Uses of Class
javajs.util.V3
Packages that use V3
Package
Description
-
Uses of V3 in com.sparshui.common
Methods in com.sparshui.common that return V3 -
Uses of V3 in javajs.api
Methods in javajs.api with parameters of type V3Modifier and TypeMethodDescriptionvoid
EigenInterface.fillFloatArrays
(V3[] eigenVectors, float[] eigenValues) -
Uses of V3 in javajs.util
Fields in javajs.util declared as V3Methods in javajs.util that return V3Modifier and TypeMethodDescriptionQuat.get3dProjection
(V3 v3d) Quat.getNormal()
Quat.getNormalDirected
(V3 v0) Quat.getVector
(int i) Quat.getVectorScaled
(int i, float scale) static V3
V3.new3
(float x, float y, float z) static V3
static V3
Methods in javajs.util with parameters of type V3Modifier and TypeMethodDescriptionfinal float
Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].static void
Measure.calcBestAxisThroughPoints
(P3[] points, int nPoints, P3 axisA, V3 axisUnitVector, V3 vectorProjection, int nTriesMax) static float
static float
Measure.distanceToPlaneV
(V3 norm, float w, P3 pt) void
Eigen.fillFloatArrays
(V3[] eigenVectors, float[] eigenValues) Specifically for 3x3 systems, returns eigenVectors as V3[3] and values as float[3]; sorted from smallest to largest value.static float
Quat.get3dProjection
(V3 v3d) static void
static float
static P3
Calculate the intersection of a line with a plane.Quat.getNormalDirected
(V3 v0) static boolean
Measure.getNormalFromCenter
(P3 ptCenter, P3 ptA, P3 ptB, P3 ptC, boolean isOutward, V3 normal, V3 vTemp) static void
Measure.getNormalToLine
(P3 pointA, P3 pointB, V3 vNormNorm) static float
Measure.getPlaneProjection
(T3 pt, P4 plane, T3 retPtProj, V3 retNorm) Project a point onto a plane, also returning the normal vector and the directed distance to the plane.static void
Measure.getPlaneThroughPoint
(T3 pt, V3 normal, P4 plane) static P4
static P3[]
Measure.getProjectedLineSegment
(P3[] points, int nPoints, P3 ptA, V3 unitVector, V3 vTemp) static final Quat
Quat.getQuaternionFrameV
(V3 vA, V3 vB, V3 vC, boolean yBased) Create a quaternion based on a framefloat
Quat.getThetaDirectedV
(V3 vector) static boolean
Measure.isInTetrahedron
(P3 pt, P3 ptA, P3 ptB, P3 ptC, P3 ptD, P4 plane, V3 vTemp, V3 vTemp2, boolean fullyEnclosed) static boolean
static A4
Constructs and initializes an AxisAngle4f from the specified axis and angle.static float
Measure.projectOntoAxis
(P3 pt, P3 ptA, V3 axisUnitVector, V3 vectorProjection) 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 vectorProjectionfinal void
Sets the value of this AxisAngle4f to the specified axis and angle. -
Uses of V3 in org.jmol.adapter.smarter
Fields in org.jmol.adapter.smarter declared as V3Methods in org.jmol.adapter.smarter that return V3Modifier and TypeMethodDescriptionAtomSetCollection.addVibrationVector
(int iatom, float x, float y, float z) protected V3[]
AtomSetCollectionReader.read3Vectors
(boolean isBohr) read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block -
Uses of V3 in org.jmol.api
Methods in org.jmol.api that return V3Modifier and TypeMethodDescriptionabstract V3
JmolViewer.getBoundBoxCornerVector()
JmolModulationSet.getV3()
JmolAdapterAtomIterator.getVib()
V3[]
SymmetryInterface.rotateAxes
(int iop, V3[] axes, P3 ptTemp, M3 mTemp) Methods in org.jmol.api with parameters of type V3Modifier and TypeMethodDescriptionfloat
JmolNMRInterface.getDipolarCouplingHz
(Atom a1, Atom a2, V3 vField) void
JmolNavigatorInterface.navigateAxis
(V3 rotAxis, float degrees) V3[]
SymmetryInterface.rotateAxes
(int iop, V3[] axes, P3 ptTemp, M3 mTemp) -
Uses of V3 in org.jmol.export
Fields in org.jmol.export declared as V3 -
Uses of V3 in org.jmol.jvxl.api
Methods in org.jmol.jvxl.api with parameters of type V3Modifier and TypeMethodDescriptionint
VertexDataServer.getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vertexA, int vertexB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn) 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. -
Uses of V3 in org.jmol.jvxl.calc
Fields in org.jmol.jvxl.calc declared as V3Modifier and TypeFieldDescriptionprotected static final V3[]
MarchingCubes.cubeVertexVectors
protected final V3[]
MarchingCubes.edgeVectors
