Serialized Form
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Package com.jcraft.jzlib
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Exception Class com.jcraft.jzlib.GZIPException
class GZIPException extends IOException implements Serializable -
Exception Class com.jcraft.jzlib.ZStreamException
class ZStreamException extends IOException implements Serializable
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Package com.sparshui.common
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Class com.sparshui.common.Location
class Location extends Object implements Serializable- serialVersionUID:
- -3472243250219991476L
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Serialized Fields
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_x
float _x
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_y
float _y
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-
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Package com.sparshui.common.messages.events
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Class com.sparshui.common.messages.events.DragEvent
class DragEvent extends Object implements Serializable- serialVersionUID:
- -2305607021385835330L
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Serialized Fields
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_dx
float _dx
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_dy
float _dy
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_nPoints
byte _nPoints
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_time
long _time
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Class com.sparshui.common.messages.events.FlickEvent
class FlickEvent extends Object implements Serializable- serialVersionUID:
- -2305607021385835330L
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Serialized Fields
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speedLevel
float speedLevel
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xDirection
float xDirection
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yDirection
float yDirection
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Class com.sparshui.common.messages.events.RelativeDragEvent
class RelativeDragEvent extends Object implements Serializable- serialVersionUID:
- 7743528698376037703L
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Serialized Fields
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_changeInX
float _changeInX
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_changeInY
float _changeInY
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Class com.sparshui.common.messages.events.RotateEvent
class RotateEvent extends Object implements Serializable- serialVersionUID:
- -5467788080845086125L
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Serialized Fields
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_center
Location _center
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_rotation
float _rotation
Rotation of this component in radians -
_time
long _time
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Class com.sparshui.common.messages.events.SpinEvent
class SpinEvent extends Object implements Serializable- serialVersionUID:
- 6394319277586792988L
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Serialized Fields
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_rotationX
float _rotationX
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_rotationY
float _rotationY
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_rotationZ
float _rotationZ
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Class com.sparshui.common.messages.events.TouchEvent
class TouchEvent extends Object implements Serializable- serialVersionUID:
- 370824346017492361L
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Serialized Fields
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_id
int _id
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_state
int _state
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_time
long _time
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_x
float _x
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_y
float _y
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Class com.sparshui.common.messages.events.ZoomEvent
class ZoomEvent extends Object implements Serializable- serialVersionUID:
- -4658011539863774168L
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Serialized Fields
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_center
Location _center
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_scale
float _scale
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_time
long _time
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-
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Package javajs.util
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Class javajs.util.A4
class A4 extends P3 implements Serializable-
Serialized Fields
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angle
float angle
The angle.
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-
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Exception Class javajs.util.JSONException
class JSONException extends RuntimeException implements Serializable -
Class javajs.util.Lst
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Class javajs.util.M3
class M3 extends M34 implements Serializable -
Class javajs.util.P3
class P3 extends T3 implements Serializable -
Class javajs.util.P3i
class P3i extends T3i implements Serializable -
Class javajs.util.P4
class P4 extends T4 implements Serializable -
Class javajs.util.T3
class T3 extends Object implements Serializable-
Serialized Fields
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x
float x
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y
float y
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z
float z
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-
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Class javajs.util.T3d
class T3d extends Object implements Serializable-
Serialized Fields
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x
double x
The x coordinate. -
y
double y
The y coordinate. -
z
double z
The z coordinate.
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-
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Class javajs.util.T3i
class T3i extends Object implements Serializable-
Serialized Fields
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x
int x
The x coordinate. -
y
int y
The y coordinate. -
z
int z
The z coordinate.
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-
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Class javajs.util.T4
class T4 extends T3 implements Serializable-
Serialized Fields
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w
float w
The w coordinate.
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-
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Class javajs.util.V3
class V3 extends T3 implements Serializable -
Class javajs.util.V3d
class V3d extends T3d implements Serializable
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Package jme
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Class jme.JME
class JME extends JPanel implements Serializable-
Serialized Fields
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aboutBox
jme.MultiBox aboutBox
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aboutBoxPoint
Point aboutBoxPoint
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action
int action
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active_an
int active_an
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actualMolecule
int actualMolecule
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afterClear
boolean afterClear
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allHs
boolean allHs
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any
JButton any
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anyBond
JButton anyBond
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anyec
JButton anyec
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apointx
int[] apointx
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apointy
int[] apointy
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application
boolean application
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aromatic
JButton aromatic
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aromaticBond
JButton aromaticBond
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arrowWidth
int arrowWidth
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atomBgColors
String atomBgColors
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atomColors
String atomColors
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atomicSymbol
JTextField atomicSymbol
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atomxBox
jme.MultiBox atomxBox
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atomxBoxPoint
Point atomxBoxPoint
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autoez
boolean autoez
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autonumber
boolean autonumber
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bpointx
int[] bpointx
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bpointy
int[] bpointy
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br
JButton br
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bwMode
boolean bwMode
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c
