModelKitPopup
 
updateBasisFromSite(int) - Method in class org.jmol.modelset.ModelSet
 
updateButton(SC, String, String) - Method in class org.jmol.popup.GenericPopup
 
updateByteAsInt(int) - Method in class com.jcraft.jzlib.Adler32
 
updateByteAsInt(int) - Method in interface com.jcraft.jzlib.Checksum
 
updateByteAsInt(int) - Method in class com.jcraft.jzlib.CRC32
 
updateCheckBoxesForModelKit(String) - Method in class org.jmol.modelkit.ModelKitPopup
 
updateCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateConsoleFont() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
updateControlPressed(int) - Method in class jspecview.common.PanelData
 
updateCoordinates(M4, BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
bs will be null if this is a set from the new isosurface MOVE [mat4] command
updateElementsComputedMenu(BS) - Method in class org.jmol.popup.JmolPopup
 
updateExisting(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
updateFileMenu() - Method in class org.jmol.popup.JmolPopup
 
updateFileTypeDependentMenus() - Method in class org.jmol.popup.JmolPopup
 
updateFontSize() - Method in class org.jmol.console.JmolConsole
 
updateFontSize() - Method in class org.jmol.console.ScriptEditor
 
updateFontSize() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateHeteroComputedMenu(Map<String, String>) - Method in class org.jmol.popup.JmolPopup
 
updateInvalidatedVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
 
updateJS() - Method in class jspecview.common.JSViewer
for JavaScript only; this is the call to draw the spectrum
updateJS() - Method in class org.jmol.viewer.Viewer
for JavaScript only
updateJS(int, int) - Method in class jspecview.app.JSVApp
 
updateLabels() - Method in class org.jmol.console.GenericConsole
 
updateLabels() - Method in class org.jmol.console.JmolConsole
 
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
updateLanguageSubmenu() - Method in class org.jmol.popup.JmolPopup
 
updateMark(int) - Method in class jme.JME
 
updateMenu() - Method in class org.jmol.modelkit.ModelKit
 
updateMenus() - Method in class org.jmol.popup.JmolPopup
 
updateMode - Variable in class jspecview.popup.JSVGenericPopup
 
updateMode - Variable in class org.jmol.popup.JmolPopup
 
updateModel(int) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateOperatorMenu() - Method in class org.jmol.modelkit.ModelKitPopup
 
updatePDBResidueComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
updateRecentMenus(String) - Method in class jspecview.application.MainFrame
 
updateRecentMenus(Lst<String>) - Method in class jspecview.application.ApplicationMenu
 
updateSceneComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateScreen() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Update screen informations
updateSelectMenu() - Method in class org.jmol.popup.JmolPopup
 
updateSignedAppletItems() - Method in class org.jmol.popup.GenericPopup
 
updateSize(boolean) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
updateSpecialMenuItem(SC) - Method in class org.jmol.popup.JmolPopup
 
updateSpectraMenu() - Method in class org.jmol.popup.JmolPopup
 
updateSurfaceData(String, float[], int, int, char) - Static method in class org.jmol.jvxl.data.JvxlData
 
updateSurfMoComputedMenu(Map<String, Object>) - Method in class org.jmol.popup.JmolPopup
 
updateSYMMETRYComputedMenus() - Method in class org.jmol.popup.JmolPopup
 
updateSYMMETRYSelectComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateSYMMETRYShowComputedMenu() - Method in class org.jmol.popup.JmolPopup
 
updateTables() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
 
updateTables() - Method in class org.openscience.jmol.app.janocchio.NoeTable
 
updateTables() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
updateToolbar(ScriptToken, boolean) - Method in class jspecview.application.MainFrame
 
updatingForShow - Variable in class org.jmol.popup.GenericPopup
 
url - Static variable in class org.jmol.script.T
 
URL_CACHE - Static variable in class javajs.util.OC
 
URL_LOCAL - Static variable in class javajs.util.OC
 
URL_LOCAL - Static variable in class jspecview.common.JSVFileManager
 
urlPrefixes - Static variable in class javajs.util.OC
 
urlTypeIndex(String) - Static method in class javajs.util.OC
 
urlTypeIndex(String) - Static method in class jspecview.common.JSVFileManager
 
USE_PALETTE - Static variable in class org.jmol.util.C
 
useAltNames - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
useAuthorChainID - Variable in class org.jmol.adapter.readers.cif.CifReader
 
useColix - Variable in class org.jmol.shape.Mesh
 
useDirLastExported - Variable in class jspecview.java.AwtFileHelper
 
useDirLastOpened - Variable in class jspecview.java.AwtFileHelper
 
useFileModelNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
useminimizationthread - Static variable in class org.jmol.script.T
 
useMinimizationThread() - Method in class org.jmol.viewer.Viewer
 
usenumberlocalization - Static variable in class org.jmol.script.T
 
usePropertyForColorRange - Variable in class org.jmol.jvxl.readers.Parameters
 
user - Static variable in class org.jmol.script.T
 
USER - Enum constant in enum class org.jmol.c.VDW
 
USER - Static variable in class org.jmol.util.ColorEncoder
 
userAction(int, Object[]) - Method in class org.jmol.viewer.ActionManager
If the user has created a function to handle this action, run it and cancel action processing if that function returns an explicit FALSE;
userActionEnabled(int) - Method in class org.jmol.viewer.ActionManager
 
usercolorscheme - Static variable in class org.jmol.script.T
 
userPropsFile - Variable in class org.openscience.jmol.app.JmolApp
 
userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
 
useScriptQueue - Variable in class org.jmol.viewer.GlobalSettings
 
useTable - Variable in class org.jmol.export._VrmlExporter
 
useThreads() - Method in class org.jmol.script.ScriptEval
 
useTimeout - Variable in class org.jmol.thread.JmolThread
 
UTF_16BE - Enum constant in enum class javajs.util.Encoding
 
UTF_16LE - Enum constant in enum class javajs.util.Encoding
 
UTF_32BE - Enum constant in enum class javajs.util.Encoding
 
UTF_32LE - Enum constant in enum class javajs.util.Encoding
 
UTF8 - Enum constant in enum class javajs.util.Encoding
 
Util - Class in org.jmol.minimize
 
Util() - Constructor for class org.jmol.minimize.Util
 

V

v1 - Variable in class org.jmol.modelset.BondCollection
 
v2 - Variable in class org.jmol.modelset.BondCollection
 
V3 - Class in javajs.util
A 3-element vector that is represented by single precision floating point x,y,z coordinates.
V3() - Constructor for class javajs.util.V3
 
V3000Rdr - Class in org.jmol.adapter.readers.molxyz
A reader for Accelrys V3000 files.
V3000Rdr() - Constructor for class org.jmol.adapter.readers.molxyz.V3000Rdr
 
