Class Symmetry

Method Details

• isBio

  public boolean isBio()

  Specified by:

  isBio in interface SymmetryInterface

• setPointGroup

  public SymmetryInterface setPointGroup(SymmetryInterface siLast, javajs.util.T3 center, javajs.util.T3[] atomset, javajs.util.BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly)

  Specified by:

  setPointGroup in interface SymmetryInterface

• getPointGroupName

  public String getPointGroupName()

  Specified by:

  getPointGroupName in interface SymmetryInterface

• getPointGroupInfo

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

  Specified by:

  getPointGroupInfo in interface SymmetryInterface

• setSpaceGroup

  public void setSpaceGroup(boolean doNormalize)

  Specified by:

  setSpaceGroup in interface SymmetryInterface

• addSpaceGroupOperation

  public int addSpaceGroupOperation(String xyz, int opId)

  Specified by:

  addSpaceGroupOperation in interface SymmetryInterface

• addBioMoleculeOperation

  public int addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse)

  Specified by:

  addBioMoleculeOperation in interface SymmetryInterface

• setLattice

  public void setLattice(int latt)

  Description copied from interface: SymmetryInterface

  set symmetry lattice type using Hall rotations

  Specified by:

  setLattice in interface SymmetryInterface

  Parameters:

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

• getSpaceGroup

  public Object getSpaceGroup()

  Specified by:

  getSpaceGroup in interface SymmetryInterface

• createSpaceGroup

  public boolean createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)

  Specified by:

  createSpaceGroup in interface SymmetryInterface

  Parameters:

  desiredSpaceGroupIndex -

  name -

  data - a Lst or Lst

  modDim - in [3+d] modulation dimension

  Returns:

  true if a known space group

• getSpaceGroupInfoObj

  public Object getSpaceGroupInfoObj(String name, float[] params, boolean isFull, boolean addNonstandard)

  Specified by:

  getSpaceGroupInfoObj in interface SymmetryInterface

• getLatticeDesignation

  public Object getLatticeDesignation()

  Specified by:

  getLatticeDesignation in interface SymmetryInterface

• setFinalOperations

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

  Specified by:

  setFinalOperations in interface SymmetryInterface

• getSpaceGroupOperation

  public javajs.util.M4 getSpaceGroupOperation(int i)

  Specified by:

  getSpaceGroupOperation in interface SymmetryInterface

• getSpaceGroupXyz

  public String getSpaceGroupXyz(int i, boolean doNormalize)

  Specified by:

  getSpaceGroupXyz in interface SymmetryInterface

• newSpaceGroupPoint

  public void newSpaceGroupPoint(javajs.util.P3 pt, int i, javajs.util.M4 o, int transX, int transY, int transZ, javajs.util.P3 retPoint)

  Specified by:

  newSpaceGroupPoint in interface SymmetryInterface

• rotateAxes

  public javajs.util.V3[] rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)

  Specified by:

  rotateAxes in interface SymmetryInterface

• getSpaceGroupOperationCode

  public String getSpaceGroupOperationCode(int iOp)

  Specified by:

  getSpaceGroupOperationCode in interface SymmetryInterface

• setTimeReversal

  public void setTimeReversal(int op, int val)

  Specified by:

  setTimeReversal in interface SymmetryInterface

• getSpinOp

  public float getSpinOp(int op)

  Specified by:

  getSpinOp in interface SymmetryInterface

• addLatticeVectors

  public boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs)

  Specified by:

  addLatticeVectors in interface SymmetryInterface

• getLatticeOp

  public int getLatticeOp()

  Specified by:

  getLatticeOp in interface SymmetryInterface

• getLatticeCentering

  public javajs.util.Lst<javajs.util.P3> getLatticeCentering()

  Specified by:

  getLatticeCentering in interface SymmetryInterface

• getOperationRsVs

  public javajs.util.Matrix getOperationRsVs(int iop)

  Specified by:

  getOperationRsVs in interface SymmetryInterface

• getSiteMultiplicity

  public int getSiteMultiplicity(javajs.util.P3 pt)

  Specified by:

  getSiteMultiplicity in interface SymmetryInterface

• addSubSystemOp

  public String addSubSystemOp(String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma)

  Specified by:

  addSubSystemOp in interface SymmetryInterface

• getMatrixFromString

  public String getMatrixFromString(String xyz, float[] rotTransMatrix, boolean allowScaling, int modDim)