JButton c
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canonize
boolean canonize
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canvasBg
Color canvasBg
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chargeImage
Image chargeImage
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choiced
JComboBox<String> choiced
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choiceh
JComboBox<String> choiceh
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cl
JButton cl
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clearImage
Image clearImage
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currentMark
int currentMark
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deleteImage
Image deleteImage
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deleterImage
Image deleterImage
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depict
boolean depict
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depictBorder
boolean depictBorder
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depictcgi
String depictcgi
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depictScale
double depictScale
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depictservlet
String depictservlet
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dimension
Dimension dimension
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doMenu
boolean doMenu
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doTags
boolean doTags
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dyMode
boolean dyMode
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embedded
boolean embedded
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endImage
Image endImage
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f
JButton f
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font
Font font
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fontBold
Font fontBold
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fontBoldMet
FontMetrics fontBoldMet
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fontMet
FontMetrics fontMet
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fontSize
int fontSize
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fontSmall
Font fontSmall
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fontSmallMet
FontMetrics fontSmallMet
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halogen
JButton halogen
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i
JButton i
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infoArea
BufferedImage infoArea
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infoImage
Image infoImage
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infoText
String infoText
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jmeh
boolean jmeh
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jmeString
String jmeString
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keepHydrogens
boolean keepHydrogens
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lastAction
int lastAction
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leftMenu
BufferedImage leftMenu
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markUsed
boolean markUsed
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mol
JMEmol mol
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molecularArea
BufferedImage molecularArea
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mols
JMEmol[] mols
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molStack
List<JMEmol> molStack
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molString
String molString
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molText
String molText
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mouseShift
boolean mouseShift
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movePossible
boolean movePossible
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multipart
boolean multipart
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myFrame
JFrame myFrame
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n
JButton n
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newMolecule
boolean newMolecule
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nmols
int nmols
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nocenter
boolean nocenter
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nonaromatic
JButton nonaromatic
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nonring
JButton nonring
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nonringBond
JButton nonringBond
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number
boolean number
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o
JButton o
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p
JButton p
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point
Point point
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polarnitro
boolean polarnitro
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psColor
Color[] psColor
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query
boolean query
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queryBox
jme.QueryBox queryBox
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rButton
boolean rButton
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reaction
boolean reaction
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relativeStereo
boolean relativeStereo
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revertStereo
boolean revertStereo
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ring
JButton ring
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ringBond
JButton ringBond
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rtemplatesImage
Image rtemplatesImage
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runsmi
boolean runsmi
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s
JButton s
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saved
int saved
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sd
int sd
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sdBond
JButton sdBond
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showAtomNumbers
boolean showAtomNumbers
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showHydrogens
boolean showHydrogens
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smartsImage
Image smartsImage
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smiImage
Image smiImage
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smiles
String smiles
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smilesBox
jme.MultiBox smilesBox
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smilesBoxPoint
Point smilesBoxPoint
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smitImage
Image smitImage
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smol
JMEmol smol
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stackPointer
int stackPointer
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star
boolean star
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stereo
boolean stereo
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stereoImage
Image stereoImage
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stereoxImage
Image stereoxImage
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template
String template
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templatesImage
Image templatesImage
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tmol
JMEmol tmol
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topMenu
BufferedImage topMenu
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undoImage
Image undoImage
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webme
boolean webme
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writemi
boolean writemi
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writemol
boolean writemol
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writesmi
boolean writesmi
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xButton
boolean xButton
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xold
int xold
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yold
int yold
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-
-
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Package jspecview.application
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Class jspecview.application.AboutDialog
class AboutDialog extends JDialog implements Serializable- serialVersionUID:
- 1L
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Class jspecview.application.ApplicationMenu
class ApplicationMenu extends JMenuBar implements Serializable- serialVersionUID:
- 1L
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Serialized Fields
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closeAllMenuItem
JMenuItem closeAllMenuItem
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closeMenuItem
JMenuItem closeMenuItem
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coordsCheckBoxMenuItem
JCheckBoxMenuItem coordsCheckBoxMenuItem
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displayMenu
JMenu displayMenu
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errorLogMenuItem
JMenuItem errorLogMenuItem
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exportAsMenu
JMenu exportAsMenu
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gridCheckBoxMenuItem
JCheckBoxMenuItem gridCheckBoxMenuItem
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integrationMenuItem