V3d - Class in javajs.util
A 3 element vector that is represented by double precision floating point x,y,z coordinates.
V3d() - Constructor for class javajs.util.V3d
 
vAB - Variable in class org.jmol.shape.Mesh
 
val - Static variable in class org.jmol.script.T
 
valence - Static variable in class org.jmol.script.T
 
validate() - Method in interface jspecview.api.AppletFrame
 
validate() - Method in class jspecview.appletjs.JSVApplet
 
validate() - Method in class org.jmol.awtjs.swing.JDialog
 
validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
 
validateAndRepaint(boolean) - Method in class jspecview.application.MainFrame
 
validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
 
validateContent(int) - Method in interface jspecview.api.AppletFrame
 
validateContent(int) - Method in class jspecview.appletjs.JSVApplet
 
validateModel(int, boolean) - Method in class org.jmol.bspt.Bspf
 
validation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
validation - Static variable in class org.jmol.script.T
 
valign - Variable in class org.jmol.modelset.Text
 
value - Variable in class jspecview.common.Measurement
 
value - Variable in class org.jmol.atomdata.RadiusData
 
value - Variable in class org.jmol.minimize.MMConstraint
 
value - Variable in class org.jmol.modelset.Measurement
 
value - Variable in class org.jmol.script.T
 
value() - Element in annotation interface javajs.J2SIgnoreImport
 
value() - Element in annotation interface javajs.J2SRequireImport
 
valueChanged() - Method in class jspecview.tree.SimpleTree
 
valueChanged(ListSelectionEvent) - Method in class jspecview.java.AwtDialogManager
ListSelectionListener callback
valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
valueExtended - Variable in class org.jmol.atomdata.RadiusData
 
valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
 
valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
 
valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
 
valueOf(String) - Static method in enum class javajs.util.Encoding
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.Annotation.AType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.ExportType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.IntegralData.IntMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.PanelData.LinkMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.ScriptToken
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class jspecview.common.Spectrum.IRMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.atomdata.RadiusData.EnumType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.CBK
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.FIL
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.HB
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.PAL
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.STER
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.STR
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.c.VDW
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.jmol.viewer.Viewer.ACCESS
Returns the enum constant of this class with the specified name.
values - Variable in class org.jmol.atomdata.RadiusData
 
values() - Static method in enum class javajs.util.Encoding
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.Annotation.AType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.ExportType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.IntegralData.IntMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.PanelData.LinkMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.ScriptToken
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class jspecview.common.Spectrum.IRMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.atomdata.RadiusData.EnumType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.CBK
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.FIL
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.HB
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.PAL
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.STER
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.STR
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.c.VDW
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.shapespecial.Draw.EnumDrawType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.jmol.viewer.Viewer.ACCESS
Returns an array containing the constants of this enum class, in the order they are declared.
vanderwaals - Static variable in class org.jmol.script.T
 
vanderwaalsMars - Static variable in class org.jmol.util.Elements
Default table of van der Waals Radii.
var - Static variable in class org.jmol.script.T
 
varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
 
variable - Static variable in class org.jmol.script.T
 
VARIABLE - Enum constant in enum class org.jmol.c.PAL
 
variables - Static variable in class org.jmol.script.T
 
varray - Static variable in class org.jmol.script.T
 
vars - Variable in class org.jmol.script.ScriptContext
 
VaspChgcarReader - Class in org.jmol.adapter.readers.xtal
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
VaspChgcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspChgcarReader
 
VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
http://cms.mpi.univie.ac.at/vasp/
VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
VaspPoscarReader - Class in org.jmol.adapter.readers.xtal
adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/
VaspPoscarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
vAtoms - Variable in class org.jmol.adapter.readers.simple.InputReader
 
vBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
vBiomolecules - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
vc - Variable in class org.jmol.util.MeshSurface
vertex count
vContours - Variable in class org.jmol.jvxl.data.JvxlData
 
vcs - Variable in class org.jmol.util.MeshSurface
vertex color index "colix" array
VDW - Enum Class in org.jmol.c
 
vdwKey - Variable in class org.jmol.minimize.MinAtom
 
VdwPROBE - Static variable in class org.jmol.util.Elements
 
vdws - Variable in class org.jmol.util.ContactPair
 
vdwType - Variable in class org.jmol.atomdata.RadiusData
 
vdwVolume - Variable in class org.jmol.util.ContactPair
 
vector - Static variable in class org.jmol.script.T
 
vector - Variable in class org.jmol.shapespecial.Dipole
 
vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
 
Vectors - Class in org.jmol.shapespecial
 
Vectors() - Constructor for class org.jmol.shapespecial.Vectors
 
vectorscale - Static variable in class org.jmol.script.T
 
vectorscentered - Static variable in class org.jmol.script.T
 
VectorsRenderer - Class in org.jmol.renderspecial
 
VectorsRenderer() - Constructor for class org.jmol.renderspecial.VectorsRenderer
 
vectorsymmetry - Static variable in class org.jmol.script.T
 
vectorT - Variable in class org.jmol.render.FontLineShapeRenderer
 
vectorT2 - Variable in class org.jmol.render.FontLineShapeRenderer
 
vectorT3 - Variable in class org.jmol.render.FontLineShapeRenderer
 
vectorTemp - Variable in class org.jmol.viewer.TransformManager
 
vectortrail - Static variable in class org.jmol.script.T
 
vendor - Variable in class jspecview.export.AMLExporter
 
vendor - Variable in class jspecview.export.CMLExporter
 
vendor - Variable in class jspecview.source.AnIMLReader
 
version - Variable in class org.jmol.jvxl.data.JvxlData
 
version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
version - Static variable in class org.jmol.viewer.JC
 
version - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
version - Static variable in class org.qcschema.QCSchemaUnits
 
version() - Static method in class com.jcraft.jzlib.JZlib
 
VERSION - Enum constant in enum class jspecview.common.ScriptToken
 
VERSION - Static variable in class jspecview.common.JSVersion
 
VERSION - Static variable in class org.openscience.jmol.app.janocchio.Nmr
 
VERSION - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
VERSION_SHORT - Static variable in class jspecview.common.JSVersion
 
versionInt - Static variable in class jspecview.common.JSVersion
 
versionInt - Static variable in class org.jmol.viewer.JC
 
VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
 
VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexColorMap - Variable in class org.jmol.shape.Mesh
 
vertexColors - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexCount - Variable in class org.jmol.render.MeshRenderer
 
vertexCount0 - Variable in class org.jmol.util.MeshSurface
 
vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
 
VertexDataServer - Interface in org.jmol.jvxl.api
 
vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
 
vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
vertexSets - Variable in class org.jmol.util.MeshSurface
 
vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
 
vertexSource - Variable in class org.jmol.util.MeshSurface
 
vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
vertexValues - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
vertices - Variable in class org.jmol.render.MeshRenderer
 
vertices - Static variable in class org.jmol.script.T
 
vertices - Variable in class org.jmol.shapespecial.Polyhedron
 
vf - Variable in class org.jmol.shape.Shape
shape visibility flag
vF - Static variable in class org.jmol.script.SV
 
vib - Variable in class org.jmol.adapter.smarter.Atom
 
vib - Variable in class org.jmol.util.ModulationSet
vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
vibration - Static variable in class org.jmol.script.T
 