  Specified by:

  getMatrixFromString in interface SymmetryInterface

• getSpaceGroupName

  public String getSpaceGroupName()

  Specified by:

  getSpaceGroupName in interface SymmetryInterface

• getSpaceGroupNameType

  public String getSpaceGroupNameType(String type)

  Specified by:

  getSpaceGroupNameType in interface SymmetryInterface

  Parameters:

  type - "Hall" or "HM" or "ITA"

  Returns:

  type or null

• setSpaceGroupName

  public void setSpaceGroupName(String name)

  Specified by:

  setSpaceGroupName in interface SymmetryInterface

• getSpaceGroupOperationCount

  public int getSpaceGroupOperationCount()

  Specified by:

  getSpaceGroupOperationCount in interface SymmetryInterface

• getLatticeType

  public char getLatticeType()

  Specified by:

  getLatticeType in interface SymmetryInterface

• getIntTableNumber

  public String getIntTableNumber()

  Specified by:

  getIntTableNumber in interface SymmetryInterface

• getCoordinatesAreFractional

  public boolean getCoordinatesAreFractional()

  Specified by:

  getCoordinatesAreFractional in interface SymmetryInterface

• getCellRange

  public int[] getCellRange()

  Specified by:

  getCellRange in interface SymmetryInterface

• getSymmetryInfoStr

  public String getSymmetryInfoStr()

  Specified by:

  getSymmetryInfoStr in interface SymmetryInterface

• getSymmetryOperations

  public SymmetryOperation[] getSymmetryOperations()

  Specified by:

  getSymmetryOperations in interface SymmetryInterface

• isSimple

  public boolean isSimple()

  Specified by:

  isSimple in interface SymmetryInterface

• setSymmetryInfo

  public SymmetryInterface setSymmetryInfo(int modelIndex, Map<String,Object> modelAuxiliaryInfo, float[] unitCellParams)

  Set space group and unit cell from the auxiliary info generated by the model adapter.

  Specified by:

  setSymmetryInfo in interface SymmetryInterface

• haveUnitCell

  public boolean haveUnitCell()

  Specified by:

  haveUnitCell in interface SymmetryInterface

• setUnitCell

  public SymmetryInterface setUnitCell(float[] unitCellParams, boolean setRelative)

  Specified by:

  setUnitCell in interface SymmetryInterface

• unitCellEquals

  public boolean unitCellEquals(SymmetryInterface uc2)

  Specified by:

  unitCellEquals in interface SymmetryInterface

• getUnitCellState

  public String getUnitCellState()

  Specified by:

  getUnitCellState in interface SymmetryInterface

• getMoreInfo

  public javajs.util.Lst<String> getMoreInfo()

  Specified by:

  getMoreInfo in interface SymmetryInterface

• getUnitsymmetryInfo

  public String getUnitsymmetryInfo()

• initializeOrientation

  public void initializeOrientation(javajs.util.M3 mat)

  Specified by:

  initializeOrientation in interface SymmetryInterface

• unitize

  public void unitize(javajs.util.T3 ptFrac)

  Specified by:

  unitize in interface SymmetryInterface

• toUnitCell

  public void toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset)

  Specified by:

  toUnitCell in interface SymmetryInterface

• toUnitCellRnd

  public void toUnitCellRnd(javajs.util.T3 pt, javajs.util.T3 offset)

  Specified by:

  toUnitCellRnd in interface SymmetryInterface

• toSupercell

  public javajs.util.P3 toSupercell(javajs.util.P3 fpt)

  Specified by:

  toSupercell in interface SymmetryInterface

• toFractional

  public void toFractional(javajs.util.T3 pt, boolean ignoreOffset)

  Specified by:

  toFractional in interface SymmetryInterface

• toFractionalM

  public void toFractionalM(javajs.util.M4 m)

  Specified by:

  toFractionalM in interface SymmetryInterface

• toCartesian

  public void toCartesian(javajs.util.T3 fpt, boolean ignoreOffset)

  Specified by:

  toCartesian in interface SymmetryInterface

• getUnitCellParams

  public float[] getUnitCellParams()

  Specified by:

  getUnitCellParams in interface SymmetryInterface

• getUnitCellAsArray

  public float[] getUnitCellAsArray(boolean vectorsOnly)