JMenuItem integrationMenuItem
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mainFrame
MainFrame mainFrame
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openRecentMenu
JMenu openRecentMenu
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overlayKeyMenuItem
JMenuItem overlayKeyMenuItem
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pointsOnlyCheckBoxMenuItem
JCheckBoxMenuItem pointsOnlyCheckBoxMenuItem
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printMenuItem
JMenuItem printMenuItem
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processingMenu
JMenu processingMenu
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revPlotCheckBoxMenuItem
JCheckBoxMenuItem revPlotCheckBoxMenuItem
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saveAsJDXMenu
JMenu saveAsJDXMenu
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saveAsMenu
JMenu saveAsMenu
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scaleXCheckBoxMenuItem
JCheckBoxMenuItem scaleXCheckBoxMenuItem
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scaleYCheckBoxMenuItem
JCheckBoxMenuItem scaleYCheckBoxMenuItem
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sidePanelCheckBoxMenuItem
JCheckBoxMenuItem sidePanelCheckBoxMenuItem
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solutionColorMenuItem
JMenuItem solutionColorMenuItem
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sourceMenuItem
JMenuItem sourceMenuItem
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statusCheckBoxMenuItem
JCheckBoxMenuItem statusCheckBoxMenuItem
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toolbarCheckBoxMenuItem
JCheckBoxMenuItem toolbarCheckBoxMenuItem
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transmittanceMenuItem
JMenuItem transmittanceMenuItem
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viewer
JSViewer viewer
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Class jspecview.application.AppToolBar
class AppToolBar extends JToolBar implements Serializable- serialVersionUID:
- 1L
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Serialized Fields
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coordsToggleButton
JToggleButton coordsToggleButton
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errorLogButton
JButton errorLogButton
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errorLogIcon
ImageIcon errorLogIcon
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errorLogRedIcon
ImageIcon errorLogRedIcon
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errorLogYellowIcon
ImageIcon errorLogYellowIcon
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gridToggleButton
JToggleButton gridToggleButton
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mainFrame
MainFrame mainFrame
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revPlotToggleButton
JToggleButton revPlotToggleButton
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spectraButton
JButton spectraButton
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vwr
JSViewer vwr
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Class jspecview.application.AwtTree
class AwtTree extends JTree implements Serializable- serialVersionUID:
- 1L
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Serialized Fields
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rootNode
JSVTreeNode rootNode
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si
ScriptInterface si
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spectraTreeModel
DefaultTreeModel spectraTreeModel
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vwr
JSViewer vwr
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Class jspecview.application.AwtTreeNode
class AwtTreeNode extends DefaultMutableTreeNode implements Serializable- serialVersionUID:
- 1L
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Serialized Fields
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index
int index
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panelNode
PanelNode panelNode
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Class jspecview.application.AwtTreePath
class AwtTreePath extends TreePath implements Serializable -
Class jspecview.application.MainFrame
class MainFrame extends JFrame implements Serializable- serialVersionUID:
- 1L
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Serialized Fields
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advancedApplet
JSVAppPro advancedApplet
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appMenu
ApplicationMenu appMenu
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commandHistory
CommandHistory commandHistory
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commandInput
JTextField commandInput
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dsp
DisplaySchemesProcessor dsp
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isAwake
boolean isAwake
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isEmbedded
boolean isEmbedded
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isHidden
boolean isHidden
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jmolDimensionNew
Dimension jmolDimensionNew
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jmolDimensionOld
Dimension jmolDimensionOld
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jmolDisplay
Component jmolDisplay
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jmolFrameHeight
int jmolFrameHeight
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jmolFrameWidth
int jmolFrameWidth
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jmolOrAdvancedApplet
JSVInterface jmolOrAdvancedApplet
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jmolPanel
JPanel jmolPanel
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jsv
JSpecView jsv
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mainborderLayout
BorderLayout mainborderLayout
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mainPanel
Component mainPanel
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mainSplitPane
JSplitPane mainSplitPane
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mainSplitPosition
int mainSplitPosition
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nullPanel
JPanel nullPanel
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recentFilePaths
Lst<String> recentFilePaths
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showExitDialog
boolean showExitDialog
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sidePanelOn
boolean sidePanelOn
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sideSplitPane
JSplitPane sideSplitPane
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spectraTreeScrollPane
JScrollPane spectraTreeScrollPane
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splitPosition
int splitPosition
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statusbarOn
boolean statusbarOn
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statusLabel
JLabel statusLabel
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statusPanel
JPanel statusPanel
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tempDS
String tempDS
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toolBar
AppToolBar toolBar
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toolbarOn
boolean toolbarOn
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tree
AwtTree tree
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vwr
JSViewer vwr
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Class jspecview.application.PreferencesDialog
class PreferencesDialog extends JDialog implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
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absTransPanel
JPanel absTransPanel
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absTransTitledBorder
TitledBorder absTransTitledBorder
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applicationPanel
JPanel applicationPanel
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AtoTRadioButton
JRadioButton AtoTRadioButton
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AutoConvertCheckBox
JCheckBox AutoConvertCheckBox
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autoIntegrateCheckBox
JCheckBox autoIntegrateCheckBox
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borderLayout6
BorderLayout borderLayout6
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buttonPanel
JPanel buttonPanel
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cancelButton
JButton cancelButton
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clearRecentButton
JButton clearRecentButton
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colorButton1
JButton colorButton1
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colorButton2
JButton colorButton2
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colorButton3
JButton colorButton3
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colorButton4
JButton colorButton4
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colorButton5
JButton colorButton5
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colorButton6
JButton colorButton6
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colorButton7
JButton colorButton7
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colorButton8
JButton colorButton8
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colorPanel
JPanel colorPanel