Vibration - Class in org.jmol.util
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.
Vibration() - Constructor for class org.jmol.util.Vibration
 
vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
vibrationOn - Variable in class org.jmol.viewer.TransformManager
 
vibrationperiod - Static variable in class org.jmol.script.T
 
vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
 
vibrations - Variable in class org.jmol.modelset.AtomCollection
 
vibrationscale - Static variable in class org.jmol.script.T
 
vibrationSteps - Variable in class org.jmol.modelset.ModelSet
 
vibrationThread - Variable in class org.jmol.viewer.TransformManager
 
VibrationThread - Class in org.jmol.thread
 
VibrationThread() - Constructor for class org.jmol.thread.VibrationThread
 
vibScale - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
vibsFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
vibx - Static variable in class org.jmol.script.T
 
vibxyz - Static variable in class org.jmol.script.T
 
viby - Static variable in class org.jmol.script.T
 
vibz - Static variable in class org.jmol.script.T
 
VIEW - Enum constant in enum class jspecview.common.ScriptToken
 
ViewCoupleTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
 
ViewData - Class in jspecview.common
Stores information that GraphSet needs to display a view with one or more spectra.
ViewData(Lst<Spectrum>, double, double, boolean) - Constructor for class jspecview.common.ViewData
 
ViewData(Lst<Spectrum>, double, double, int[], int[], boolean, boolean) - Constructor for class jspecview.common.ViewData
 
viewer - Variable in class jspecview.appletjs.JSVApplet
 
viewer - Variable in class jspecview.application.ApplicationMenu
 
viewer - Variable in class org.jmol.util.GenericApplet
 
viewer - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
 
Viewer - Class in org.jmol.viewer
 
Viewer(Map<String, Object>) - Constructor for class org.jmol.viewer.Viewer
new way...
Viewer.ACCESS - Enum Class in org.jmol.viewer
 
viewerOptions - Variable in class jspecview.appletjs.JSVApplet
 
viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
 
ViewNoeTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
 
viewOffset - Variable in class jspecview.common.Parameters
 
viewpoint - Variable in class org.jmol.export.__CartesianExporter
 
Views - Enum constant in enum class jspecview.common.Annotation.AType
 
ViewsDialog - Class in jspecview.dialog
Dialog for managing overlaying spectra and closing files
ViewsDialog() - Constructor for class jspecview.dialog.ViewsDialog
 
viewSelected() - Method in class jspecview.dialog.ViewsDialog
 
VIS_BACKBONE_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_BALLS_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_BOND_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_CARTOON_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_LABEL_FLAG - Static variable in class org.jmol.viewer.JC
 
visibilityFlags - Variable in class org.jmol.shape.Mesh
 
visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
 
visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedron
 
visible - Variable in class org.jmol.modelset.Text
 
visible - Static variable in class org.jmol.script.T
 
visible - Variable in class org.jmol.shape.Mesh
 
visible - Variable in class org.jmol.shapespecial.Ellipsoid
 
Visible - Class in jspecview.common
Visible class - for prediction of colour from visible spectrum see Robert J.
Visible() - Constructor for class jspecview.common.Visible
 
VisibleInterface - Interface in jspecview.api
 
visualrange - Static variable in class org.jmol.script.T
 
visualRangeAngstroms - Variable in class org.jmol.viewer.TransformManager
 
VK_ALT - Static variable in class org.jmol.awtjs.Event
 
VK_BACK_SPACE - Static variable in class org.jmol.awtjs.Event
 
VK_CONTROL - Static variable in class org.jmol.awtjs.Event
 
VK_DELETE - Static variable in class org.jmol.awtjs.Event
 
VK_DOWN - Static variable in class org.jmol.awtjs.Event
 
VK_ESCAPE - Static variable in class org.jmol.awtjs.Event
 
VK_LEFT - Static variable in class org.jmol.awtjs.Event
 
VK_META - Static variable in class org.jmol.awtjs.Event
 
VK_PAGE_DOWN - Static variable in class org.jmol.awtjs.Event
 
VK_PAGE_UP - Static variable in class org.jmol.awtjs.Event
 
VK_PERIOD - Static variable in class org.jmol.awtjs.Event
 
VK_RIGHT - Static variable in class org.jmol.awtjs.Event
 
VK_SHIFT - Static variable in class org.jmol.awtjs.Event
 
VK_SPACE - Static variable in class org.jmol.awtjs.Event
 
VK_UP - Static variable in class org.jmol.awtjs.Event
 
vNaN - Static variable in class org.jmol.script.SV
 
vNorm - Variable in class org.jmol.symmetry.CIPData
 
vOcc - Variable in class org.jmol.util.ModulationSet
the current value of the occupancy modulation
volume - Variable in class org.jmol.quantum.QuantumCalculation
 
volume - Static variable in class org.jmol.script.T
 
volume - Variable in class org.jmol.util.BZone
 
volume - Variable in class org.jmol.util.ContactPair
 
volume - Variable in class org.jmol.util.SimpleUnitCell
 
volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
volumeData - Variable in class org.jmol.jvxl.readers.Parameters
 
VolumeData - Class in org.jmol.jvxl.data
 
VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
 
volumeDataTemp - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
volumeRender - Variable in class org.jmol.render.MeshRenderer
 
volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
volumeRender(boolean) - Method in class org.jmol.export.Export3D
 
volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
 
volumeRender4(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
volumeRender4(int, int, int, int) - Method in class org.jmol.export.Export3D
 
volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
volumeRenderPointSize - Variable in class org.jmol.shape.Mesh
 
volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricOrigin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelData - Variable in class org.jmol.quantum.QuantumCalculation
 
VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
 
voxelDataTemp - Variable in class org.jmol.quantum.QuantumCalculation
 
voxelPtToXYZ(int, int, int, T3) - Method in class org.jmol.jvxl.data.VolumeData
 
voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
 
voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
 
vs - Variable in class org.jmol.util.MeshSurface
vertices
vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
vT - Static variable in class org.jmol.script.SV
 
vTemp - Variable in class org.jmol.renderspecial.DrawRenderer
 
vTemp - Variable in class org.jmol.shape.Mesh
 
vTemp - Variable in class org.jmol.symmetry.CIPData
 
vTemp2 - Variable in class org.jmol.renderspecial.DrawRenderer
 
vvs - Variable in class org.jmol.util.MeshSurface
vertex values
vwr - Variable in class jspecview.app.JSVApp
 
vwr - Variable in class jspecview.application.AppToolBar
 
vwr - Variable in class jspecview.application.AwtTree
 
vwr - Variable in class jspecview.dialog.DialogManager
 
vwr - Variable in class jspecview.dialog.JSVDialog
 
vwr - Variable in class jspecview.export.AMLExporter
 
vwr - Variable in class jspecview.export.CMLExporter
 
vwr - Variable in class jspecview.export.SVGExporter
 
vwr - Variable in class jspecview.popup.JSVGenericPopup
 
vwr - Variable in class jspecview.tree.SimpleTree
 
vwr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
vwr - Variable in class org.jmol.adapter.writers.CMLWriter
 
