Interface SymmetryInterface

Method Details

• addBioMoleculeOperation

  int addBioMoleculeOperation(M4 mat, boolean isReverse)

• addSpaceGroupOperation

  int addSpaceGroupOperation(String xyz, int opId)

• calculateCIPChiralityForAtoms

  void calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms)

• calculateCIPChiralityForSmiles

  String[] calculateCIPChiralityForSmiles(String smiles) throws Exception

  Throws:

  Exception

• checkPeriodic

  boolean checkPeriodic(P3 pt, float packing, float packing2)

• convertTransform

  Object convertTransform(String transform, M4 trm)

• findSpaceGroup

  Object findSpaceGroup(BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags)

• fixUnitCell

  boolean fixUnitCell(float[] unitCellParams)

• geCIFWriterValue

  String geCIFWriterValue(String type)

• generateCrystalClass

  Lst<P3> generateCrystalClass(P3 pt0)

• getAdditionalOperations

  M4[] getAdditionalOperations()

• getAdditionalOperationsCount

  int getAdditionalOperationsCount()

• getCanonicalCopy

  P3[] getCanonicalCopy(float scale, boolean allow2D)

• getCartesianOffset

  P3 getCartesianOffset()

• getCellRange

  int[] getCellRange()

• getCellWeight

  float getCellWeight(P3 pt)

• getConstrainableEquivAtom

  Atom getConstrainableEquivAtom(Atom a)

• getCoordinatesAreFractional

  boolean getCoordinatesAreFractional()

• getDimensionality

  int getDimensionality()

• getEquivPointList

  void getEquivPointList(int nIgnore, String flags, M4[] opsCtr, float packing, Lst<Point3fi> pts, SymmetryInterface uc)

• getEquivPoints

  Lst<Point3fi> getEquivPoints(Point3fi pt, String flags, float packing)

• getFinalOperationCount

  int getFinalOperationCount()

• getFractionalOffset

  P3 getFractionalOffset(boolean onlyIfFractional)

• getFractionalOrigin

  P3 getFractionalOrigin()

• getGroupType

  int getGroupType()

• getIntTableIndex

  String getIntTableIndex()

• getIntTableNumber

  String getIntTableNumber()

• getIntTableTransform

  String getIntTableTransform()

• getInvariantSymops

  int[] getInvariantSymops(P3 p3, int[] v0)

• getIterator

  AtomIndexIterator getIterator(Viewer vwr, Atom atom, BS bstoms, float radius)

• getLatticeCentering

  Lst<P3> getLatticeCentering()

• getLatticeDesignation

  Object getLatticeDesignation()

• getLatticeOp

  int getLatticeOp()

• getLatticeType

  char getLatticeType()

• getMoreInfo

  Lst<String> getMoreInfo()

• getOperationRsVs

  Matrix getOperationRsVs(int op)

• getPeriodicity

  int getPeriodicity()

• getPointGroupInfo

  Object getPointGroupInfo(int modelIndex, String drawID, boolean asInfo, String type, int index, float scale)

• getPointGroupName

  String getPointGroupName()

• getPrecision

  float getPrecision()

• getQuaternionRotation

  Quat getQuaternionRotation(String abc)

• getSiteMultiplicity

  int getSiteMultiplicity(P3 a)

• getSpaceGroup

  Object getSpaceGroup()

• getSpaceGroupClegId

  String getSpaceGroupClegId()

• getSpaceGroupInfo

  Map<String,Object> getSpaceGroupInfo(ModelSet modelSet, String spaceGroup, int modelIndex, boolean isFull, float[] cellParams)

• getSpaceGroupInfoObj

  Object getSpaceGroupInfoObj(String name, Object params, boolean isFull, boolean addNonstandard)

• getSpaceGroupJmolId

  String getSpaceGroupJmolId()

• getSpaceGroupJSON

  Object getSpaceGroupJSON(String name, String data, int index)

• getSpaceGroupName

  String getSpaceGroupName()

• getSpaceGroupOperation

  M4 getSpaceGroupOperation(int i)

• getSpaceGroupOperationCount

  int getSpaceGroupOperationCount()

• getSpaceGroupXyzOriginal

  String getSpaceGroupXyzOriginal(int i, boolean doNormalize)

• getSpinIndex

  int getSpinIndex(int op)

• getSpinOp

  int getSpinOp(int op)

• getSpinSym

  SymmetryInterface getSpinSym()

• getState

  boolean getState(ModelSet ms, int modelIndex, SB commands)

• getSubgroupJSON

  Object getSubgroupJSON(String nameFrom, String nameTo, int index1, int index2, int flags, Map<String,Object> retMap, Lst<Object> retLst)

• getSymmetryInfoAtom

  Object getSymmetryInfoAtom(ModelSet ms, int iatom, String xyz, int op, P3 translation, P3 pt, P3 pt2, String id, int type, float scaleFactor, int nth, int options, int[] oplist)

  Parameters:

  ms -

  iatom -

  xyz -

  op -

  translation - TODO

  pt -

  pt2 - a second point or an offset

  id -

  type - T.point, T.lattice, or T.draw, T.matrix4f, T.label, T.list, T.info, T.translation, T.axis, T.plane, T.angle, T.center

  scaleFactor -

  nth - TODO

  options - could be T.offset

  oplist -

  Returns:

  a variety of object types

• getSymmetryInfoStr

  String getSymmetryInfoStr()