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colorPanel1
JPanel colorPanel1
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colorSchemePanel
JPanel colorSchemePanel
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confirmExitCheckBox
JCheckBox confirmExitCheckBox
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contentBorderLayout
BorderLayout contentBorderLayout
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contentpanel
JPanel contentpanel
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contentTitledBorder
TitledBorder contentTitledBorder
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conversionButtonGroup
ButtonGroup conversionButtonGroup
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coordinatesCheckBox
JCheckBox coordinatesCheckBox
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currentColorButton
JButton currentColorButton
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currentDS
ColorParameters currentDS
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customButton
JButton customButton
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defaultColorCheckBox
JCheckBox defaultColorCheckBox
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defaultDSName
String defaultDSName
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defaultFontCheckBox
JCheckBox defaultFontCheckBox
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deleteButton
JButton deleteButton
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displayFontPanel
JPanel displayFontPanel
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displayPanel
JPanel displayPanel
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dsp
DisplaySchemesProcessor dsp
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elementLabel
JLabel elementLabel
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elementList
JList<String> elementList
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elementPanel
JPanel elementPanel
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elModel
DefaultListModel<String> elModel
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exportDirCheckBox
JCheckBox exportDirCheckBox
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fontComboBox
JComboBox<String> fontComboBox
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fontTitledBorder
TitledBorder fontTitledBorder
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generalPanel
JPanel generalPanel
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gridBagLayout1
GridBagLayout gridBagLayout1
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gridBagLayout2
GridBagLayout gridBagLayout2
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gridBagLayout3
GridBagLayout gridBagLayout3
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gridBagLayout4
GridBagLayout gridBagLayout4
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gridBagLayout5
GridBagLayout gridBagLayout5
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gridBagLayout6
GridBagLayout gridBagLayout6
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gridBagLayout7
GridBagLayout gridBagLayout7
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gridCheckBox
JCheckBox gridCheckBox
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gridLayout1
GridLayout gridLayout1
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gridLayout2
GridLayout gridLayout2
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integFactorTextField
JTextField integFactorTextField
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integOffsetTextField
JTextField integOffsetTextField
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integratinTitledBorder
TitledBorder integratinTitledBorder
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integrationPanel
JPanel integrationPanel
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isSpectrumDisplayApplyNowEnabled
boolean isSpectrumDisplayApplyNowEnabled
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jLabel1
JLabel jLabel1
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jLabel2
JLabel jLabel2
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jLabel3
JLabel jLabel3
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jLabel4
JLabel jLabel4
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jLabel5
JLabel jLabel5
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jLabel6
JLabel jLabel6
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jLabel7
JLabel jLabel7
-
jLabel8
JLabel jLabel8
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jLabel9
JLabel jLabel9
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legendCheckBox
JCheckBox legendCheckBox
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listScrollPane
JScrollPane listScrollPane
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minYTextField
JTextField minYTextField
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okButton
JButton okButton
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openedDirCheckBox
JCheckBox openedDirCheckBox
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overlayCheckBox
JCheckBox overlayCheckBox
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panel
JPanel panel
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plotColorButton
JButton plotColorButton
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preferences
Properties preferences
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preferencesTabbedPane
JTabbedPane preferencesTabbedPane
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previewPanel
AwtPanel previewPanel
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procColorButton1
JButton procColorButton1
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procColorButton2
JButton procColorButton2
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procColorButton3
JButton procColorButton3
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procColorButton4
JButton procColorButton4
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procColorButton5
JButton procColorButton5
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procColorButton6
JButton procColorButton6
-
procColorButton7
JButton procColorButton7
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procColorButton8
JButton procColorButton8
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processingCustomButton
JButton processingCustomButton
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processingPanel
JPanel processingPanel
-
saveButton
JButton saveButton
-
scaleXCheckBox
JCheckBox scaleXCheckBox
-
scaleYCheckBox
JCheckBox scaleYCheckBox
-
schemeComboBox
JComboBox<String> schemeComboBox
-
separateWindowCheckBox
JCheckBox separateWindowCheckBox
-
sidePanelCheckBox
JCheckBox sidePanelCheckBox
-
spectrumDisplayApplyNowCheckBox
JCheckBox spectrumDisplayApplyNowCheckBox
-
spectrumPanel
JPanel spectrumPanel
-
statusBarCheckBox
JCheckBox statusBarCheckBox
-
svgForInkscapeCheckBox
JCheckBox svgForInkscapeCheckBox
-
toolbarCheckBox
JCheckBox toolbarCheckBox
-
topPanel
JPanel topPanel
-
TtoARadioButton
JRadioButton TtoARadioButton
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uiPanel
JPanel uiPanel
-
-
-
Package jspecview.common
-
Class jspecview.common.IntegralData
class IntegralData extends MeasurementData implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
haveRegions
boolean haveRegions
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integralTotal
double integralTotal
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intRange
double intRange
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normalizationFactor
double normalizationFactor
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offset
double offset
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percentMinY
double percentMinY
-
percentOffset
double percentOffset
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percentRange
double percentRange
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xyCoords
Coordinate[] xyCoords
-
-
Class jspecview.common.MeasurementData
- serialVersionUID:
- 1L
-
Serialized Fields
-
isON
boolean isON
-
key
String key
-
myParams
Parameters myParams
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precision
int precision
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spec
Spectrum spec
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type
Annotation.AType type
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units
String units
-
-
Class jspecview.common.PeakData
class PeakData extends MeasurementData implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
maxY
double maxY
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minY
double minY
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thresh
double thresh
-
-
Class jspecview.common.PeakPickEvent
class PeakPickEvent extends EventObject implements Serializable-
Serialized Fields
-
coord
Coordinate coord
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peakInfo
PeakInfo peakInfo
-
-
-
-
Package jspecview.exception
-
Exception Class jspecview.exception.JSVException
class JSVException extends Exception implements Serializable
-
-
Package jspecview.java
-
Class jspecview.java.AwtColor
class AwtColor extends Color implements Serializable-
Serialized Fields
-
opacity
int opacity
-
-
-
Class jspecview.java.AwtDialog
class AwtDialog extends JDialog implements Serializable-
Serialized Fields
-
buttonInsets
Insets buttonInsets