protected final V3[]
MarchingCubes.voxelVertexVectors
-
Uses of V3 in org.jmol.jvxl.data
Fields in org.jmol.jvxl.data declared as V3Modifier and TypeFieldDescriptionV3[]
VolumeData.oabc
final V3[]
VolumeData.unitVolumetricVectors
final V3[]
VolumeData.volumetricVectors
Methods in org.jmol.jvxl.data with parameters of type V3 -
Uses of V3 in org.jmol.jvxl.readers
Fields in org.jmol.jvxl.readers declared as V3Methods in org.jmol.jvxl.readers that return V3Methods in org.jmol.jvxl.readers with parameters of type V3Modifier and TypeMethodDescriptionprotected float
SurfaceReader.getSPF
(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, T3 ptReturn) protected float
JvxlXmlReader.getSurfacePointAndFraction
(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, T3 ptReturn) protected float
SurfaceReader.getSurfacePointAndFraction
(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, T3 ptReturn) int
SurfaceReader.getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vA, int vB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn) -
Uses of V3 in org.jmol.modelset
Fields in org.jmol.modelset declared as V3Methods in org.jmol.modelset that return V3Modifier and TypeMethodDescriptionModelSet.calculateMolecularDipole
(int modelIndex, BS bsAtoms) ModelSet.getBoundBoxCornerVector()
ModelSet.getModelDipole
(int modelIndex) Methods in org.jmol.modelset with parameters of type V3Modifier and TypeMethodDescriptionModelSet.addAtom
(int modelIndex, Group group, int atomicAndIsotopeNumber, String atomName, String atomType, int atomSerial, int atomSeqID, int atomSite, P3 xyz, float radius, V3 vib, int formalCharge, float partialCharge, float occupancy, float bfactor, Lst<Object> tensors, boolean isHetero, byte specialAtomID, BS atomSymmetry, float bondRadius) AtomCollection.getHybridizationAndAxes
(int atomIndex, int atomicNumber, V3 z, V3 x, String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ, boolean isQuick, T3 ref) void
ModelSet.moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, BS bs, P3 center, boolean isInternal, boolean translationOnly) -
Uses of V3 in org.jmol.modelsetbio
Fields in org.jmol.modelsetbio declared as V3Modifier and TypeFieldDescriptionprotected V3
ProteinStructure.axisUnitVector
protected V3
ProteinStructure.vectorProjection
protected V3[]
BioPolymer.wingVectors
Methods in org.jmol.modelsetbio that return V3Methods in org.jmol.modelsetbio with parameters of type V3Modifier and TypeMethodDescriptionprotected P3
AlphaPolymer.getControlPoint
(int i, V3 v) protected P3
BioPolymer.getControlPoint
(int i, V3 v) boolean
AminoMonomer.getNHPoint
(P3 aminoHydrogenPoint, V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens) void
-
Uses of V3 in org.jmol.quantum
Methods in org.jmol.quantum with parameters of type V3Modifier and TypeMethodDescriptionfloat
NMRCalculation.getDipolarCouplingHz
(Atom a1, Atom a2, V3 vField) -
Uses of V3 in org.jmol.render
Fields in org.jmol.render declared as V3 -
Uses of V3 in org.jmol.renderbio
Fields in org.jmol.renderbio declared as V3Modifier and TypeFieldDescriptionprotected V3[]
BioShapeRenderer.wingVectors
protected V3[]
BioShapeRenderer.wingVectors
protected V3[]
BioShapeRenderer.wingVectors
protected V3[]
BioShapeRenderer.wingVectors
protected V3[]
BioShapeRenderer.wingVectors
protected V3[]
BioShapeRenderer.wingVectors
protected V3[]
BioShapeRenderer.wingVectors
-
Uses of V3 in org.jmol.renderspecial
Fields in org.jmol.renderspecial declared as V3 -
Uses of V3 in org.jmol.script
Methods in org.jmol.script with parameters of type V3 -
Uses of V3 in org.jmol.shape
Fields in org.jmol.shape declared as V3Methods in org.jmol.shape that return V3Modifier and TypeMethodDescriptionV3[]
Mesh.getNormals
(T3[] vertices, P4 plane) V3[]
Mesh.getNormalsTemp()
Methods in org.jmol.shape with parameters of type V3Modifier and TypeMethodDescriptionshort[]
Mesh.setNormixes
(V3[] normals) protected void
Mesh.sumVertexNormals
(T3[] vertices, V3[] normals) protected static void
Mesh.sumVertexNormals2
(Mesh m, T3[] vertices, V3[] normals) -
Uses of V3 in org.jmol.shapebio
Fields in org.jmol.shapebio declared as V3 -
Uses of V3 in org.jmol.shapespecial