vwr - Variable in class org.jmol.console.GenericConsole
 
vwr - Variable in class org.jmol.console.ImageDialog
 
vwr - Variable in class org.jmol.dialog.Dialog
 
vwr - Variable in class org.jmol.export.___Exporter
 
vwr - Variable in class org.jmol.minimize.Minimizer
 
vwr - Variable in class org.jmol.modelkit.ModelKit
 
vwr - Variable in class org.jmol.modelset.AtomCollection
 
vwr - Variable in class org.jmol.popup.JmolGenericPopup
 
vwr - Variable in class org.jmol.render.ShapeRenderer
 
vwr - Variable in class org.jmol.script.ScriptError
 
vwr - Variable in class org.jmol.script.ScriptCompiler
 
vwr - Variable in class org.jmol.scriptext.ScriptExt
 
vwr - Variable in class org.jmol.shape.Shape
 
vwr - Variable in class org.jmol.thread.JmolThread
 
vwr - Variable in class org.jmol.util.GData
 
vwr - Variable in class org.jmol.util.MeshSurface
 
vwr - Variable in class org.jmol.viewer.ActionManager
 
vwr - Variable in class org.jmol.viewer.AnimationManager
 
vwr - Variable in class org.jmol.viewer.FileManager
 
vwr - Variable in class org.jmol.viewer.OutputManagerAwt
 
vwr - Variable in class org.jmol.viewer.OutputManagerJS
 
vwr - Variable in class org.jmol.viewer.ShapeManager
 
vwr - Variable in class org.jmol.viewer.StateManager
 
vwr - Variable in class org.jmol.viewer.StatusManager
 
vwr - Variable in class org.jmol.viewer.TransformManager
 
vwr - Variable in class org.molecularplayground.MPJmolApp
 
vwr - Variable in class org.openscience.jmol.app.JmolData
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
vwr - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
vwrFrame - Variable in class org.jmol.console.JmolConsole
 
vwrOptions - Variable in class org.jmol.util.GenericApplet
 
vwrOptions - Variable in class org.jmol.viewer.Viewer
 
vwrOptions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 

W

w - Variable in class javajs.util.T4
The w coordinate.
w - Static variable in class org.jmol.script.T
 
waitForDisplay(Object, Object) - Method in class jspecview.java.AwtPlatform
 
waitForDisplay(Object, Object) - Method in class jspecview.js2d.JsPlatform
 
waitForDisplay(Object, Object) - Method in interface org.jmol.api.GenericPlatform
can be ignored (return false) if platform cannot save images
waitForDisplay(Object, Object) - Method in class org.jmol.awt.Platform
 
waitForDisplay(Object, Object) - Method in class org.jmol.awtjs2d.Platform
 
waitformoveto - Static variable in class org.jmol.script.T
 
waitForMoveTo - Variable in class org.jmol.viewer.GlobalSettings
 
waitForQueue() - Method in interface org.jmol.api.JmolScriptManager
 
waitForQueue() - Method in class org.jmol.script.ScriptManager
 
warn(String) - Method in class org.jmol.util.DefaultLogger
 
warn(String) - Static method in class org.jmol.util.Logger
Writes a log at WARN level.
warn(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level.
warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
warnEx(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at WARN level with detail on exception.
warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level with detail on exception.
warning(int, String, String) - Method in class org.jmol.script.ScriptError
 
warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
WARNING_MESSAGE - Static variable in class jspecview.dialog.DialogManager
 
wasClicked(int, int) - Method in class org.jmol.shape.Frank
 
wasClicked(int, int) - Method in class org.jmol.shape.Shape
 
wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
 
wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
 
wasmInchiHack(String) - Method in class org.jmol.viewer.Viewer
WASM inchi must be initialized asynchronously
wasPerspective - Variable in class org.jmol.export._PovrayExporter
 
wasPerspective - Variable in class org.jmol.export._TachyonExporter
 
wasRotating() - Method in class org.jmol.modelkit.ModelKit
 
wasSpinOn - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
 
wasUnquoted - Variable in class javajs.util.CifDataParser
whether we are processing an unquoted value or key
wasX - Variable in class org.jmol.script.ScriptMathProcessor
 
WB - Static variable in class org.jmol.util.ColorEncoder
 
WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WebExport - Class in org.openscience.jmol.app.webexport
 
webme - Variable in class jme.JME
 
WebMOReader - Class in org.jmol.adapter.readers.quantum
A molecular orbital reader for WebMO files.
WebMOReader() - Constructor for class org.jmol.adapter.readers.quantum.WebMOReader
 
WEST - Static variable in class org.jmol.awtjs.swing.BorderLayout
 
WEST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
 
whatsnewAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WhatsNewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
 
WhatsNewDialog - Class in org.openscience.jmol.app.jmolpanel
 
WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
 
WHEEL - Static variable in class org.jmol.viewer.binding.Binding
 
wheeled(long, int, int) - Method in class jspecview.app.GenericMouse
 
WHEELED - Static variable in class org.jmol.awtjs.Event
 
when - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
 
whilecmd - Static variable in class org.jmol.script.T
 
WHITE - Static variable in class jspecview.common.ColorParameters
 
WHITE - Static variable in class org.jmol.util.C
 
why - Variable in class org.jmol.script.ScriptContext
 
width - Variable in class javajs.img.ImageEncoder
 
width - Variable in class org.jmol.awtjs.swing.Component
 
width - Variable in class org.jmol.awtjs.swing.Dimension
 
width - Variable in class org.jmol.render.FontLineShapeRenderer
 
width - Variable in class org.jmol.render.MeshRenderer
 
width - Static variable in class org.jmol.script.T
 
width - Variable in class org.jmol.shape.Mesh
 
width - Variable in class org.jmol.util.GData
 
width - Variable in class org.jmol.util.Rectangle
 
width - Variable in class org.jmol.viewer.TransformManager
 
WIDTHSCALE - Static variable in class org.jmol.shapecgo.CGOMesh
 
Wien2kReader - Class in org.jmol.adapter.readers.xtal
A reader for Wein2k DFT files.
Wien2kReader() - Constructor for class org.jmol.adapter.readers.xtal.Wien2kReader
 
wigner - Static variable in class org.jmol.script.T
 
window - Static variable in class org.jmol.script.T
 
WINDOW - Enum constant in enum class jspecview.common.ScriptToken
 
windowActivated(WindowEvent) - Method in class jspecview.java.AwtDialogManager
 
windowActivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
 
windowActivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowActivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowcentered - Static variable in class org.jmol.script.T
 
windowCentered - Variable in class org.jmol.viewer.TransformManager
 
windowClosed(WindowEvent) - Method in class jspecview.java.AwtDialogManager
 
windowClosed(WindowEvent) - Method in class org.jmol.console.ImageDialog
 
windowClosed(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowClosed(WindowEvent) - Method in class org.jmol.console.ScriptEditor
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowClosing(WindowEvent) - Method in class jspecview.java.AwtDialogManager
WindowListener callback
windowClosing(WindowEvent) - Method in class org.jmol.console.ImageDialog
 