-
dataTable
JTable dataTable
-
defaultHeight
int defaultHeight
-
haveColors
boolean haveColors
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haveTwoPanels
boolean haveTwoPanels
-
iRow
int iRow
-
leftPanel
JPanel leftPanel
-
mainSplitPane
JSplitPane mainSplitPane
-
manager
DialogManager manager
-
optionKey
String optionKey
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options
Map<String,
Object> options -
panelInsets
Insets panelInsets
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registryKey
String registryKey
-
rightPanel
JPanel rightPanel
-
selectedRow
int selectedRow
-
tableCellAlignLeft
boolean tableCellAlignLeft
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tableModel
jspecview.java.DialogTableModel tableModel
-
thisPanel
JPanel thisPanel
-
type
Annotation.AType type
-
-
-
Class jspecview.java.AwtMainPanel
class AwtMainPanel extends JPanel implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
currentPanelIndex
int currentPanelIndex
-
selectedPanel
JSVPanel selectedPanel
-
-
Class jspecview.java.AwtPanel
class AwtPanel extends JPanel implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
apiPlatform
GenericPlatform apiPlatform
-
bgcolor
GenericColor bgcolor
-
mouse
GenericMouseInterface mouse
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pd
PanelData pd
-
vwr
JSViewer vwr
-
-
Class jspecview.java.AwtPrintDialog
class AwtPrintDialog extends JDialog implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
cancelButton
JButton cancelButton
-
centerRadioButton
JRadioButton centerRadioButton
-
chooseFontRadioButton
JRadioButton chooseFontRadioButton
-
defaultFontRadioButton
JRadioButton defaultFontRadioButton
-
fitToPageRadioButton
JRadioButton fitToPageRadioButton
-
fontButtonGroup
ButtonGroup fontButtonGroup
-
gridCheckBox
JCheckBox gridCheckBox
-
landscapeRadioButton
JRadioButton landscapeRadioButton
-
layoutButtonGroup
ButtonGroup layoutButtonGroup
-
pdfButton
JButton pdfButton
-
pl
PrintLayout pl
-
plNew
PrintLayout plNew
-
portraitRadioButton
JRadioButton portraitRadioButton
-
positionButtonGroup
ButtonGroup positionButtonGroup
-
previewButton
JButton previewButton
-
printButton
JButton printButton
-
scaleXCheckBox
JCheckBox scaleXCheckBox
-
scaleYCheckBox
JCheckBox scaleYCheckBox
-
titleCheckBox
JCheckBox titleCheckBox
-
topLeftRadioButton
JRadioButton topLeftRadioButton
-
-
-
Package org.jmol.adapter.smarter
-
Class org.jmol.adapter.smarter.Atom
class Atom extends P3 implements Serializable-
Serialized Fields
-
altLoc
char altLoc
-
anisoBorU
float[] anisoBorU
-
atomName
String atomName
-
atomSerial
int atomSerial
-
atomSetIndex
int atomSetIndex
-
atomSite
int atomSite
-
bfactor
float bfactor
-
bondingRadius
float bondingRadius
-
bsSymmetry
BS bsSymmetry
-
chainID
int chainID
-
elementNumber
short elementNumber
-
elementSymbol
String elementSymbol
-
foccupancy
float foccupancy
-
formalCharge
int formalCharge
-
group3
String group3
-
index
int index
-
insertionCode
char insertionCode
-
isHetero
boolean isHetero
-
isNegDisorder
boolean isNegDisorder
-
partialCharge
float partialCharge
-
radius
float radius
-
sequenceNumber
int sequenceNumber
-
tensors
Lst<Object> tensors
-
typeSymbol
String typeSymbol
-
vib
V3 vib
-
-
-
-
Package org.jmol.awt
-
Class org.jmol.awt.AwtColor
class AwtColor extends Color implements Serializable-
Serialized Fields
-
opacity
int opacity
-
-
-
-
Package org.jmol.console
-
Class org.jmol.console.ImageDialog
class ImageDialog extends JDialog implements Serializable-
Serialized Fields
-
canvas
org.jmol.console.ImageDialog.ImageCanvas canvas
-
console
JmolAppConsoleInterface console
-
image
Image image
-
imageMap
Map<String,
GenericImageDialog> imageMap -
menubar
JMenuBar menubar
-
title
String title
-
vwr
Viewer vwr
-
-
-
Class org.jmol.console.JmolButton
class JmolButton extends JButton implements Serializable -
Class org.jmol.console.JmolLabel
class JmolLabel extends JLabel implements Serializable -
Class org.jmol.console.JmolToggleButton
class JmolToggleButton extends JToggleButton implements Serializable -
Class org.jmol.console.KeyJCheckBox
class KeyJCheckBox extends JCheckBox implements Serializable-
Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.KeyJCheckBoxMenuItem
class KeyJCheckBoxMenuItem extends JCheckBoxMenuItem implements Serializable-
Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.KeyJMenu
class KeyJMenu extends JMenu implements Serializable -
Class org.jmol.console.KeyJMenuItem
class KeyJMenuItem extends JMenuItem implements Serializable-
Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.KeyJRadioButtonMenuItem
class KeyJRadioButtonMenuItem extends JRadioButtonMenuItem implements Serializable-
Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.ScriptEditor
class ScriptEditor extends JDialog implements Serializable-
Serialized Fields
-
attEcho
SimpleAttributeSet attEcho
-
attError
SimpleAttributeSet attError
-
attHighlight
SimpleAttributeSet attHighlight
-
buttonPanel
JPanel buttonPanel
-
checkButton
JButton checkButton
-
clearButton
JButton clearButton
-
closeButton
JButton closeButton
-
consoleButton
JButton consoleButton
-
editor
org.jmol.console.ScriptEditor.EditorTextPane editor
-
filename
String filename
-
fontButton
JButton fontButton
-
fontSize
int fontSize
-
haltButton
JButton haltButton
-
jmolConsole
JmolConsole jmolConsole
-
lastIndices
int lastIndices
-
loadButton
JButton loadButton
-
map
Map<String,
Object> map -
noPrefs
boolean noPrefs
-
openButton
JButton openButton
-
parsedContext
ScriptContext parsedContext
-
parsedData
String parsedData
-
pauseButton
JButton pauseButton
-
resumeButton
JButton resumeButton
-
runButton
JButton runButton
-
saveAsButton
JButton saveAsButton
-
saveButton
JButton saveButton
-
state
int state
-
stateButton
JButton stateButton
-
stepButton
JButton stepButton
-
title
String title
-
topButton
JButton topButton
-
vwr
Viewer vwr
-
zipFileName
String zipFileName
-
-
-
-
Package org.jmol.dialog
-
Class org.jmol.dialog.Dialog
class Dialog extends JPanel implements Serializable-
Serialized Fields
-
cb
JComboBox<String> cb
-
choice
String choice
-
dialogType
String dialogType
-
extension
String extension
-
extensions
String[] extensions
-
imageChoices
String[] imageChoices
-
imageExtensions
String[] imageExtensions
-
imageType
String imageType
-
initialFile
File initialFile
-
inputFileName
String inputFileName
-
openPreview
FilePreview openPreview
-
outputFileName
String outputFileName
-
qPanelJPEG
JPanel qPanelJPEG
-
qPanelPNG
JPanel qPanelPNG
-
qSliderJPEG
JSlider qSliderJPEG
-
qSliderPNG
JSlider qSliderPNG
-
qualityJ
int qualityJ
-
qualityP
int qualityP
-
vwr
Viewer vwr
-
-
-
Class org.jmol.dialog.FileChooser
class FileChooser extends JFileChooser implements Serializable -
Class org.jmol.dialog.FilePreview
class FilePreview extends JPanel implements Serializable-
Serialized Fields
-
active
JCheckBox active
-
append
JCheckBox append
-
cartoons
JCheckBox cartoons
-
chooser
JFileChooser chooser
-
display
org.jmol.dialog.FilePreview.FPPanel display
-
vwr
Viewer vwr
-
-
-
-
Package org.jmol.modelset
-
Class org.jmol.modelset.Atom
class Atom extends Point3fi implements Serializable-
Serialized Fields
-
altloc
char altloc
-
atomID
byte atomID
-
atomNumberFlags
short atomNumberFlags
atomNumberFlags encodes atomic number (a), isotope number(i) as: iiii iiii iaaa aaaa -
atomSite
int atomSite
-
atomSymmetry
BS atomSymmetry
-
bonds
Bond[] bonds
MAY BE NULL -
clickabilityFlags
int clickabilityFlags
-
colixAtom
short colixAtom
-
formalChargeAndFlags
int formalChargeAndFlags
-
group
Group group
-
madAtom
short madAtom
-
nBackbonesDisplayed
int nBackbonesDisplayed
-
nBondsDisplayed
int nBondsDisplayed
-
paletteID
byte paletteID
-
shapeVisibilityFlags
int shapeVisibilityFlags
-
userDefinedVanDerWaalRadius
float userDefinedVanDerWaalRadius
-
valence
byte valence
-
-
-
-
Package org.jmol.script
-
Exception Class org.jmol.script.ScriptException
class ScriptException extends Exception implements Serializable-
Serialized Fields
-
eval
ScriptEval eval
-
isError
boolean isError
-
message
String message
-
untranslated
String untranslated
-
-
-
Exception Class org.jmol.script.ScriptInterruption
class ScriptInterruption extends ScriptException implements Serializable
-
-
Package org.jmol.smiles
-
Exception Class org.jmol.smiles.InvalidSmilesException
class InvalidSmilesException extends Exception implements Serializable -
Class org.jmol.smiles.SmilesAtom
class SmilesAtom extends P3 implements Serializable-
Serialized Fields
-
aromaticAmbiguous
boolean aromaticAmbiguous
-
atomClass
float atomClass
-
atomicMass
int atomicMass
-
atomNumber
int atomNumber
-
atomSite
int atomSite
-
atomType
String atomType
-
bioAtomName
String bioAtomName
-
bioType
char bioType
-
bondCount
int bondCount
-
bonds
SmilesBond[] bonds
-
charge
int charge
-
cipChirality
int cipChirality
-
component
int component
-
connectivity
int connectivity
-
covalentHydrogenCount
int covalentHydrogenCount
-
degree
int degree
-
elementDefined
boolean elementDefined
-
elementNumber
int elementNumber
-
explicitHydrogenCount
int explicitHydrogenCount
-
hasDoubleBond
boolean hasDoubleBond
-
hasSubpattern
boolean hasSubpattern
-
hasSymbol
boolean hasSymbol
-
implicitHydrogenCount
int implicitHydrogenCount
-
index
int index
-
iNested
int iNested
-
insCode
char insCode
-
isAND
boolean isAND
-
isAromatic
boolean isAromatic
-
isBioAtom
boolean isBioAtom