  Specified by:

  getUnitCellAsArray in interface SymmetryInterface

• getTensor

  public Tensor getTensor(Viewer vwr, float[] parBorU)

  Specified by:

  getTensor in interface SymmetryInterface

• getUnitCellVerticesNoOffset

  public javajs.util.P3[] getUnitCellVerticesNoOffset()

  Specified by:

  getUnitCellVerticesNoOffset in interface SymmetryInterface

• getCartesianOffset

  public javajs.util.P3 getCartesianOffset()

  Specified by:

  getCartesianOffset in interface SymmetryInterface

• getFractionalOffset

  public javajs.util.P3 getFractionalOffset()

  Specified by:

  getFractionalOffset in interface SymmetryInterface

• setOffsetPt

  public void setOffsetPt(javajs.util.T3 pt)

  Specified by:

  setOffsetPt in interface SymmetryInterface

• setOffset

  public void setOffset(int nnn)

  Specified by:

  setOffset in interface SymmetryInterface

• getUnitCellMultiplier

  public javajs.util.T3 getUnitCellMultiplier()

  Specified by:

  getUnitCellMultiplier in interface SymmetryInterface

• getUnitCellMultiplied

  public SymmetryInterface getUnitCellMultiplied()

  Specified by:

  getUnitCellMultiplied in interface SymmetryInterface

• getCanonicalCopy

  public javajs.util.P3[] getCanonicalCopy(float scale, boolean withOffset)

  Specified by:

  getCanonicalCopy in interface SymmetryInterface

• getUnitCellInfoType

  public float getUnitCellInfoType(int infoType)

  Specified by:

  getUnitCellInfoType in interface SymmetryInterface

• getUnitCellInfo

  public String getUnitCellInfo(boolean scaled)

  Specified by:

  getUnitCellInfo in interface SymmetryInterface

• isSlab

  public boolean isSlab()

  Specified by:

  isSlab in interface SymmetryInterface

• isPolymer

  public boolean isPolymer()

  Specified by:

  isPolymer in interface SymmetryInterface

• checkDistance

  public boolean checkDistance(javajs.util.P3 f1, javajs.util.P3 f2, float distance, float dx, int iRange, int jRange, int kRange, javajs.util.P3 ptOffset)

  Specified by:

  checkDistance in interface SymmetryInterface

• getUnitCellVectors

  public javajs.util.P3[] getUnitCellVectors()

  Specified by:

  getUnitCellVectors in interface SymmetryInterface

• getUnitCell

  public SymmetryInterface getUnitCell(javajs.util.T3[] oabc, boolean setRelative, String name)

  Specified by:

  getUnitCell in interface SymmetryInterface

  Parameters:

  oabc - [ptorigin, va, vb, vc]

  setRelative - a flag only set true for IsosurfaceMesh

  name -

  Returns:

  this SymmetryInterface

• isSupercell

  public boolean isSupercell()

  Specified by:

  isSupercell in interface SymmetryInterface

• notInCentroid

  public javajs.util.BS notInCentroid(ModelSet modelSet, javajs.util.BS bsAtoms, int[] minmax)

  Specified by:

  notInCentroid in interface SymmetryInterface

• isNotCentroid

  private boolean isNotCentroid(javajs.util.P3 center, int n, int[] minmax, boolean centroidPacked)

• getDesc

  private SymmetryDesc getDesc(ModelSet modelSet)

• getSymmetryInfoAtom

  public Object getSymmetryInfoAtom(ModelSet modelSet, int iatom, String xyz, int op, javajs.util.P3 translation, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type, float scaleFactor, int nth, int options)

  Specified by:

  getSymmetryInfoAtom in interface SymmetryInterface

  translation - TODO

  pt2 - a second point or an offset

  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

  nth - TODO

  options - could be T.offset

  Returns:

  a variety of object types

• getSpaceGroupInfo

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

  Specified by:

  getSpaceGroupInfo in interface SymmetryInterface

• fcoord

  public String fcoord(javajs.util.T3 p)

  Specified by:

  fcoord in interface SymmetryInterface

• getV0abc

  public javajs.util.T3[] getV0abc(Object def, javajs.util.M4 retMatrix)

  Specified by:

  getV0abc in interface SymmetryInterface

• getQuaternionRotation

  public javajs.util.Quat getQuaternionRotation(String abc)