windowClosing(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowClosing(WindowEvent) - Method in class org.jmol.console.ScriptEditor
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowClosing(HTMLElement) - Method in interface org.jmol.awtjs.swing.SwingController
Called by clicking the [x] in the corner of the dialog; send a notification back to the manager via processWindowClosing(key) var id = $("div.JDialog:has(#" + element.id + ")")[0].id var dialog = Jmol.Swing.htDialogs[id]; dialog.manager.processWindowClosing(dialog.registryKey);
windowClosing_actionPerformed() - Method in class jspecview.application.MainFrame
 
windowDeactivated(WindowEvent) - Method in class jspecview.java.AwtDialogManager
 
windowDeactivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
 
windowDeactivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowDeactivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowDeiconified(WindowEvent) - Method in class jspecview.java.AwtDialogManager
 
windowDeiconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
 
windowDeiconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowDeiconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowHeight - Variable in class org.jmol.modelset.Text
 
windowHeight - Variable in class org.jmol.util.GData
 
windowIconified(WindowEvent) - Method in class jspecview.java.AwtDialogManager
 
windowIconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
 
windowIconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowIconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowName - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
windowOpened(WindowEvent) - Method in class jspecview.java.AwtDialogManager
 
windowOpened(WindowEvent) - Method in class org.jmol.console.ImageDialog
 
windowOpened(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowOpened(WindowEvent) - Method in class org.jmol.console.ScriptEditor
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolJME
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowWidth - Variable in class org.jmol.modelset.Text
 
windowWidth - Variable in class org.jmol.util.GData
 
wingVectors - Variable in class org.jmol.modelsetbio.BioPolymer
 
wingVectors - Variable in class org.jmol.renderbio.BackboneRenderer
 
wingVectors - Variable in class org.jmol.renderbio.CartoonRenderer
 
wingVectors - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
wingVectors - Variable in class org.jmol.renderbio.RibbonsRenderer
 
wingVectors - Variable in class org.jmol.renderbio.RocketsRenderer
 
wingVectors - Variable in class org.jmol.renderbio.StrandsRenderer
 
wingVectors - Variable in class org.jmol.renderbio.TraceRenderer
 
wingVectors - Variable in class org.jmol.shapebio.BioShape
 
wireframe - Static variable in class org.jmol.script.T
 
wireframeOnly - Variable in class org.jmol.renderbio.BackboneRenderer
 
wireframeOnly - Variable in class org.jmol.renderbio.CartoonRenderer
 
wireframeOnly - Variable in class org.jmol.renderbio.MeshRibbonRenderer
 
wireframeOnly - Variable in class org.jmol.renderbio.RibbonsRenderer
 
wireframeOnly - Variable in class org.jmol.renderbio.RocketsRenderer
 
wireframeOnly - Variable in class org.jmol.renderbio.StrandsRenderer
 
wireframeOnly - Variable in class org.jmol.renderbio.TraceRenderer
 
wireframerotation - Static variable in class org.jmol.script.T
 
within - Static variable in class org.jmol.script.T
 
within(float, P3, Lst<P3>) - Static method in class org.jmol.util.BZone
 
withinDistPoints(float, P3, P3[], P3[], BS, Object[]) - Static method in class org.jmol.bspt.PointIterator
carry out various functions of the within() script function
words - Variable in class org.jmol.popup.PopupResource
 
wrap(String, SB) - Static method in class org.jmol.symmetry.WyckoffFinder
Just wrap the coordinate with parentheses.
wrapCdata(Object) - Static method in class javajs.util.XmlUtil
wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
wrapCData(String) - Static method in class org.jmol.adapter.writers.CDXMLWriter
wrap the string as character data, with replacements for [ noted as a list starting with * after the CDATA termination
wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManagerAwt
 
wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManagerJS
 
write - Static variable in class org.jmol.script.T
 
write(byte[], int, int) - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
write(byte[], int, int) - Method in interface javajs.api.GenericOutputChannel
 
write(byte[], int, int) - Method in class javajs.util.OC
 
write(int) - Method in class javajs.util.OC
Deprecated.
write(BS) - Method in class org.jmol.adapter.writers.CDXMLWriter
 
write(BS) - Method in class org.jmol.adapter.writers.CIFWriter
 
write(BS) - Method in class org.jmol.adapter.writers.CMLWriter
 
write(BS) - Method in class org.jmol.adapter.writers.PDBWriter
 
write(BS) - Method in class org.jmol.adapter.writers.PWMATWriter
 
write(BS) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
write(BS) - Method in class org.jmol.adapter.writers.XSFWriter
 
write(BS) - Method in interface org.jmol.api.JmolWriter
 
write(JSViewer, Lst<String>, boolean) - Method in interface jspecview.api.ExportInterface
from EXPORT command
write(JSViewer, Lst<String>, boolean) - Method in class jspecview.export.Exporter
 
WRITE - Enum constant in enum class jspecview.common.ScriptToken
 
writeAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WriteAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
 
writeActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
writeArray(Object) - Method in class org.jmol.util.JSONWriter
 
writeAtoms(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeBonds(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeBoolean(Boolean) - Method in class org.jmol.util.JSONWriter
 
writeByte(int) - Method in class javajs.img.PngEncoder
Write a single byte into the pngBytes array at a given position.
writeByteAsInt(int) - Method in class com.jcraft.jzlib.DeflaterOutputStream
 
writeByteAsInt(int) - Method in interface javajs.api.GenericOutputChannel
 
writeByteAsInt(int) - Method in class javajs.util.OC
 
writeBytes(byte[]) - Method in class javajs.img.PngEncoder
Write an array of bytes into the pngBytes array.
writeCRC() - Method in class javajs.img.PngEncoder
 
writeFile(String, Object, String) - Method in class org.jmol.viewer.Viewer
 
writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
 
writeFloat(float) - Method in class javajs.util.OC
 
writeForm(String) - Method in class jspecview.export.AMLExporter
 
writeForm(String) - Method in class jspecview.export.CMLExporter
 
writeForm(String) - Method in class jspecview.export.SVGExporter
 
writeInt(int) - Method in interface javajs.api.GenericOutputChannel
 
writeInt(int) - Method in class javajs.util.OC
 
writeInt2(int) - Method in class javajs.img.PngEncoder
Write a two-byte integer into the pngBytes array at a given position.
writeInt4(int) - Method in class javajs.img.PngEncoder
Write a four-byte integer into the pngBytes array at a given position.
writeJob(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeJobMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeJobs() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeJSON() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeList(List<Object>) - Method in class org.jmol.util.JSONWriter
 
writeLong(long) - Method in interface javajs.api.GenericOutputChannel
 
writeLong(long) - Method in class javajs.util.OC
 
writeMagic() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeMap(Map<String, Object>) - Method in class org.jmol.util.JSONWriter
 
writemi - Variable in class jme.JME
 
writeMOBases() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeModel(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeModelMetadata(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeModels() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writemol - Variable in class jme.JME
 
WriteNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
 
writeNamfisFiles(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
writeNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
 
writeNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
 
writeNull() - Method in class org.jmol.util.JSONWriter
 
writeNumber(Number) - Method in class org.jmol.util.JSONWriter
 
writeObject(Object) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeObject(Object) - Method in class org.jmol.util.JSONWriter
 
writeSchemaMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeShort(short) - Method in interface javajs.api.GenericOutputChannel
 
writeShort(short) - Method in class javajs.util.OC
 
writesmi - Variable in class jme.JME
 
writeStatus(String) - Method in interface jspecview.api.JSVAppletInterface
Writes a message to the status label
writeStatus(String) - Method in interface jspecview.api.ScriptInterface
 
writeStatus(String) - Method in class jspecview.app.JSVApp
Writes a message to the status label
writeStatus(String) - Method in class jspecview.appletjs.JSVApplet
 
writeStatus(String) - Method in class jspecview.application.JSpecView
 
writeStatus(String) - Method in class jspecview.application.MainFrame
Writes a message to the status bar
writeString(String) - Method in class javajs.img.PngEncoder
Write a string into the pngBytes array at a given position.
writeString(String) - Method in class org.jmol.util.JSONWriter
 
writeString(String, SB) - Method in class org.jmol.util.JSONWriter
 
writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
 
writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
 
writeTopology(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
writeVibrations(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
 
wyckoff - Static variable in class org.jmol.script.T
 
WYCKOFF_RET_CENTERING - Static variable in class org.jmol.symmetry.WyckoffFinder
 
WYCKOFF_RET_CENTERING_STRING - Static variable in class org.jmol.symmetry.WyckoffFinder
 
WYCKOFF_RET_COORD - Static variable in class org.jmol.symmetry.WyckoffFinder
 
WYCKOFF_RET_COORDS - Static variable in class org.jmol.symmetry.WyckoffFinder
 
WYCKOFF_RET_COORDS_ALL - Static variable in class org.jmol.symmetry.WyckoffFinder
 
WYCKOFF_RET_GENERAL - Static variable in class org.jmol.symmetry.WyckoffFinder
 
WYCKOFF_RET_LABEL - Static variable in class org.jmol.symmetry.WyckoffFinder
positive numbers will be label characters or '*'
WYCKOFF_RET_WITH_MULT - Static variable in class org.jmol.symmetry.WyckoffFinder
 
WyckoffFinder - Class in org.jmol.symmetry
A class to calculate, store, and retrieve Wyckoff information as per BCS nph-trgen at https://www.cryst.ehu.es/cgi-bin/cryst/programs//nph-trgen?gnum=146invalid input: '&what'=wposinvalid input: '&trmat'=2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3cinvalid input: '&unconv'=R%203%20:Rinvalid input: '&from'=ita For the 611 standard setting in ITA GENPOS, we are just reading the json file and loading its information.
WyckoffFinder() - Constructor for class org.jmol.symmetry.WyckoffFinder
 
wyckoffm - Static variable in class org.jmol.script.T
 

X

x - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
 
x - Variable in class javajs.util.T3
 
x - Variable in class javajs.util.T3d
The x coordinate.
x - Variable in class javajs.util.T3i
The x coordinate.
x - Variable in class org.jmol.quantum.SlaterData
 
x - Static variable in class org.jmol.script.T
 
x - Variable in class org.jmol.util.Rectangle
 
x - Variable in class org.jmol.viewer.MouseState
 
X - Variable in class org.jmol.quantum.QuantumCalculation
 
X - Static variable in class org.jmol.util.BoxInfo
 
X2 - Variable in class org.jmol.quantum.QuantumCalculation
 
xaxisData - Variable in class jspecview.source.AnIMLReader
 
xAxisLeftToRight - Variable in class jspecview.common.PanelData
 
xBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
xButton - Variable in class jme.JME
 
XcrysdenReader - Class in org.jmol.adapter.readers.xtal
 
XcrysdenReader() - Constructor for class org.jmol.adapter.readers.xtal.XcrysdenReader
 
xFactor - Variable in class jspecview.source.JDXDataObject
Also used in JDXExport
xFactor - Variable in class jspecview.source.AnIMLReader
 
xGT - Static variable in class org.jmol.util.GData
 
xLabel - Variable in class jspecview.source.JDXDataObject
 
xLast - Variable in class org.jmol.util.GData
 
xlateAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
xLT - Static variable in class org.jmol.util.GData
 
xMax - Variable in class org.jmol.quantum.QuantumCalculation
 
xMin - Variable in class org.jmol.quantum.QuantumCalculation
 
XmlArgusReader - Class in org.jmol.adapter.readers.xml
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
 
XmlCdxReader - Class in org.jmol.adapter.readers.xml
A reader for CambridgeSoft CDXML files.
XmlCdxReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCdxReader
 
XmlChem3dReader - Class in org.jmol.adapter.readers.xml
An chem3d c3xml reader
XmlChem3dReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
 
XmlCmlReader - Class in org.jmol.adapter.readers.xml
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
 
xmlData - Variable in class org.jmol.jvxl.data.VolumeData
 
XmlHandler - Class in org.jmol.adapter.readers.xml
a SAX handler -- Java only
XmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlHandler
 
XmlMagResReader - Class in org.jmol.adapter.readers.xml
 
XmlMagResReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMagResReader
 
XmlMolproReader - Class in org.jmol.adapter.readers.xml
A Molpro 2005 reader
XmlMolproReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
 
XmlMOReader - Class in org.jmol.adapter.readers.xml
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
XmlMOReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMOReader
 
XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
An Odyssey xodydata reader
XmlOdysseyReader() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
XMLParser - Class in jspecview.source
 
XMLParser(BufferedReader) - Constructor for class jspecview.source.XMLParser
 
XmlQEReader - Class in org.jmol.adapter.readers.xml
QuantumEspresso XML reader
XmlQEReader() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader
 
XmlReader - Class in org.jmol.adapter.readers.xml
A generic XML reader template -- by itself, does nothing.
XmlReader - Class in org.jmol.jvxl.readers
 
XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
 
XmlReader(BufferedReader) - Constructor for class org.jmol.jvxl.readers.XmlReader
 
XmlUtil - Class in javajs.util
A very simplistic XML generator
XmlUtil() - Constructor for class javajs.util.XmlUtil
 
XmlVaspReader - Class in org.jmol.adapter.readers.xml
Vasp vasprun.xml reader
XmlVaspReader() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader
 
XmlXsdReader - Class in org.jmol.adapter.readers.xml
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
XmlXsdReader() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader
 
xor(BS) - Method in class javajs.util.BS
Performs a logical XOR of this bit set with the bit set argument.
xPixelClicked - Variable in class jspecview.common.PanelData
 
XSCALEON - Enum constant in enum class jspecview.common.ScriptToken
 
XSFWriter - Class in org.jmol.adapter.writers
An XCrysDen XSF writer.
XSFWriter() - Constructor for class org.jmol.adapter.writers.XSFWriter
 
xtalSymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
XtalSymmetry - Class in org.jmol.adapter.smarter
A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.
XtalSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry
 
XtalSymmetry.FileSymmetry - Class in org.jmol.adapter.smarter
A class only used by adapter.smarter.XtalSymmetry while building the file-based model.
XtlWriter - Class in org.jmol.adapter.writers
 