-
isBioAtomWild
boolean isBioAtomWild
-
isBioResidue
boolean isBioResidue
-
isFirst
boolean isFirst
true if this atom is the first SMILES atom or first after a . with no connector -
isLeadAtom
boolean isLeadAtom
-
isTopoAtom
boolean isTopoAtom
-
jmolIndex
int jmolIndex
-
mapIndex
int mapIndex
-
matchingComponent
int matchingComponent
-
matchingIndex
int matchingIndex
-
matchingNode
Node matchingNode
-
missingHydrogenCount
int missingHydrogenCount
-
nonhydrogenDegree
int nonhydrogenDegree
-
not
boolean not
-
notBondedIndex
int notBondedIndex
-
notCrossLinked
boolean notCrossLinked
-
nSubAtoms
int nSubAtoms
-
parent
SmilesAtom parent
-
pattern
String pattern
-
patternIndex
int patternIndex
-
primitiveType
int primitiveType
-
referance
String referance
-
residueChar
String residueChar
-
residueName
String residueName
-
residueNumber
int residueNumber
-
ringConnectivity
int ringConnectivity
-
ringMembership
int ringMembership
-
ringSize
int ringSize
-
selected
boolean selected
-
stereo
SmilesStereo stereo
-
subAtoms
SmilesAtom[] subAtoms
-
symbol
String symbol
-
valence
int valence
-
-
-
-
Package org.jmol.util
-
Class org.jmol.util.ModulationSet
class ModulationSet extends Vibration implements Serializable-
Serialized Fields
-
axesLengths
float[] axesLengths
unit cell axes -- used in Modulation for calculating magnetic modulations -
enabled
boolean enabled
indicates state of modulated or unmodulated -
fileOcc
double fileOcc
-
gammaE
M3 gammaE
-
gammaIinv
Matrix gammaIinv
-
htUij
Map<String,
Float> htUij current value of anisotropic parameter modulation -
id
String id
an identifier for this modulation -
iop
int iop
the symmetry operation used to generate this atom -
isCommensurate
boolean isCommensurate
commensurate modulations cannot be "undone" and they cannot be turned off -
isQ
boolean isQ
-
isSubsystem
boolean isSubsystem
subsystems can deliver their own unique unit cell; they are commensurate -
modCalc
ModulationSet modCalc
modCalc is used for calculations independent of what the current setting is -
mods
Lst<Modulation> mods
the list of all modulations associated with this atom -
mxyz
V3 mxyz
the modulated magnetic spin -
nOps
int nOps
the number of operators in this space group -- needed for occupancy calculation -
occAbsolute
boolean occAbsolute
for Crenels (simple occupational modulation or Legendre displacement modulation, the value determined here is absolute (0 or 1), not an adjustment; set in calculate() by one of the modulations -
occParams
double[] occParams
-
occSiteMultiplicity
double occSiteMultiplicity
-
ptTemp
P3 ptTemp
-
qtOffset
P3 qtOffset
-
r0
P3 r0
the unmodulated original position of this atom; note that x,y,z extended from Vibration(V3) is the current displacement modulation itself -
rI
Matrix rI
-
rsvs
Matrix rsvs
the matrix representation for this atom's symmetry operation -
scale
float scale
an adjustable scaling factor, as for vibrations -
sigma
Matrix sigma
-
spinOp
float spinOp
the spin operation for this atom: +1/0/-1 -
strop
String strop
a string description of the atom's symmetry operator -
symmetry
SymmetryInterface symmetry
the space group appropriate to this atom -
tau
Matrix tau
-
tFactorInv
Matrix tFactorInv
-
v0
V3 v0
-
vib
Vibration vib
vib is a spin vector when the model has modulation; otherwise an unmodulated vibration. -
vOcc
float vOcc
the current value of the occupancy modulation
-
-
-
Class org.jmol.util.Point3fi
class Point3fi extends P3 implements Serializable-
Serialized Fields
-
i
int i
index in full collection -
mi
short mi
model index -- may be to a trajectory -
sD
short sD
screen diameter -
sX
int sX
screen X -
sY
int sY
screen Y -
sZ
int sZ
screen Z
-
-
-
Class org.jmol.util.Vibration
class Vibration extends V3 implements Serializable-
Serialized Fields
-
modDim
int modDim
modDim will be > 0 for modulation -
modScale
float modScale
-
showTrace
boolean showTrace
-
trace
P3[] trace
-
tracePt
int tracePt
-
-
-
-
Package org.jmol.viewer
-
Exception Class org.jmol.viewer.JmolAsyncException
class JmolAsyncException extends IOException implements Serializable-
Serialized Fields
-
fileName
String fileName
-
-
-
-
Package org.openscience.jmol.app
-
Class org.openscience.jmol.app.Jmol
class Jmol extends JmolPanel implements Serializable
-
-
Package org.openscience.jmol.app.janocchio
-
Class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
class CoupleColourSelectionPanel extends JPanel implements Serializable-
Serialized Fields
-
coupleTable
CoupleTable coupleTable
-
jLabel1
JLabel jLabel1
-
jLabel2
JLabel jLabel2
-
redField
JTextField redField
-
redLabel
JLabel redLabel
-
setAllButton
JButton setAllButton
-
yellowField
JTextField yellowField
-
yellowLabel
JLabel yellowLabel
-
-
-
Class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
class CoupleParameterSelectionPanel extends JPanel implements Serializable-
Serialized Fields
-
chButtonGroup
ButtonGroup chButtonGroup
-
coupleTable
CoupleTable coupleTable
-
eq0RadioButton
JRadioButton eq0RadioButton
-
eq1RadioButton
JRadioButton eq1RadioButton
-
eq2RadioButton
JRadioButton eq2RadioButton
-
eq3RadioButton
JRadioButton eq3RadioButton
-
jLabel1
JLabel jLabel1
-
jLabel2
JLabel jLabel2
-
jLabel3
JLabel jLabel3
-
jLabel4
JLabel jLabel4
-
titleLabel
JLabel titleLabel
-
-
-
Class org.openscience.jmol.app.janocchio.CoupleTable
class CoupleTable extends JTabbedPane implements Serializable-
Serialized Fields
-
calcProps
NmrMolecule calcProps
-
CHequation
String CHequation
-
colorCellRenderer
org.openscience.jmol.app.janocchio.NMRTableCellRenderer colorCellRenderer
-
coupleAddAllButton
JButton coupleAddAllButton
-
coupleColourSelectionPanel
CoupleColourSelectionPanel coupleColourSelectionPanel
-
coupledeleteAllButton
JButton coupledeleteAllButton
-
coupledeleteButton
JButton coupledeleteButton
-
coupleSelection
ListSelectionModel coupleSelection
-
coupleTable
JTable coupleTable
-
coupleTableModel
org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel coupleTableModel
-
degtorad
double degtorad
-
expCouples
String[][] expCouples
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
labelArray
String[] labelArray
-
molCDKuptodate
boolean molCDKuptodate
-
natomsPerModel
int natomsPerModel
-
nmrPanel
NMR_JmolPanel nmrPanel
-
redValue
double redValue
-
selectedCoupleRow
int[] selectedCoupleRow
-
viewer
NMR_Viewer viewer
-
yellowValue
double yellowValue
-
-
-
Class org.openscience.jmol.app.janocchio.FrameCounter
class FrameCounter extends JPanel implements Serializable-
Serialized Fields
-
field
JTextField field
-
frameCount
int frameCount
-
frameNumber
int frameNumber
-
label
JLabel label
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
class FrameDeltaDisplay extends JPanel implements Serializable-
Serialized Fields
-
coupleWeight
double coupleWeight
-
coupleWeightField
JTextField coupleWeightField
-
frameDeltaCouple
double frameDeltaCouple
-
frameDeltaNoe
double frameDeltaNoe
-
label
JLabel label
-
noeWeight
double noeWeight
-
noeWeightField
JTextField noeWeightField
-
totalfield
JTextField totalfield
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.LabelSetter
class LabelSetter extends JPanel implements Serializable-
Serialized Fields
-
coupleTable
CoupleTable coupleTable
-
field
JTextField field
-
label
JLabel label
-
labelArray
String[] labelArray
-
minindex
int minindex
-
noeTable
NoeTable noeTable
-
selectedAtomIndex
int selectedAtomIndex
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.NamfisReader
class NamfisReader extends JPanel implements Serializable -
Class org.openscience.jmol.app.janocchio.NamfisSaver
class NamfisSaver extends JPanel implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
class NMR_DisplayPanel extends DisplayPanel implements Serializable-
Serialized Fields
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
guimap
NmrGuiMap guimap
-
populationDisplay
PopulationDisplay populationDisplay
-
status
StatusBar status
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel
class NMR_JmolPanel extends JmolPanel implements Serializable-
Serialized Fields
-
coupleTable
CoupleTable coupleTable
-
exportChooser
JFileChooser exportChooser
-
frameCounter
FrameCounter frameCounter
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
htMessageCallbacks
Map<String,
Thread> htMessageCallbacks -
isApplet
boolean isApplet
-
labelSetter
LabelSetter labelSetter
-
mainSplitPane
JSplitPane mainSplitPane
-
nmrApplet
NmrApplet nmrApplet
-
nmrDisplay
NMR_DisplayPanel nmrDisplay
-
nmrguimap
NmrGuiMap nmrguimap
-
noeTable
NoeTable noeTable
-
openChooser
FileChooser openChooser
-
populationDisplay
PopulationDisplay populationDisplay
-
readNamfisChooser
JFileChooser readNamfisChooser
-
readNmrChooser
JFileChooser readNmrChooser
-
saveNamfisChooser
JFileChooser saveNamfisChooser
-
saveNmrChooser
JFileChooser saveNmrChooser
-
-
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
class DetachAppletAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
class JumpBestFrameAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
class LabelNmrAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
class ReadNamfisAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
class ReadNmrAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
class ReattachAppletAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
class ViewCoupleTableAction extends org.openscience.jmol.app.janocchio.NMR_JmolPanel.MoleculeDependentAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
