Uses of Class
javajs.util.M4
Packages that use M4
Package
Description
Provides a software implementation of complete 3D graphics engine
for rendering molecules and associated shapes.
-
Uses of M4 in javajs.util
Methods in javajs.util that return M4Modifier and TypeMethodDescriptionM4.invert()
Sets the value of this matrix to its inverse.static M4
M4.newA16
(float[] v) Constructs and initializes a Matrix4f from the specified 16 element array.static M4
Constructs a new matrix with the same values as the Matrix4f parameter.static M4
Constructs and initializes a Matrix4f from the rotation matrix and translation.M4.round
(float f) M4.setAsXYRotation
(float angle) Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.M4.setAsXZRotation
(float angle) Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.M4.setAsYZRotation
(float angle) Sets the value of this matrix to a rotation matrix about the w axis by the passed angle.Sets the value of this matrix to a copy of the passed matrix m1.Methods in javajs.util with parameters of type M4Modifier and TypeMethodDescriptionstatic float
Fills a 4x4 matrix with rotation-translation of mapped points A to B.void
Sets the value of this matrix to the result of multiplying itself with matrix m1.void
Sets the value of this matrix to the result of multiplying the two argument matrices together.static M4
Constructs a new matrix with the same values as the Matrix4f parameter.Sets the value of this matrix to a copy of the passed matrix m1.void
Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).Measure.transformPoints
(Lst<P3> vPts, M4 m4, P3 center) -
Uses of M4 in org.jmol.adapter.readers.cif
Methods in org.jmol.adapter.readers.cif with parameters of type M4 -
Uses of M4 in org.jmol.adapter.smarter
Fields in org.jmol.adapter.smarter with type parameters of type M4Methods in org.jmol.adapter.smarter with parameters of type M4 -
Uses of M4 in org.jmol.api
Methods in org.jmol.api that return M4Modifier and TypeMethodDescriptionM4[]
SymmetryInterface.getAdditionalOperations()
SymmetryInterface.getSpaceGroupOperation
(int i) M4[]
SymmetryInterface.getSymmetryOperations()
SymmetryInterface.getTransform
(P3 fracA, P3 fracB, boolean debug) SymmetryInterface.replaceTransformMatrix
(M4 trm) SymmetryInterface.staticGetMatrixTransform
(String cleg) Methods in org.jmol.api with parameters of type M4Modifier and TypeMethodDescriptionint
SymmetryInterface.addBioMoleculeOperation
(M4 mat, boolean isReverse) SymmetryInterface.convertTransform
(String transform, M4 trm) void
JmolRendererInterface.fillEllipsoid
(P3 center, P3[] points, int x, int y, int z, int diameter, M3 mToEllipsoidal, double[] coef, M4 mDeriv, int selectedOctant, P3[] octantPoints) void
SymmetryInterface.getEquivPointList
(Lst<P3> pts, int nIgnore, String flags, M4[] opsCtr) T3[]
void
SymmetryInterface.newSpaceGroupPoint
(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint) SymmetryInterface.replaceTransformMatrix
(M4 trm) SymmetryInterface.staticConvertOperation
(String string, M4 matrix) -
Uses of M4 in org.jmol.atomdata
Methods in org.jmol.atomdata with parameters of type M4Modifier and TypeMethodDescriptionvoid
AtomData.transformXYZ
(M4 mat, BS bs) allow for transformed XYZ -
Uses of M4 in org.jmol.export
Fields in org.jmol.export declared as M4Methods in org.jmol.export with parameters of type M4Modifier and TypeMethodDescriptionvoid
Export3D.fillEllipsoid
(P3 center, P3[] points, int x, int y, int z, int diameter, M3 mToEllipsoidal, double[] coef, M4 mDeriv, int selectedOctant, P3[] octantPoints) protected void
__CartesianExporter.setSphereMatrix
(T3 center, float rx, float ry, float rz, A4 a, M4 sphereMatrix) -
Uses of M4 in org.jmol.g3d
Methods in org.jmol.g3d with parameters of type M4 -
Uses of M4 in org.jmol.jvxl.readers
Fields in org.jmol.jvxl.readers declared as M4 -
Uses of M4 in org.jmol.modelset
Fields in org.jmol.modelset declared as M4Modifier and TypeFieldDescriptionModel.mat4
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelectedMethods in org.jmol.modelset that return M4Methods in org.jmol.modelset with parameters of type M4 -
Uses of M4 in org.jmol.script
Methods in org.jmol.script that return M4Modifier and TypeMethodDescriptionstatic M4
ScriptMathProcessor.getMatrix4f
(M3 matRotate, T3 vTranslate) Methods in org.jmol.script with parameters of type M4Modifier and TypeMethodDescriptionboolean
static double
Fills a 4x4 matrix with rotation-translation of mapped points A to B.ScriptParam.transformPoints