XtlWriter() - Constructor for class org.jmol.adapter.writers.XtlWriter
 
xUnitExponent - Variable in class jspecview.export.AMLExporter
 
xUnitExponent - Variable in class jspecview.export.CMLExporter
 
xUnitFactor - Variable in class jspecview.export.AMLExporter
 
xUnitFactor - Variable in class jspecview.export.CMLExporter
 
xUnitLabel - Variable in class jspecview.export.AMLExporter
 
xUnitLabel - Variable in class jspecview.export.CMLExporter
 
xUnits - Variable in class jspecview.export.AMLExporter
 
xUnits - Variable in class jspecview.export.CMLExporter
 
xUnits - Variable in class jspecview.source.JDXDataObject
 
xUnits - Variable in class jspecview.source.AnIMLReader
 
XUNITSON - Enum constant in enum class jspecview.common.ScriptToken
 
xVdwClash - Variable in class org.jmol.util.ContactPair
 
xWhenPressed - Variable in class jspecview.app.GenericMouse
 
xy - Variable in class org.jmol.render.LabelsRenderer
 
xy - Variable in class org.jmol.shape.Hover
 
XY - Enum constant in enum class jspecview.common.ExportType
 
XY_RANGE - Static variable in class org.jmol.viewer.ActionManager
 
XY_ZTOP - Static variable in class org.jmol.viewer.JC
 
xyCoords - Variable in class jspecview.export.AMLExporter
 
xyCoords - Variable in class jspecview.export.CMLExporter
 
xyCoords - Variable in class jspecview.source.JDXDataObject
array of x,y coordinates
xyData - Variable in class jspecview.dialog.JSVDialog
 
xypParameter(int) - Method in class org.jmol.script.ScriptParam
 
xyz - Variable in class org.jmol.atomdata.AtomData
 
xyz - Variable in class org.jmol.modelset.Text
 
xyz - Static variable in class org.jmol.script.T
 
XYZ - Static variable in class org.jmol.util.BoxInfo
 
xyzIsSlabbedInternal(T3) - Method in class org.jmol.viewer.TransformManager
 
xyzMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
xyzMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
xyzpParameter(int) - Method in class org.jmol.script.ScriptParam
 
XyzReader - Class in org.jmol.adapter.readers.molxyz
Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
 
xyzToLab(P3, P3) - Method in class javajs.img.GifEncoder
 
xyzToRgb(P3, P3) - Method in class javajs.img.GifEncoder
 
xyzToVoxelPt(float, float, float, T3i) - Method in class org.jmol.jvxl.data.VolumeData
 

Y

y - Variable in class com.sparshui.inputdevice.JmolTouchSimulator.TouchData
 
y - Variable in class javajs.util.T3
 
y - Variable in class javajs.util.T3d
The y coordinate.
y - Variable in class javajs.util.T3i
The y coordinate.
y - Variable in class org.jmol.quantum.SlaterData
 
y - Static variable in class org.jmol.script.T
 
y - Variable in class org.jmol.util.Rectangle
 
y - Variable in class org.jmol.viewer.MouseState
 
Y - Variable in class org.jmol.quantum.QuantumCalculation
 
Y - Static variable in class org.jmol.util.BoxInfo
 
Y2 - Variable in class org.jmol.quantum.QuantumCalculation
 
y2DUnits - Variable in class jspecview.source.JDXDataObject
 
yaxisData - Variable in class jspecview.source.AnIMLReader
 
yBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
YELLOW - Static variable in class org.jmol.util.C
 
yFactor - Variable in class jspecview.source.JDXDataObject
Also used in JDXExport
yFactor - Variable in class jspecview.source.AnIMLReader
 
yGT - Static variable in class org.jmol.util.GData
 
yLabel - Variable in class jspecview.source.JDXDataObject
 
yLast - Variable in class org.jmol.util.GData
 
yLT - Static variable in class org.jmol.util.GData
 
yMax - Variable in class org.jmol.quantum.QuantumCalculation
 
yMin - Variable in class org.jmol.quantum.QuantumCalculation
 
YSCALE - Enum constant in enum class jspecview.common.ScriptToken
 
YSCALEON - Enum constant in enum class jspecview.common.ScriptToken
 
yUnitLabel - Variable in class jspecview.export.AMLExporter
 
yUnitLabel - Variable in class jspecview.export.CMLExporter
 
yUnits - Variable in class jspecview.export.AMLExporter
 
yUnits - Variable in class jspecview.export.CMLExporter
 
yUnits - Variable in class jspecview.source.JDXDataObject
 
yUnits - Variable in class jspecview.source.AnIMLReader
 
YUNITSON - Enum constant in enum class jspecview.common.ScriptToken
 
yWhenPressed - Variable in class jspecview.app.GenericMouse
 
yzCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
yzPlanePts - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzPlanes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 

Z

z - Variable in class javajs.util.T3
 
z - Variable in class javajs.util.T3d
The z coordinate.
z - Variable in class javajs.util.T3i
The z coordinate.
z - Variable in class org.jmol.modelset.Text
 
z - Variable in class org.jmol.quantum.SlaterData
 
z - Static variable in class org.jmol.script.T
 
Z - Variable in class org.jmol.quantum.QuantumCalculation
 
Z - Static variable in class org.jmol.util.BoxInfo
 
Z_ASCII - Static variable in class com.jcraft.jzlib.JZlib
 
Z_BEST_COMPRESSION - Static variable in class com.jcraft.jzlib.JZlib
 
Z_BEST_SPEED - Static variable in class com.jcraft.jzlib.JZlib
 
Z_BINARY - Static variable in class com.jcraft.jzlib.JZlib
 
Z_BUF_ERROR - Static variable in class com.jcraft.jzlib.JZlib
 
Z_DATA_ERROR - Static variable in class com.jcraft.jzlib.JZlib
 
Z_DEFAULT_COMPRESSION - Static variable in class com.jcraft.jzlib.JZlib
 
Z_DEFAULT_STRATEGY - Static variable in class com.jcraft.jzlib.JZlib
 
Z_ERRNO - Static variable in class com.jcraft.jzlib.JZlib
 
Z_FILTERED - Static variable in class com.jcraft.jzlib.JZlib
 
Z_FINISH - Static variable in class com.jcraft.jzlib.JZlib
 
Z_FULL_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
 
Z_HUFFMAN_ONLY - Static variable in class com.jcraft.jzlib.JZlib
 
Z_MEM_ERROR - Static variable in class com.jcraft.jzlib.JZlib
 
Z_NEED_DICT - Static variable in class com.jcraft.jzlib.JZlib
 
Z_NO_COMPRESSION - Static variable in class com.jcraft.jzlib.JZlib
 
Z_NO_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
 
Z_OK - Static variable in class com.jcraft.jzlib.JZlib
 
Z_PARTIAL_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
 
Z_STREAM_END - Static variable in class com.jcraft.jzlib.JZlib
 
Z_STREAM_ERROR - Static variable in class com.jcraft.jzlib.JZlib
 
Z_SYNC_FLUSH - Static variable in class com.jcraft.jzlib.JZlib
 
Z_UNKNOWN - Static variable in class com.jcraft.jzlib.JZlib
 
Z_VERSION_ERROR - Static variable in class com.jcraft.jzlib.JZlib
 
Z2 - Variable in class org.jmol.quantum.QuantumCalculation
 
zap - Static variable in class org.jmol.script.T
 
zap() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
zap() - Method in class org.jmol.console.GenericConsole
 
zap(boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
ZAP_TITLE - Static variable in class org.jmol.viewer.JC
 
