Field Detail

• spaceGroup

  SpaceGroup spaceGroup

• pointGroup

  private PointGroup pointGroup

• symmetryInfo

  private SymmetryInfo symmetryInfo

• unitCell

  private UnitCell unitCell

• cip

  private CIPChirality cip

• isBio

  private boolean isBio

• desc

  private SymmetryDesc desc

• nullDesc

  private static SymmetryDesc nullDesc

Constructor Detail

• Symmetry

  public Symmetry()

Method Detail

• 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 java.lang.String getPointGroupName()

  Specified by:

  getPointGroupName in interface SymmetryInterface

• getPointGroupInfo

  public java.lang.Object getPointGroupInfo​(int modelIndex,
                                            java.lang.String drawID,
                                            boolean asInfo,
                                            java.lang.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​(java.lang.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 java.lang.Object getSpaceGroup()

  Specified by:

  getSpaceGroup in interface SymmetryInterface

• createSpaceGroup

  public boolean createSpaceGroup​(int desiredSpaceGroupIndex,
                                  java.lang.String name,
                                  java.lang.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 java.lang.Object getSpaceGroupInfoObj​(java.lang.String name,
                                               float[] params,
                                               boolean isFull,
                                               boolean addNonstandard)

  Specified by:

  getSpaceGroupInfoObj in interface SymmetryInterface

• getLatticeDesignation

  public java.lang.Object getLatticeDesignation()

  Specified by:

  getLatticeDesignation in interface SymmetryInterface

• setFinalOperations

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

  Specified by:

  setFinalOperations in interface SymmetryInterface

• getSpaceGroupOperation

  public javajs.util.M4 getSpaceGroupOperation​(int i)

  Specified by:

  getSpaceGroupOperation in interface SymmetryInterface

• getSpaceGroupXyz

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

  Specified by:

  addSubSystemOp in interface SymmetryInterface

• getMatrixFromString

  public java.lang.String getMatrixFromString​(java.lang.String xyz,
                                              float[] rotTransMatrix,
                                              boolean allowScaling,
                                              int modDim)

  Specified by:

  getMatrixFromString in interface SymmetryInterface

• getSpaceGroupName

  public java.lang.String getSpaceGroupName()

  Specified by:

  getSpaceGroupName in interface SymmetryInterface

• getSpaceGroupNameType

  public java.lang.String getSpaceGroupNameType​(java.lang.String type)

  Specified by:

  getSpaceGroupNameType in interface SymmetryInterface

  Parameters:

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

  Returns:

  type or null

• setSpaceGroupName

  public void setSpaceGroupName​(java.lang.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 java.lang.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 java.lang.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,
                                           java.util.Map<java.lang.String,​java.lang.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 java.lang.String getUnitCellState()

  Specified by:

  getUnitCellState in interface SymmetryInterface

• getMoreInfo

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

  Specified by:

  getMoreInfo in interface SymmetryInterface

• getUnitsymmetryInfo

  public java.lang.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 java.lang.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,
                                       java.lang.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 java.lang.Object getSymmetryInfoAtom​(ModelSet modelSet,
                                              int iatom,
                                              java.lang.String xyz,
                                              int op,
                                              javajs.util.P3 translation,
                                              javajs.util.P3 pt,
                                              javajs.util.P3 pt2,
                                              java.lang.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 java.util.Map<java.lang.String,​java.lang.Object> getSpaceGroupInfo​(ModelSet modelSet,
                                                                                  java.lang.String sgName,
                                                                                  int modelIndex,
                                                                                  boolean isFull,
                                                                                  float[] cellParams)

  Specified by:

  getSpaceGroupInfo in interface SymmetryInterface

• fcoord

  public java.lang.String fcoord​(javajs.util.T3 p)

  Specified by:

  fcoord in interface SymmetryInterface

• getV0abc

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

  Specified by:

  getV0abc in interface SymmetryInterface

• getQuaternionRotation

  public javajs.util.Quat getQuaternionRotation​(java.lang.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 java.lang.String[] calculateCIPChiralityForSmiles​(Viewer vwr,
                                                           java.lang.String smiles)
                                                    throws java.lang.Exception

  Specified by:

  calculateCIPChiralityForSmiles in interface SymmetryInterface

  Throws:

  java.lang.Exception

• getCIPChirality

  private CIPChirality getCIPChirality​(Viewer vwr)

• getConventionalUnitCell

  public javajs.util.T3[] getConventionalUnitCell​(java.lang.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 java.util.Map<java.lang.String,​java.lang.Object> getUnitCellInfoMap()

  Specified by:

  getUnitCellInfoMap in interface SymmetryInterface

• setUnitCell

  public void setUnitCell​(SymmetryInterface uc)

  Specified by:

  setUnitCell in interface SymmetryInterface

• findSpaceGroup

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

  Specified by:

  findSpaceGroup in interface SymmetryInterface

• setSpaceGroupTo

  public void setSpaceGroupTo​(java.lang.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,
                                                        java.lang.String flags)

  Specified by:

  getEquivPoints in interface SymmetryInterface

• getEquivPointList

  public void getEquivPointList​(javajs.util.Lst<javajs.util.P3> pts,
                                int nIgnored,
                                java.lang.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)