  Specified by:

  getQuaternionRotation in interface SymmetryInterface

• getFractionalOrigin

  public javajs.util.T3 getFractionalOrigin()

  Specified by:

  getFractionalOrigin in interface SymmetryInterface

• getState

  public boolean getState(ModelSet ms, int modelIndex, javajs.util.SB commands)

  Specified by:

  getState in interface SymmetryInterface

• getIterator

  public AtomIndexIterator getIterator(Viewer vwr, Atom atom, javajs.util.BS bsAtoms, float radius)

  Specified by:

  getIterator in interface SymmetryInterface

• toFromPrimitive

  public boolean toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] oabc, javajs.util.M3 primitiveToCrystal)

  Specified by:

  toFromPrimitive in interface SymmetryInterface

• generateCrystalClass

  public javajs.util.Lst<javajs.util.P3> generateCrystalClass(javajs.util.P3 pt0)

  Specified by:

  generateCrystalClass in interface SymmetryInterface

• calculateCIPChiralityForAtoms

  public void calculateCIPChiralityForAtoms(Viewer vwr, javajs.util.BS bsAtoms)

  Specified by:

  calculateCIPChiralityForAtoms in interface SymmetryInterface

• calculateCIPChiralityForSmiles

  public String[] calculateCIPChiralityForSmiles(Viewer vwr, String smiles) throws Exception

  Specified by:

  calculateCIPChiralityForSmiles in interface SymmetryInterface

  Throws:

  Exception

• getCIPChirality

  private CIPChirality getCIPChirality(Viewer vwr)

• getConventionalUnitCell

  public javajs.util.T3[] getConventionalUnitCell(String latticeType, javajs.util.M3 primitiveToCrystal)

  return a conventional lattice from a primitive

  Specified by:

  getConventionalUnitCell in interface SymmetryInterface

  Parameters:

  latticeType - "A" "B" "C" "R" etc.

  Returns:

  [origin va vb vc]

• getUnitCellInfoMap

  public Map<String,Object> getUnitCellInfoMap()

  Specified by:

  getUnitCellInfoMap in interface SymmetryInterface

• setUnitCell

  public void setUnitCell(SymmetryInterface uc)

  Specified by:

  setUnitCell in interface SymmetryInterface

• findSpaceGroup

  public Object findSpaceGroup(Viewer vwr, javajs.util.BS atoms, String xyzList, float[] unitCell, boolean asString, boolean isAssign)

  Specified by:

  findSpaceGroup in interface SymmetryInterface

• setSpaceGroupTo

  public void setSpaceGroupTo(Object sg)

  Specified by:

  setSpaceGroupTo in interface SymmetryInterface

  Parameters:

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

• removeDuplicates

  public javajs.util.BS removeDuplicates(ModelSet ms, javajs.util.BS bs, boolean highPrec)

  Specified by:

  removeDuplicates in interface SymmetryInterface

• getEquivPoints

  public javajs.util.Lst<javajs.util.P3> getEquivPoints(javajs.util.Lst<javajs.util.P3> pts, javajs.util.P3 pt, String flags)

  Specified by:

  getEquivPoints in interface SymmetryInterface

• getEquivPointList

  public void getEquivPointList(javajs.util.Lst<javajs.util.P3> pts, int nIgnored, String flags)

  Specified by:

  getEquivPointList in interface SymmetryInterface

• getInvariantSymops

  public int[] getInvariantSymops(javajs.util.P3 pt, int[] v0)

  Specified by:

  getInvariantSymops in interface SymmetryInterface

• getTransform

  public javajs.util.M4 getTransform(javajs.util.P3 fracA, javajs.util.P3 fracB, boolean best)

  Specified by:

  getTransform in interface SymmetryInterface

  Parameters:

  fracA -

  fracB -

  Returns:

  matrix

• newPoint

  static void newPoint(javajs.util.M4 m, javajs.util.P3 atom1, int x, int y, int z, javajs.util.P3 atom2)

• isWithinUnitCell

  public boolean isWithinUnitCell(javajs.util.P3 pt, float a, float b, float c)

  Specified by:

  isWithinUnitCell in interface SymmetryInterface

• checkPeriodic

  public boolean checkPeriodic(javajs.util.P3 pt)

  Specified by:

  checkPeriodic in interface SymmetryInterface