Fields in org.jmol.shapespecial declared as V3Methods in org.jmol.shapespecial with parameters of type V3Modifier and TypeMethodDescriptionstatic void
Ellipsoid.getEquationForQuadricWithCenter
(float x, float y, float z, M3 mToElliptical, V3 vTemp, M3 mTemp, double[] coef, M4 mDeriv) -
Uses of V3 in org.jmol.shapesurface
Methods in org.jmol.shapesurface with parameters of type V3Modifier and TypeMethodDescriptionint
Isosurface.getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vA, int vB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn) protected void
IsosurfaceMesh.sumVertexNormals
(T3[] vertices, V3[] vectorSums) -
Uses of V3 in org.jmol.symmetry
Fields in org.jmol.symmetry declared as V3Methods in org.jmol.symmetry that return V3Modifier and TypeMethodDescriptionSymmetryOperation.getOpAxis()
SymmetryOperation.getOpTrans()
V3[]
Symmetry.rotateAxes
(int iop, V3[] axes, P3 ptTemp, M3 mTemp) Methods in org.jmol.symmetry with parameters of type V3Modifier and TypeMethodDescriptionstatic void
SymmetryOperation.normalize12ths
(V3 vtrans) V3[]
Symmetry.rotateAxes
(int iop, V3[] axes, P3 ptTemp, M3 mTemp) -
Uses of V3 in org.jmol.util
Subclasses of V3 in org.jmol.utilModifier and TypeClassDescriptionclass
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 occupancyclass
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.Fields in org.jmol.util declared as V3Modifier and TypeFieldDescriptionV3[]
Tensor.eigenVectors
ModulationSet.mxyz
the modulated magnetic spinV3[]
MeshSurface.normalsTemp
V3[]
MeshSurface.oabc
protected V3[]
GData.transformedVectors
Methods in org.jmol.util that return V3Modifier and TypeMethodDescriptionBoxInfo.getBoundBoxCornerVector()
GData.getLightSource()
V3[]
GData.getTransformedVertexVectors()
ModulationSet.getV3()
static V3
Geodesic.getVertexVector
(int i) static V3[]
Geodesic.getVertexVectors()
static V3[]
Normix.getVertexVectors()
Methods in org.jmol.util with parameters of type V3Modifier and TypeMethodDescriptionstatic void
SimpleUnitCell.fillParams
(V3 va, V3 vb, V3 vc, float[] p) static short
Normix.get2SidedNormix
(V3 v, BS bsTemp) static short
Normix.getNormixV
(V3 v, BS bsTemp) P3[]
Triangulator.intersectLine
(P3[] points, int nPoints, P3 ptA, V3 unitVector) Tensor.setFromAxes
(V3[] axes) Standard constructor for ellipsoids based on axes -
Uses of V3 in org.jmol.viewer
Fields in org.jmol.viewer declared as V3Modifier and TypeFieldDescriptionstatic final V3
JC.axisNX
static final V3
JC.axisNY
static final V3
JC.axisNZ
static final V3
JC.axisX
static final V3
JC.axisY
static final V3
JC.axisZ
static final V3
JC.center
protected V3
TransformManager.internalTranslation
static final V3[]
protected final V3
TransformManager.vectorTemp
Methods in org.jmol.viewer that return V3Modifier and TypeMethodDescriptionViewer.calculateMolecularDipole
(BS bsAtoms) Viewer.getBoundBoxCornerVector()
Viewer.getModelDipole()
Methods in org.jmol.viewer with parameters of type V3Modifier and TypeMethodDescriptionViewer.getHybridizationAndAxes
(int atomIndex, V3 z, V3 x, String lcaoType) boolean
TransformManager.isInPosition
(V3 axis, float degrees) void
Viewer.move
(JmolScriptEvaluator eval, V3 dRot, float dZoom, V3 dTrans, float dSlab, float floatSecondsTotal, int fps) void
Viewer.moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly, boolean useModelKit) void
Viewer.moveTo
(JmolScriptEvaluator eval, float floatSecondsTotal, P3 center, V3 rotAxis, float degrees, M3 rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY) void
TransformManager.navigateAxis
(V3 rotAxis, float degrees) scripted entry point for navigationvoid
Viewer.navigateAxis
(V3 rotAxis, float degrees) boolean
Viewer.rotateAboutPointsInternal
(JmolScriptEvaluator eval, P3 point1, P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, V3 translation, Lst<P3> finalPoints, float[] dihedralList, M4 m4, boolean useModelKit) void
TransformManager.rotateAxisAngle
(V3 rotAxis, float radians) boolean
Viewer.rotateAxisAngleAtCenter
(JmolScriptEvaluator eval, P3 rotCenter, V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected) -
Uses of V3 in org.openscience.jvxl.simplewriter
Methods in org.openscience.jvxl.simplewriter with parameters of type V3