class ViewNoeTableAction extends org.openscience.jmol.app.janocchio.NMR_JmolPanel.MoleculeDependentAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
class WriteNamfisAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.janocchio.NmrReader
class NmrReader extends JPanel implements Serializable -
Class org.openscience.jmol.app.janocchio.NmrSaver
class NmrSaver extends JPanel implements Serializable -
Class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
class NoeColourSelectionPanel extends JPanel implements Serializable-
Serialized Fields
-
-
Class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
class NoeParameterSelectionPanel extends JPanel implements Serializable-
Serialized Fields
-
cutoffField
JTextField cutoffField
-
cutoffLabel
JLabel cutoffLabel
-
freqField
JTextField freqField
-
freqLabel
JLabel freqLabel
-
noesyComboBox
JComboBox<String> noesyComboBox
-
noesyLabel
JLabel noesyLabel
-
noeTable
NoeTable noeTable
-
refSingleComboBox
JComboBox<String> refSingleComboBox
-
refSingleLabel
JLabel refSingleLabel
-
rhoStarField
JTextField rhoStarField
-
rhoStarLabel
JLabel rhoStarLabel
-
setAllButton
JButton setAllButton
-
tauField
JTextField tauField
-
tauLabel
JLabel tauLabel
-
titleLabel
JLabel titleLabel
-
tMixField
JTextField tMixField
-
tMixLabel
JLabel tMixLabel
-
-
-
Class org.openscience.jmol.app.janocchio.NoeTable
class NoeTable extends JTabbedPane implements Serializable-
Serialized Fields
-
calcProps
NmrMolecule calcProps
-
colorCellRenderer
org.openscience.jmol.app.janocchio.NMRTableCellRenderer colorCellRenderer
-
cutoff
double cutoff
-
expDists
String[][] expDists
-
expNoes
String[][] expNoes
-
expOrDistButton
JComboBox<String> expOrDistButton
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
freq
double freq
-
labelArray
String[] labelArray
-
lexpNoes
boolean lexpNoes
-
lrefSingle
boolean lrefSingle
-
molCDKuptodate
boolean molCDKuptodate
-
natomsPerModel
int natomsPerModel
-
nmrPanel
NMR_JmolPanel nmrPanel
-
noeColourSelectionPanel
NoeColourSelectionPanel noeColourSelectionPanel
-
noedeleteAllButton
JButton noedeleteAllButton
-
noedeleteButton
JButton noedeleteButton
-
noeExprefValue
double noeExprefValue
-
noeNPrefIndices
int[] noeNPrefIndices
-
noeNPrefValue
double noeNPrefValue
-
noeParameterSelectionPanel
NoeParameterSelectionPanel noeParameterSelectionPanel
-
noeSelection
ListSelectionModel noeSelection
-
noesetRefButton
JButton noesetRefButton
-
noesy
boolean noesy
-
noeTable
JTable noeTable
-
noeTableModel
org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel noeTableModel
-
redValue
double redValue
-
rhoStar
double rhoStar
-
selectedNoeRow
int[] selectedNoeRow
-
tau
double tau
-
tMix
double tMix
-
viewer
NMR_Viewer viewer
-
yellowValue
double yellowValue
-
-
-
Class org.openscience.jmol.app.janocchio.PopulationDisplay
class PopulationDisplay extends JPanel implements Serializable-
Serialized Fields
-
field
JTextField field
-
frameNumber
int frameNumber
-
imaxp
int imaxp
-
label
JLabel label
-
maxp
double maxp
-
population
double[] population
-
populationFrames
JCheckBox populationFrames
-
storedFrameNumber
int storedFrameNumber
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.TableSorter
class TableSorter extends AbstractTableModel implements Serializable-
Serialized Fields
-
columnComparators
Map columnComparators
-
modelToView
int[] modelToView
-
mouseListener
MouseListener mouseListener
-
sortingColumns
List sortingColumns
-
tableHeader
JTableHeader tableHeader
-
tableModel
TableModel tableModel
-
tableModelListener
TableModelListener tableModelListener
-
viewToModel
org.openscience.jmol.app.janocchio.TableSorter.Row[] viewToModel
-
-
-
-
Package org.openscience.jmol.app.jmolpanel
-
Class org.openscience.jmol.app.jmolpanel.AboutDialog
class AboutDialog extends JDialog implements Serializable-
Serialized Fields
-
vwr
JmolViewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.AtomSetChooser
class AtomSetChooser extends JFrame implements Serializable-
Serialized Fields
-
amplitudeSlider
JSlider amplitudeSlider
-
animThread
Thread animThread
-
currentIndex
int currentIndex
-
fpsSlider
JSlider fpsSlider
-
indexes
int[] indexes
Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf. -
infoLabel
JLabel infoLabel
-
periodSlider
JSlider periodSlider
-
propertiesTextArea
JTextArea propertiesTextArea
-
radiusSlider
JSlider radiusSlider
-
radiusValue
int radiusValue
-
repeatCheckBox
JCheckBox repeatCheckBox
-
saveChooser
JFileChooser saveChooser
-
scaleSlider
JSlider scaleSlider
-
selectSlider
JSlider selectSlider
-
tree
JTree tree
-
treeModel
DefaultTreeModel treeModel
-
vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.CreditsDialog
class CreditsDialog extends HelpDialog implements Serializable -
Class org.openscience.jmol.app.jmolpanel.DisplayPanel
class DisplayPanel extends JPanel implements Serializable-
Serialized Fields
-
axesAction
Action axesAction
-
bottomAction
Action bottomAction
-
boundboxAction
Action boundboxAction
-
buttonModelkit
AbstractButton buttonModelkit
-
buttonRotate
AbstractButton buttonRotate
-
defineCenterAction
org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction defineCenterAction
-
deleteAction
Action deleteAction
-
dimSize
Dimension dimSize
-
displaySpeed
String displaySpeed
-
frame
JFrame frame
-
frontAction
Action frontAction
-
haveDisplay
boolean haveDisplay
-
homeAction
org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction homeAction
-
hydrogensAction
Action hydrogensAction
-
jmolPanel
JmolPanel jmolPanel
-
lastMotionEventNumber
int lastMotionEventNumber
-
leftAction
Action leftAction
-
measurementsAction
Action measurementsAction
-
perspectiveAction
Action perspectiveAction
-
rectClip
Rectangle rectClip
-
rightAction
Action rightAction
-
showPaintTime
boolean showPaintTime
-
startupDim
Dimension startupDim
-
timeBegin
long timeBegin
-
toolbarButtonGroup
ButtonGroup toolbarButtonGroup
-
topAction
Action topAction
-
vwr
Viewer vwr
-
xlateAction
Action xlateAction
-
zoomAction
Action zoomAction
-
-
-
Class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
class CheckBoxMenuItemAction extends AbstractAction implements Serializable-
Serialized Fields
-
action
String action
-
-
-
Class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
class MoveToAction extends AbstractAction implements Serializable-
Serialized Fields
-
action
String action
-
-
-
Class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
class SetStatusAction extends AbstractAction implements Serializable-
Serialized Fields
-
statusText
String statusText
-
-
-
Class org.openscience.jmol.app.jmolpanel.GaussianDialog
class GaussianDialog extends JDialog implements Serializable-
Serialized Fields
-
basisBox
JComboBox<String> basisBox
-
charge
String charge
-
chargeSpinner
JSpinner chargeSpinner
-
check
String check
-
checkField
JTextField checkField
-
closeButton
JButton closeButton
-
container
JPanel container
-
dfBox
JComboBox<String> dfBox
-
editArea
JTextPane editArea
-
editPane
JScrollPane editPane
-
file
String file
-
fileButton
JButton fileButton
-
fileChooser
JFileChooser fileChooser
-
fileField
JTextField fileField
-
iscroll
int iscroll
-
mem
String mem
-
memBox
JComboBox<String> memBox
-
meth
String meth
-
methBox
JComboBox<String> methBox
-
mult
String mult
-
multSpinner
JSpinner multSpinner
-
optsField
JTextField optsField
-
proc
String proc
-
procSpinner
JSpinner procSpinner
-
refreshButton
JButton refreshButton
-
route
String route
-
saveButton
JButton saveButton
-
select
String select
-
selectField
JTextField selectField
-
vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.HelpDialog
class HelpDialog extends JDialog implements Serializable-
Serialized Fields
-
html
JEditorPane html
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolJME
class JmolJME extends JME implements Serializable-
Serialized Fields
-
allowClean
boolean allowClean
debug flag; set to false to see an actual 2D structure before SMILES-based cleaning. -
cleaning
boolean cleaning
-
fileName
String fileName
-
headless
boolean headless
allows working headlessly if no frame is defined; set false if a frame is present -
parentWindow
Container parentWindow
-
vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel
class JmolPanel extends JPanel implements Serializable-
Serialized Fields
-
appletContext
String appletContext
-
atomSetChooser
AtomSetChooser atomSetChooser
-
clientService
JsonNioServer clientService
-
commands
Map<String,
Action> commands -
consoleframe
JFrame consoleframe
-
copyImageAction
JmolPanel.CopyImageAction copyImageAction
-
copyScriptAction
JmolPanel.CopyScriptAction copyScriptAction
-
display
DisplayPanel display
-
executeScriptAction
JmolPanel.ExecuteScriptAction executeScriptAction
-
exportAction
JmolPanel.ExportAction exportAction
-
frame
JFrame frame
-
gaussianDialog
GaussianDialog gaussianDialog
-
guimap
GuiMap guimap
-
imageType
String imageType
-
isPlugin
boolean isPlugin
-
jmolApp
JmolApp jmolApp
-
jmolJME
JmolJME jmolJME
-
measurementTable
MeasurementTable measurementTable
-
menubar
JMenuBar menubar
-
menuItems
Map<String,
JMenuItem> menuItems -
modelAdapter
JmolAdapter modelAdapter
-
myStatusListener
StatusListener myStatusListener
-
pasteClipboardAction
JmolPanel.PasteClipboardAction pasteClipboardAction
-
pcs
PropertyChangeSupport pcs
-
pluginMenu
JMenu pluginMenu
-
plugins
Map<String,
