Uses of Interface
org.jmol.api.SymmetryInterface
Packages that use SymmetryInterface
Package
Description
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Uses of SymmetryInterface in org.jmol.adapter.smarter
Classes in org.jmol.adapter.smarter that implement SymmetryInterfaceModifier and TypeClassDescriptionstatic class
A class only used by adapter.smarter.XtalSymmetry while building the file-based model. -
Uses of SymmetryInterface in org.jmol.api
Methods in org.jmol.api that return SymmetryInterfaceModifier and TypeMethodDescriptionJmolModulationSet.getSubSystemUnitCell()
static SymmetryInterface
Interface.getSymmetry
(Viewer vwr, String state) SymmetryInterface.getUnitCell
(T3[] points, boolean setRelative, String name) SymmetryInterface.getUnitCellMultiplied()
SymmetryInterface.setPointGroup
(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) SymmetryInterface.setUnitCellFromParams
(float[] params, boolean setRelative, float slop) for Viewer.getSymStatic onlyMethods in org.jmol.api with parameters of type SymmetryInterfaceModifier and TypeMethodDescriptionboolean
SymmetryInterface.isSymmetryCell
(SymmetryInterface sym) SymmetryInterface.setPointGroup
(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) void
SymmetryInterface.setUnitCell
(SymmetryInterface uc) boolean
SymmetryInterface.unitCellEquals
(SymmetryInterface uc2) -
Uses of SymmetryInterface in org.jmol.modelkit
Methods in org.jmol.modelkit that return SymmetryInterfaceMethods in org.jmol.modelkit with parameters of type SymmetryInterfaceModifier and TypeMethodDescriptionvoid
ModelKit.addLockedAtoms
(SymmetryInterface sg, BS bsLocked) Only for the current modelprotected org.jmol.modelkit.ModelKit.Constraint
ModelKit.setConstraint
(SymmetryInterface sym, int ia, int mode) This constraint will be set for the site only.boolean
ModelKit.transformAtomsToUnitCell
(SymmetryInterface sym, T3[] oabc, String ucname) Transform the atoms to fractional coordinate, set the unit cell to a new cell, and then transform them back to Cartesians. -
Uses of SymmetryInterface in org.jmol.modelset
Fields in org.jmol.modelset declared as SymmetryInterfaceModifier and TypeFieldDescriptionModel.biosymmetry
protected SymmetryInterface
AtomCollection.pointGroup
Model.simpleCage
ModelSet.unitCells
Methods in org.jmol.modelset that return SymmetryInterfaceModifier and TypeMethodDescriptionModelSet.getUnitCell
(int modelIndex) ModelSet.getUnitCellForAtom
(int index) ModelSet.setModelCage
(int modelIndex, SymmetryInterface simpleCage) This is the model-specific cage created by a UNITCELL or MODELKIT UNITCELL command.ModelSet.setModelCagePts
(int iModel, T3[] originABC, String name) Methods in org.jmol.modelset with parameters of type SymmetryInterfaceModifier and TypeMethodDescriptionModelSet.getSymmetryEquivAtoms
(BS bsAtoms, SymmetryInterface sym, BS bsModelAtoms) Return a bitset of equivalent atomsModelSet.setModelCage
(int modelIndex, SymmetryInterface simpleCage) This is the model-specific cage created by a UNITCELL or MODELKIT UNITCELL command.void
Model.setSimpleCage
(SymmetryInterface ucell) void
ModelSet.setSpaceGroup
(int mi, SymmetryInterface sg, BS basis) Set up all the model-related fields in association with a new space group. -
Uses of SymmetryInterface in org.jmol.shape
Fields in org.jmol.shape declared as SymmetryInterfaceMethods in org.jmol.shape that return SymmetryInterface -
Uses of SymmetryInterface in org.jmol.shapesurface
Methods in org.jmol.shapesurface that return SymmetryInterface -
Uses of SymmetryInterface in org.jmol.symmetry
Classes in org.jmol.symmetry that implement SymmetryInterfaceFields in org.jmol.symmetry declared as SymmetryInterfaceMethods in org.jmol.symmetry that return SymmetryInterfaceModifier and TypeMethodDescriptionSymmetry.getUnitCell
(T3[] oabc, boolean setRelative, String name) Symmetry.getUnitCellMultiplied()
Note, this has no origin shift.Symmetry.setPointGroup
(Viewer vwr, SymmetryInterface siLast, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) Symmetry.setUnitCellFromParams
(float[] unitCellParams, boolean setRelative, float slop) for the vwr.getSymTemp() onlyMethods in org.jmol.symmetry with parameters of type SymmetryInterfaceModifier and TypeMethodDescriptionstatic boolean
CLEG.checkFullSyntax
(String[] tokens, SymmetryInterface sym, boolean allow300) Test nodes and transforms for valid syntax.boolean
Symmetry.isSymmetryCell
(SymmetryInterface sym) UnitCellIterator.set
(SymmetryInterface unitCell, Atom atom, Atom[] atoms, BS bsAtoms, float distance) Symmetry.setPointGroup
(Viewer vwr, SymmetryInterface siLast, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) void
Symmetry.setUnitCell
(SymmetryInterface uc) boolean
Symmetry.unitCellEquals
(SymmetryInterface uc2) Constructors in org.jmol.symmetry with parameters of type SymmetryInterface -
Uses of SymmetryInterface in org.jmol.util
Methods in org.jmol.util that return SymmetryInterfaceMethods in org.jmol.util with parameters of type SymmetryInterfaceModifier and TypeMethodDescriptionModulationSet.setMod
(String id, P3 r00, P3 r0, int d, Lst<Modulation> mods, M3 gammaE, Matrix[] factors, SymmetryInterface symmetry, int nOps, int iop, Vibration v, boolean isCommensurate) A collection of modulations for a specific atom. -
Uses of SymmetryInterface in org.jmol.viewer
Methods in org.jmol.viewer that return SymmetryInterfaceModifier and TypeMethodDescriptionViewer.getCurrentUnitCell()
Viewer.getOperativeSymmetry()
Only return symmetry that has operators.Viewer.getSymStatic()
Retrieve the static Symmetry object, which should be used only staticallyViewer.getSymTemp()
Retrieve a new Symmetry object.Methods in org.jmol.viewer with parameters of type SymmetryInterfaceModifier and TypeMethodDescriptionViewer.findSpaceGroup
(SymmetryInterface sym, BS bsAtoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) Viewer.getMotionFixedAtoms
(SymmetryInterface sym, BS bsFixed) For the current SINGLE model only.void
Viewer.toCartesianUC
(SymmetryInterface unitCell, T3 pt, boolean ignoreOffset) void
Viewer.toFractionalUC
(SymmetryInterface unitCell, T3 pt, boolean ignoreOffset)