(Lst<P3> vPts, M4 m4, P3 center) -
Uses of M4 in org.jmol.scriptext
Methods in org.jmol.scriptext with parameters of type M4Modifier and TypeMethodDescriptionfloat
SmilesExt.getSmilesCorrelation
(BS bsA, BS bsB, String smiles, Lst<P3> ptsA, Lst<P3> ptsB, M4 m4, Lst<BS> vReturn, boolean asMap, int[][] mapSet, P3 center, boolean bestMap, int flags) The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.float
SmilesExt.mapPolyhedra
(int i1, int i2, boolean isSmiles, M4 m) -
Uses of M4 in org.jmol.shape
Fields in org.jmol.shape declared as M4 -
Uses of M4 in org.jmol.shapespecial
Methods in org.jmol.shapespecial with parameters of type M4Modifier and TypeMethodDescriptionstatic void
Ellipsoid.getEquationForQuadricWithCenter
(float x, float y, float z, M3 mToElliptical, V3 vTemp, M3 mTemp, double[] coef, M4 mDeriv) -
Uses of M4 in org.jmol.shapesurface
Methods in org.jmol.shapesurface with parameters of type M4Modifier and TypeMethodDescriptionvoid
IsosurfaceMesh.updateCoordinates
(M4 m, BS bs) bs will be null if this is a set from the new isosurface MOVE [mat4] command -
Uses of M4 in org.jmol.symmetry
Subclasses of M4 in org.jmol.symmetryFields in org.jmol.symmetry declared as M4Methods in org.jmol.symmetry that return M4Modifier and TypeMethodDescriptionCLEG.ClegData.addSGTransform
(String tr, String what) M4[]
Symmetry.getAdditionalOperations()
static M4
SymmetryOperation.getMatrixFromXYZ
(String xyz, float[] v, boolean halfOrLess) HallInfo.HallReceiver.getMatrixOperation
(int k) Get the 4x4 matrix for the kth operation.SpaceGroup.getMatrixOperation
(int i) Symmetry.getSpaceGroupOperation
(int i) Symmetry.getTransform
(P3 fracA, P3 fracB, boolean best) SymmetryDesc.getTransform
(UnitCell uc, SymmetryOperation[] ops, P3 fracA, P3 fracB, boolean best) Symmetry.replaceTransformMatrix
(M4 trm) Symmetry.staticGetMatrixTransform
(String cleg) static M4
Methods in org.jmol.symmetry with parameters of type M4Modifier and TypeMethodDescriptionint
Symmetry.addBioMoleculeOperation
(M4 mat, boolean isReverse) boolean
HallInfo.HallReceiver.addHallOperationCheckDuplicates
(M4 operation) Add a (possibly) new operation, checking for duplicates.boolean
SpaceGroup.addHallOperationCheckDuplicates
(M4 operation) Symmetry.convertTransform
(String transform, M4 trm) void
Symmetry.getEquivPointList
(Lst<P3> pts, int nInitial, String flags, M4[] opsCtr) static T3[]
UnitCell.getMatrixAndUnitCell
(SimpleUnitCell uc, Object def, M4 retMatrix) T3[]
static final String
SymmetryOperation.getXYZFromMatrix
(M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess) static final String
SymmetryOperation.getXYZFromMatrixFrac
(M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess, boolean allowFractions) void
Symmetry.newSpaceGroupPoint
(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint) static void
SymmetryOperation.normalizeOperationToCentroid
(int dim, M4 m, P3[] fracPts, int i0, int n) Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.Symmetry.replaceTransformMatrix
(M4 trm) Symmetry.staticConvertOperation
(String xyz, M4 matrix) static M4
void
Symmetry.transformUnitCell
(M4 trm) -
Uses of M4 in org.jmol.util
Fields in org.jmol.util declared as M4Modifier and TypeFieldDescriptionMeshSurface.mat4
SimpleUnitCell.matrixCartesianToFractional
protected M4
SimpleUnitCell.matrixCtoFNoOffset
SimpleUnitCell.matrixFractionalToCartesian
protected M4
SimpleUnitCell.matrixFtoCNoOffset
Methods in org.jmol.util with parameters of type M4Modifier and TypeMethodDescriptionint
Shader.getEllipsoidShade
(float x, float y, float z, int radius, M4 mDeriv) void
SimpleUnitCell.toFractionalM
(M4 m) -
Uses of M4 in org.jmol.viewer
Fields in org.jmol.viewer declared as M4Modifier and TypeFieldDescriptionprotected final M4
TransformManager.matrixTemp
final M4
TransformManager.matrixTransform
final M4
TransformManager.matrixTransformInv
Methods in org.jmol.viewer with parameters of type M4Modifier and TypeMethodDescriptionvoid
Viewer.moveAtoms
(M4 m4, M3 mNew, M3 rotation, V3 translation, P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly, boolean useModelKit) void
ShapeManager.notifyAtomPositionsChanged
(int baseModel, BS bs, M4 mat) 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, P3[][] centerAndPoints) void
TransformManager.rotateAxisAngleRadiansInternal
(float radians, BS bsAtoms, M4 m4, boolean useModelKit) void
TransformManager4D.setAsBallRotation
(M4 m, float scale, float dx, float dy, float dz) 4D ball rotation from nominal dx, dy, dz motion.