JmolPlugin> plugins -
pluginsSet
boolean pluginsSet
-
povrayAction
JmolPanel.PovrayAction povrayAction
-
preferencesDialog
PreferencesDialog preferencesDialog
-
printAction
JmolPanel.PrintAction printAction
-
qualityJPG
int qualityJPG
-
qualityPNG
int qualityPNG
-
recentFiles
org.openscience.jmol.app.jmolpanel.RecentFilesDialog recentFiles
-
serverService
JsonNioServer serverService
-
splash
SplashInterface splash
-
startupHeight
int startupHeight
-
startupWidth
int startupWidth
-
status
StatusBar status
-
surfaceTool
SurfaceTool surfaceTool
-
surfaceToolAction
JmolPanel.SurfaceToolAction surfaceToolAction
-
toolbar
JToolBar toolbar
-
touchHandler
JsonNioClient.TouchHandler touchHandler
-
toWebAction
JmolPanel.ToWebAction toWebAction
-
twoDEditorAction
JmolPanel.TwoDEditorAction twoDEditorAction
-
viewMeasurementTableAction
JmolPanel.ViewMeasurementTableAction viewMeasurementTableAction
-
vwr
Viewer vwr
-
vwrOptions
Map<String,
Object> vwrOptions -
webExport
WebExport webExport
-
windowName
String windowName
-
writeAction
JmolPanel.WriteAction writeAction
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
class AboutAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
class AnimButton extends JmolButton implements Serializable-
Serialized Fields
-
lastPressTime
long lastPressTime
-
script
String script
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
class AtomSetChooserAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
class CloseAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
class ConsoleAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
class CopyImageAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
class CopyScriptAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
class CreditsAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
class ExecuteScriptAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
class ExitAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
class ExportAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
class GaussianAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
class NewAction extends AbstractAction implements Serializable-
Serialized Fields
-
script
String script
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
class NewwinAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
class OpenAction extends JmolPanel.NewAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
class OpenMolAction extends JmolPanel.NewAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
class OpenPdbAction extends JmolPanel.NewAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
class OpenUrlAction extends JmolPanel.NewAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
class PasteClipboardAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
class PovrayAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
class PrintAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
class RecentFilesAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
class ResizeAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
class ScriptEditorAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
class ScriptWindowAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
class SurfaceToolAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
class ToWebAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.TwoDEditorAction
class TwoDEditorAction extends AbstractAction implements Serializable-
Serialized Fields
-
jmolPanel
JmolPanel jmolPanel
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
class UguideAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
class ViewMeasurementTableAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
class WhatsNewAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
class WriteAction extends AbstractAction implements Serializable -
Class org.openscience.jmol.app.jmolpanel.MeasurementTable
class MeasurementTable extends JDialog implements Serializable-
Serialized Fields
-
container
JPanel container
-
deleteAllButton
JButton deleteAllButton
-
deleteButton
JButton deleteButton
-
measurementTable
JTable measurementTable
-
measurementTableModel
org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel measurementTableModel
-
selectedMeasurementRow
int selectedMeasurementRow
-
stringClass
Class<? extends String> stringClass
-
vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.PovrayDialog
class PovrayDialog extends JDialog implements Serializable-
Serialized Fields
-
allFramesCheck
JCheckBox allFramesCheck
-
antiAliasCheck
JCheckBox antiAliasCheck
-
displayWhileRenderingCheck
JCheckBox displayWhileRenderingCheck
-
goButton
JButton goButton
-
imageSizeHeight
JLabel imageSizeHeight
-
imageSizeRatioBox
JCheckBox imageSizeRatioBox
-
imageSizeRatioCombo
JComboBox<String> imageSizeRatioCombo
-
imageSizeTextHeight
JFormattedTextField imageSizeTextHeight
-
imageSizeTextWidth
JFormattedTextField imageSizeTextWidth
-
imageSizeWidth
JLabel imageSizeWidth
-
mosaicPreviewCheck
JCheckBox mosaicPreviewCheck
-
mosaicPreviewComboEnd
JComboBox<String> mosaicPreviewComboEnd
-
mosaicPreviewComboStart
JComboBox<String> mosaicPreviewComboStart
-
mosaicPreviewEnd
JLabel mosaicPreviewEnd
-
mosaicPreviewStart
JLabel mosaicPreviewStart
-
outputAlphaCheck
JCheckBox outputAlphaCheck
-
outputExtension
String outputExtension
-
outputFileType
String outputFileType
-
outputFormatCheck
JCheckBox outputFormatCheck
-
outputFormatCombo
JComboBox<String> outputFormatCombo
-
outputHeight
int outputHeight
-
outputWidth
int outputWidth
-
povrayPathButton
JButton povrayPathButton
-
povrayPathLabel
JTextField povrayPathLabel
-
runPovCheck
JCheckBox runPovCheck
-
saveField
JTextField saveField
-
savePathLabel
JTextField savePathLabel
-
-
-
Class org.openscience.jmol.app.jmolpanel.PreferencesDialog
class PreferencesDialog extends JDialog implements Serializable-
Serialized Fields
-
abNo
JRadioButton abNo
-
abYes
JRadioButton abYes
-
actions
List<Action> actions
-
antialiasDisplay
boolean antialiasDisplay
-
applyButton
JButton applyButton
-
autoBond
boolean autoBond
-
axesOrientationRasmol
boolean axesOrientationRasmol
-
bButton
JButton bButton
-
bdSlider
JSlider bdSlider
-
bondingVersion
int bondingVersion
-
bondTolerance
float bondTolerance
-
btSlider
JSlider btSlider
-
bwSlider
JSlider bwSlider
-
cancelButton
JButton cancelButton
-
cbAntialias
JCheckBox cbAntialias
-
cbAxesOrientationRasmol
JCheckBox cbAxesOrientationRasmol
-
cbClearHistory
JCheckBox cbClearHistory
-
cbMeasureAngstroms
JCheckBox cbMeasureAngstroms
-
cbOpenFilePreview
JCheckBox cbOpenFilePreview
-
cbPerspectiveDepth
JCheckBox cbPerspectiveDepth
-
cbShowAxes
JCheckBox cbShowAxes
-
cbShowBoundingBox
JCheckBox cbShowBoundingBox
-
cH
JCheckBox cH
-
checkBoxListener
ItemListener checkBoxListener
-
clearHistory
boolean clearHistory
-
cM
JCheckBox cM
-
commands
Map<String,
Action> commands -
currentProperties
Properties currentProperties
-
eButton
JButton eButton
-
fontScale
int fontScale
-
guimap
GuiMap guimap
-
jmol
JmolPanel jmol
-
jmolDefaultProperties
Properties jmolDefaultProperties
-
jmolDefaultsButton
JButton jmolDefaultsButton
-
marBond
short marBond
-
measureAngstroms
boolean measureAngstroms
-
minBondDistance
float minBondDistance
-
okButton
JButton okButton
-
openFilePreview
boolean openFilePreview
-
pButton
JButton pButton
-
percentVdwAtom
int percentVdwAtom
-
perspectiveDepth
boolean perspectiveDepth
-
prefsAction
org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction prefsAction
-
rasmolDefaultsButton
JButton rasmolDefaultsButton
-
showAxes
boolean showAxes
-
showBoundingBox
boolean showBoundingBox
-
showHydrogens
boolean showHydrogens
-
showMeasurements
boolean showMeasurements
-
tButton
JButton tButton
-
vButton
JButton vButton
-
vdwPercentSlider
JSlider vdwPercentSlider
-
vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.Splash
class Splash extends Window implements Serializable -
Class org.openscience.jmol.app.jmolpanel.StatusBar
class StatusBar extends JPanel implements Serializable-
Serialized Fields
-
status
JLabel[] status
-
-
-
Class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
class WhatsNewDialog extends HelpDialog implements Serializable
-
-
Package org.openscience.jmol.app.jmolpanel.console
-
Class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
class ConsoleTextArea extends JTextArea implements Serializable
-
-
Package org.openscience.jmol.app.jsonkiosk
-
Class org.openscience.jmol.app.jsonkiosk.BannerFrame
class BannerFrame extends JFrame implements Serializable-
Serialized Fields
-
bannerLabel
JLabel bannerLabel
-
-
-
Class org.openscience.jmol.app.jsonkiosk.KioskFrame
class KioskFrame extends JFrame implements Serializable
-
-
Package org.openscience.jmol.app.webexport
-
Class org.openscience.jmol.app.webexport.Orbitals
class Orbitals extends JPanel implements Serializable -
Class org.openscience.jmol.app.webexport.Test
class Test extends JPanel implements Serializable- serialVersionUID:
- 1L
-
Serialized Fields
-
appletPath
JTextField appletPath
-
arrayListHandler
org.openscience.jmol.app.webexport.ArrayListTransferHandler arrayListHandler
-
fc
JFileChooser fc
-
FileButton
JButton FileButton
-
movetoTime
JButton movetoTime
-
PathButton
JButton PathButton
-
StateButton
JButton StateButton
-
StringtoScriptButton
JButton StringtoScriptButton
-
vwr
Viewer vwr
-
-
Class org.openscience.jmol.app.webexport.WebExport
class WebExport extends JPanel implements Serializable
-