ZAPPED - Enum constant in enum class org.jmol.c.FIL
 
zBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
zbuf - Variable in class org.jmol.g3d.Graphics3D
 
zbufT - Variable in class org.jmol.g3d.Graphics3D
 
zdepth - Static variable in class org.jmol.script.T
 
zDepthPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zDepthValue - Variable in class org.jmol.viewer.TransformManager
 
zerobasedxyzrasmol - Static variable in class org.jmol.script.T
 
zeroFontId - Variable in class org.jmol.shape.Labels
 
zeta - Variable in class org.jmol.quantum.SlaterData
 
zGT - Static variable in class org.jmol.util.GData
 
ZInputStream - Interface in javajs.api
 
ZipData - Class in javajs.util
 
ZipData(int) - Constructor for class javajs.util.ZipData
 
ZipTools - Class in javajs.util
Note the JSmol/HTML5 must use its own version of java.util.zip.ZipOutputStream.
ZipTools() - Constructor for class javajs.util.ZipTools
 
zLT - Static variable in class org.jmol.util.GData
 
zMargin - Variable in class org.jmol.g3d.Graphics3D
 
zMax - Variable in class org.jmol.quantum.QuantumCalculation
 
zMin - Variable in class org.jmol.quantum.QuantumCalculation
 
zmPct - Variable in class org.jmol.viewer.TransformManager
zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled
zoom - Static variable in class org.jmol.script.T
 
ZOOM - Enum constant in enum class jspecview.common.ScriptToken
 
ZOOM_EVENT - Static variable in class com.sparshui.common.messages.events.EventType
 
ZOOM_EVENT - Static variable in class com.sparshui.GestureType
 
ZOOM_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
ZOOM_GESTURE - Static variable in class com.sparshui.GestureType
 
ZOOM_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
zoomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
zoomBoxColor - Variable in class jspecview.common.PanelData
 
ZOOMBOXCOLOR - Enum constant in enum class jspecview.common.ScriptToken
 
zoomBoxColor2 - Variable in class jspecview.common.PanelData
 
ZOOMBOXCOLOR2 - Enum constant in enum class jspecview.common.ScriptToken
 
zoomBy(int) - Method in class org.jmol.viewer.TransformManager
standard response to user mouse vertical shift-drag
zoomByFactor(float, int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
 
zoomByFactor(float, int, int) - Method in class org.jmol.navigate.Navigator
 
zoomByFactor(int, int, int) - Method in class org.jmol.viewer.ActionManager
 
zoomenabled - Static variable in class org.jmol.script.T
 
zoomEnabled - Variable in class org.jmol.viewer.TransformManager
 
ZoomEvent - Class in com.sparshui.common.messages.events
 
ZoomEvent - Class in jspecview.common
 
ZoomEvent() - Constructor for class com.sparshui.common.messages.events.ZoomEvent
 
ZoomEvent(byte[]) - Constructor for class com.sparshui.common.messages.events.ZoomEvent
Constructs a ZoomEvent from a serialized version of ZoomEvent.
ZoomEvent(float, Location, long) - Constructor for class com.sparshui.common.messages.events.ZoomEvent
 
zoomFactor - Variable in class org.jmol.viewer.TransformManager
 
zoomheight - Static variable in class org.jmol.script.T
 
zoomlarge - Static variable in class org.jmol.script.T
 
zoomTo - Static variable in class org.jmol.script.T
 
zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
 
zoomTrigger - Variable in class org.jmol.viewer.ActionManager
 
zshade - Static variable in class org.jmol.script.T
 
zShadeEnabled - Variable in class org.jmol.viewer.TransformManager
 
zshadepower - Static variable in class org.jmol.script.T
 
zslab - Static variable in class org.jmol.script.T
 
zSlab - Variable in class org.jmol.modelset.Text
 
zSlab - Variable in class org.jmol.render.LabelsRenderer
 
zSlabPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zSlabPoint - Variable in class org.jmol.viewer.TransformManager
 
zSlabValue - Variable in class org.jmol.viewer.TransformManager
 
ZStream - Class in com.jcraft.jzlib
Bob Hanson -- using this for Jmol; added ZStream.getBytes(s) ZStream deprecated? Not for public use in the future.
ZStream() - Constructor for class com.jcraft.jzlib.ZStream
 
ZStreamException - Exception Class in com.jcraft.jzlib
 
ZStreamException() - Constructor for exception class com.jcraft.jzlib.ZStreamException
 
ZStreamException(String) - Constructor for exception class com.jcraft.jzlib.ZStreamException
 
zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager
 

_

__ - Static variable in class org.jmol.script.T
 
___Exporter - Class in org.jmol.export
 
___Exporter() - Constructor for class org.jmol.export.___Exporter
 
__CartesianExporter - Class in org.jmol.export
 
__CartesianExporter() - Constructor for class org.jmol.export.__CartesianExporter
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.AdfReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.AmsReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.DgridReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.QCJSONReader
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
_active - Variable in class com.sparshui.inputdevice.JmolTouchSimulator
 
_args - Static variable in class org.jmol.script.T
 
_atomPickedCallback(int, int) - Method in interface org.jmol.api.js.JSmolAppletObject
 
_IdtfExporter - Class in org.jmol.export
 
_IdtfExporter() - Constructor for class org.jmol.export._IdtfExporter
 
_in - Variable in class com.sparshui.common.ClientProtocol
 
_MayaExporter - Class in org.jmol.export
 
_MayaExporter() - Constructor for class org.jmol.export._MayaExporter
 
_ObjExporter - Class in org.jmol.export
Class to export Wavefront OBJ files.
_ObjExporter() - Constructor for class org.jmol.export._ObjExporter
 
_offset - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_offsetCentroid - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_out - Variable in class com.sparshui.common.ClientProtocol
 
_PovrayExporter - Class in org.jmol.export
 
_PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
 
_refresh() - Method in interface org.jmol.api.js.JSmolAppletObject
 
_search(String) - Method in interface jspecview.api.js.JSVAppletObject
 
_showStatus(String, String) - Method in interface jspecview.api.js.JSVAppletObject
 
_showTooltip(String, int, int) - Method in interface jspecview.api.js.JSVAppletObject
 
_socket - Variable in class com.sparshui.common.ClientProtocol
 
_StlExporter - Class in org.jmol.export
STereoLithography file format exporter for 3D printing.
_StlExporter() - Constructor for class org.jmol.export._StlExporter
 
_TachyonExporter - Class in org.jmol.export
 
_TachyonExporter() - Constructor for class org.jmol.export._TachyonExporter
 
_updateView(Object, String) - Method in interface jspecview.api.js.JSVAppletObject
 
_VrmlExporter - Class in org.jmol.export
A basic VRML generator.
_VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
 
_X3dExporter - Class in org.jmol.export
 
_X3dExporter() - Constructor for class org.jmol.export._X3dExporter
 
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