• getSymmetryOperations

  M4[] getSymmetryOperations()

• getSymopList

  String[] getSymopList(boolean normalize)

• getTransform

  M4 getTransform(P3 fracA, P3 fracB, boolean debug)

• getUnitCell

  SymmetryInterface getUnitCell(T3[] oabc, boolean setRelative, String name)

• getUnitCellAsArray

  float[] getUnitCellAsArray(boolean vectorsOnly)

• getUnitCellCenter

  P3 getUnitCellCenter()

• getUnitCellDisplayName

  String getUnitCellDisplayName()

• getUnitCellInfo

  String getUnitCellInfo(boolean scaled)

• getUnitCellInfoMap

  Map<String,Object> getUnitCellInfoMap()

• getUnitCellInfoStr

  float getUnitCellInfoStr(String type)

• getUnitCellInfoType

  float getUnitCellInfoType(int infoType)

• getUnitCellMultiplied

  SymmetryInterface getUnitCellMultiplied()

• getUnitCellMultiplier

  T3 getUnitCellMultiplier()

• getUnitCellParams

  float[] getUnitCellParams()

• getUnitCellState

  String getUnitCellState()

• getUnitCellVectors

  P3[] getUnitCellVectors()

• getUnitCellVerticesNoOffset

  P3[] getUnitCellVerticesNoOffset()

• getV0abc

  T3[] getV0abc(Object def, M4 m)

• getWyckoffPosition

  Object getWyckoffPosition(P3 pt, String letter)

• haveUnitCell

  boolean haveUnitCell()

• initializeOrientation

  void initializeOrientation(M3 matUnitCellOrientation)

• isBio

  boolean isBio()

• isPolymer

  boolean isPolymer()

• isSimple

  boolean isSimple()

• isSlab

  boolean isSlab()

• isSupercell

  boolean isSupercell()

• isSymmetryCell

  boolean isSymmetryCell(SymmetryInterface sym)

• isWithinUnitCell

  boolean isWithinUnitCell(P3 pt, float x, float y, float z, float packing)

• newSpaceGroupPoint

  void newSpaceGroupPoint(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint)

• notInCentroid

  BS notInCentroid(ModelSet modelSet, BS bsAtoms, int[] minmax)

• removeDuplicates

  BS removeDuplicates(ModelSet ms, BS bs, boolean highPrec)

• saveOrRetrieveTransformMatrix

  M4 saveOrRetrieveTransformMatrix(M4 trmat)

• setFinalOperations

  void setFinalOperations(int dim, String name, P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, String filterSymop)

• setLattice

  void setLattice(int latt)

  set symmetry lattice type using Hall rotations

  Parameters:

  latt - SHELX index or character lattice character P I R F A B C S T or \0

• setOffset

  void setOffset(int nnn)

• setOffsetPt

  void setOffsetPt(T3 pt)

• setPointGroup

  SymmetryInterface setPointGroup(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly)

• setSpaceGroup

  void setSpaceGroup(boolean doNormalize)

• setSpaceGroupName

  void setSpaceGroupName(String name)

• setSpaceGroupTo

  void setSpaceGroupTo(Object spaceGroup)

  Parameters:

  spaceGroup - ITA number, ITA full name ("48:1")

• setSpinAxisAngle

  void setSpinAxisAngle(A4 aa)

• setUnitCell

  void setUnitCell(SymmetryInterface uc)

• setUnitCellFromParams

  SymmetryInterface setUnitCellFromParams(float[] params, boolean setRelative, float slop)

• setViewer

  SymmetryInterface setViewer(Viewer vwr, String id)

  for Viewer.getSymStatic only

  Parameters:

  vwr -

  id - TODO

  Returns:

  this

• staticCleanTransform

  String staticCleanTransform(String trm)

• staticConvertOperation

  Object staticConvertOperation(String xyz, M34 matrix, String labels)

• staticGetMatrixTransform

  M4 staticGetMatrixTransform(String cleg, Object retLstOrMap)

• staticGetTransformABC

  String staticGetTransformABC(M4 transform, boolean normalize)

• staticToRationalXYZ

  String staticToRationalXYZ(P3 fPt, String sep)

• staticTransformSpaceGroup

  String staticTransformSpaceGroup(BS bs, String cleg, Object paramsOrUC, SB sb)

• toCartesian

  void toCartesian(T3 pt, boolean ignoreOffset)

• toFractional

  void toFractional(T3 pt, boolean ignoreOffset)

• toFromPrimitive

  boolean toFromPrimitive(boolean toPrimitive, char type, T3[] oabc, M3 primitiveToCrystal)

• toSupercell

  P3 toSupercell(P3 fpt)

• toUnitCell

  void toUnitCell(T3 pt, T3 offset)

• unitCellEquals

  boolean unitCellEquals(SymmetryInterface uc2)

• unitize

  void unitize(T3 ptFrac)

• adjustRangeMinMax

  void adjustRangeMinMax(T3[] oabc, float packingRange, P3i minXYZ, P3i maxXYZ, P3 rmin, P3 rmax, P3i newMin, P3i newMax)

• updatePointGroup

  String updatePointGroup()

• toFractionalSpin

  void toFractionalSpin(T3 v)

• toCartesianSpin

  void toCartesianSpin(T3 v)