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.
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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 M4M4.newA16(float[] v) Constructs and initializes a Matrix4f from the specified 16 element array.static M4Constructs a new matrix with the same values as the Matrix4f parameter.static M4Constructs 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 floatFills a 4x4 matrix with rotation-translation of mapped points A to B.voidSets the value of this matrix to the result of multiplying itself with matrix m1.voidSets the value of this matrix to the result of multiplying the two argument matrices together.static M4Constructs 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.voidSets 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.saveOrRetrieveTransformMatrix(M4 trmat) SymmetryInterface.staticGetMatrixTransform(String cleg, Object retLstOrMap) Methods in org.jmol.api with parameters of type M4Modifier and TypeMethodDescriptionintSymmetryInterface.addBioMoleculeOperation(M4 mat, boolean isReverse) SymmetryInterface.convertTransform(String transform, M4 trm) voidJmolRendererInterface.fillEllipsoid(P3 center, P3[] points, int x, int y, int z, int diameter, M3 mToEllipsoidal, double[] coef, M4 mDeriv, int selectedOctant, P3[] octantPoints) voidSymmetryInterface.getEquivPointList(int nIgnore, String flags, M4[] opsCtr, float packing, Lst<Point3fi> pts, SymmetryInterface uc) T3[]voidSymmetryInterface.newSpaceGroupPoint(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint) SymmetryInterface.saveOrRetrieveTransformMatrix(M4 trmat) SymmetryInterface.staticGetTransformABC(M4 transform, boolean normalize) -
Uses of M4 in org.jmol.atomdata
Methods in org.jmol.atomdata with parameters of type M4Modifier and TypeMethodDescriptionvoidAtomData.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 TypeMethodDescriptionvoidExport3D.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.mat4mat4 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 M4ScriptMathProcessor.getMatrix4f(M3 matRotate, T3 vTranslate) Methods in org.jmol.script with parameters of type M4Modifier and TypeMethodDescriptionbooleanstatic doubleFills 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 TypeMethodDescriptionfloatSmilesExt.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.floatSmilesExt.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 voidEllipsoid.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 TypeMethodDescriptionvoidIsosurfaceMesh.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 M4SymmetryOperation.getMatrixFromXYZ(String xyz, float[] v, boolean halfOrLess) static M4SymmetryOperation.getMatrixFromXYZScaled(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.saveOrRetrieveTransformMatrix(M4 trm) Saved by CLEG.assignSpaceGroup; retrieved by SpaceGroupFinder.Symmetry.staticGetMatrixTransform(String cleg, Object retLstOrMap) static M4Methods in org.jmol.symmetry with parameters of type M4Modifier and TypeMethodDescriptionintSymmetry.addBioMoleculeOperation(M4 mat, boolean isReverse) booleanHallInfo.HallReceiver.addHallOperationCheckDuplicates(M4 operation) Add a (possibly) new operation, checking for duplicates.booleanSpaceGroup.addHallOperationCheckDuplicates(M4 operation) Symmetry.convertTransform(String transform, M4 trm) A general method to handle converstions between string-based and matrix-based representations of transformations.voidSymmetry.getEquivPointList(int nInitial, String flags, M4[] opsCtr, float packing, Lst<Point3fi> pts, SymmetryInterface uc) Load a list of initial current points, and one or more starting points with equivalent points.static T3[]UnitCell.getMatrixAndUnitCell(Viewer vwr, SimpleUnitCell uc, Object def, M4 retMatrix) static StringSymmetryOperation.getTransformABC(M4 transform, boolean normalize) This method properly transposes the matrix for ABC format, converting columns to rows before passing the information to getXYZFromMatrixFrac(...,"ABC").static StringSymmetryOperation.getTransformABCd(M4 transform, boolean normalize, boolean fractionAsDecimal) static StringSymmetryOperation.getTransformUVW(M4 spin) static StringSymmetryOperation.getTransformXYZ(M4 op) T3[]static final StringSymmetryOperation.getXYZFromMatrix(M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess) static booleanSymmetryOperation.isTranslation(M4 op) voidSymmetry.newSpaceGroupPoint(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint) static voidSymmetryOperation.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.saveOrRetrieveTransformMatrix(M4 trm) Saved by CLEG.assignSpaceGroup; retrieved by SpaceGroupFinder.Symmetry.staticGetTransformABC(M4 transform, boolean normalize) static M4voidSymmetry.transformUnitCell(M4 trm) Transform the unit cell based on the calculated transformation matrix. -
Uses of M4 in org.jmol.util
Fields in org.jmol.util declared as M4Modifier and TypeFieldDescriptionMeshSurface.mat4SimpleUnitCell.matrixCartesianToFractionalprotected M4SimpleUnitCell.matrixCtoFNoOffsetSimpleUnitCell.matrixFractionalToCartesianprotected M4SimpleUnitCell.matrixFtoCNoOffsetMethods in org.jmol.util with parameters of type M4Modifier and TypeMethodDescriptionintShader.getEllipsoidShade(float x, float y, float z, int radius, M4 mDeriv) voidSimpleUnitCell.toFractionalM(M4 m) -
Uses of M4 in org.jmol.viewer
Fields in org.jmol.viewer declared as M4Modifier and TypeFieldDescriptionprotected final M4TransformManager.matrixTempfinal M4TransformManager.matrixTransformfinal M4TransformManager.matrixTransformInvMethods in org.jmol.viewer with parameters of type M4Modifier and TypeMethodDescriptionvoidViewer.moveAtoms(M4 m4, M3 mNew, M3 rotation, V3 translation, P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly, boolean useModelKit) voidShapeManager.notifyAtomPositionsChanged(int baseModel, BS bs, M4 mat) booleanViewer.rotateAboutPointsInternal(JmolScriptEvaluator eval, P3 point1, P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, V3 translation, Lst<P3> finalPoints, float[] dihedralList, M3 vectorMatrix, M4 m4, boolean useModelKit, P3[][] centerAndPoints) voidTransformManager.rotateAxisAngleRadiansInternal(float radians, BS bsAtoms, M4 m4, boolean useModelKit) voidTransformManager4D.setAsBallRotation(M4 m, float scale, float dx, float dy, float dz) 4D ball rotation from nominal dx, dy, dz motion.