Class Symmetry

Method Details

• getSymopList

  public String[] getSymopList(boolean doNormalize)

  Specified by:

  getSymopList in interface SymmetryInterface

• isBio

  public boolean isBio()

  Specified by:

  isBio in interface SymmetryInterface

• setPointGroup

  public SymmetryInterface setPointGroup(Viewer vwr, SymmetryInterface siLast, T3 center, T3[] atomset, 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(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

• getSpaceGroupInfoObj

  public Object getSpaceGroupInfoObj(String name, Object 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, P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, String filterSymop)

  Specified by:

  setFinalOperations in interface SymmetryInterface

• getSpaceGroupOperation

  public M4 getSpaceGroupOperation(int i)

  Specified by:

  getSpaceGroupOperation in interface SymmetryInterface

• getSpaceGroupXyzOriginal

  public String getSpaceGroupXyzOriginal(int i, boolean doNormalize)

  Specified by:

  getSpaceGroupXyzOriginal in interface SymmetryInterface

• newSpaceGroupPoint

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

  Specified by:

  newSpaceGroupPoint in interface SymmetryInterface

• getSpinOp

  public int getSpinOp(int op)

  Specified by:

  getSpinOp in interface SymmetryInterface

• getLatticeOp

  public int getLatticeOp()

  Specified by:

  getLatticeOp in interface SymmetryInterface

• getLatticeCentering

  public Lst<P3> getLatticeCentering()

  Specified by:

  getLatticeCentering in interface SymmetryInterface

• getOperationRsVs

  public Matrix getOperationRsVs(int iop)

  Specified by:

  getOperationRsVs in interface SymmetryInterface

• getSiteMultiplicity

  public int getSiteMultiplicity(P3 pt)

  Specified by:

  getSiteMultiplicity in interface SymmetryInterface

• getSpaceGroupName

  public String getSpaceGroupName()

  Specified by:

  getSpaceGroupName in interface SymmetryInterface

• geCIFWriterValue

  public String geCIFWriterValue(String type)

  Specified by:

  geCIFWriterValue in interface SymmetryInterface

• getLatticeType

  public char getLatticeType()

  Specified by:

  getLatticeType in interface SymmetryInterface

• getIntTableNumber

  public String getIntTableNumber()

  Specified by:

  getIntTableNumber in interface SymmetryInterface

• getIntTableIndex

  public String getIntTableIndex()

  Specified by:

  getIntTableIndex in interface SymmetryInterface

• getIntTableTransform

  public String getIntTableTransform()

  Specified by:

  getIntTableTransform in interface SymmetryInterface

• getSpaceGroupClegId

  public String getSpaceGroupClegId()

  Specified by:

  getSpaceGroupClegId in interface SymmetryInterface

• getSpaceGroupJmolId

  public String getSpaceGroupJmolId()

  Specified by:

  getSpaceGroupJmolId 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()

  When information is desired about the space group, we use SymmetryInfo.

  Specified by:

  getSymmetryInfoStr in interface SymmetryInterface

• getSpaceGroupOperationCount

  public int getSpaceGroupOperationCount()

  Specified by:

  getSpaceGroupOperationCount in interface SymmetryInterface

• getSymmetryOperations

  public SymmetryOperation[] getSymmetryOperations()

  Specified by:

  getSymmetryOperations in interface SymmetryInterface

• getAdditionalOperationsCount

  public int getAdditionalOperationsCount()

  Specified by:

  getAdditionalOperationsCount in interface SymmetryInterface

• getAdditionalOperations

  public M4[] getAdditionalOperations()

  Specified by:

  getAdditionalOperations in interface SymmetryInterface

• isSimple

  public boolean isSimple()

  Specified by:

  isSimple in interface SymmetryInterface

• haveUnitCell

  public boolean haveUnitCell()

  Specified by:

  haveUnitCell in interface SymmetryInterface

• setUnitCellFromParams

  public SymmetryInterface setUnitCellFromParams(float[] unitCellParams, boolean setRelative, float slop)

  Specified by:

  setUnitCellFromParams in interface SymmetryInterface

• unitCellEquals

  public boolean unitCellEquals(SymmetryInterface uc2)

  Specified by:

  unitCellEquals in interface SymmetryInterface

• isSymmetryCell

  public boolean isSymmetryCell(SymmetryInterface sym)

  Specified by:

  isSymmetryCell in interface SymmetryInterface

• getUnitCellState

  public String getUnitCellState()

  Specified by:

  getUnitCellState in interface SymmetryInterface

• getMoreInfo

  public Lst<String> getMoreInfo()

  Specified by:

  getMoreInfo in interface SymmetryInterface

• initializeOrientation

  public void initializeOrientation(M3 mat)

  Specified by:

  initializeOrientation in interface SymmetryInterface

• unitize

  public void unitize(T3 ptFrac)

  Specified by:

  unitize in interface SymmetryInterface

• toUnitCell

  public void toUnitCell(T3 pt, T3 offset)

  Specified by:

  toUnitCell in interface SymmetryInterface

• toSupercell

  public P3 toSupercell(P3 fpt)

  Specified by:

  toSupercell in interface SymmetryInterface

• toFractional

  public void toFractional(T3 pt, boolean ignoreOffset)

  Specified by:

  toFractional in interface SymmetryInterface

• toCartesian

  public void toCartesian(T3 pt, 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

• getUnitCellVerticesNoOffset

  public P3[] getUnitCellVerticesNoOffset()

  Specified by:

  getUnitCellVerticesNoOffset in interface SymmetryInterface

• getCartesianOffset

  public P3 getCartesianOffset()

  Specified by:

  getCartesianOffset in interface SymmetryInterface

• getFractionalOffset

  public P3 getFractionalOffset(boolean onlyIfFractional)

  determine if an offset cell is a unit translation, so that the space group can be continued

  Specified by:

  getFractionalOffset in interface SymmetryInterface

• setOffsetPt

  public void setOffsetPt(T3 pt)

  Specified by:

  setOffsetPt in interface SymmetryInterface

• setOffset

  public void setOffset(int nnn)

  Specified by:

  setOffset in interface SymmetryInterface

• getUnitCellMultiplier

  public T3 getUnitCellMultiplier()

  Specified by:

  getUnitCellMultiplier in interface SymmetryInterface

• getUnitCellMultiplied

  public SymmetryInterface getUnitCellMultiplied()

  Note, this has no origin shift.

  Specified by:

  getUnitCellMultiplied in interface SymmetryInterface

• getCanonicalCopy

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

  Specified by:

  getCanonicalCopy in interface SymmetryInterface

• getUnitCellInfoType

  public float getUnitCellInfoType(int infoType)

  Specified by:

  getUnitCellInfoType in interface SymmetryInterface

• getUnitCellInfoStr

  public float getUnitCellInfoStr(String type)

  Specified by:

  getUnitCellInfoStr 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

• getUnitCellVectors

  public P3[] getUnitCellVectors()

  Specified by:

  getUnitCellVectors in interface SymmetryInterface

• getUnitCell

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

  Specified by:

  notInCentroid in interface SymmetryInterface

• getSymmetryInfoAtom

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

  Specified by:

  getSymmetryInfoAtom in interface SymmetryInterface

  Parameters:

  modelSet -

  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

• getSpaceGroupInfo

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

  Specified by:

  getSpaceGroupInfo in interface SymmetryInterface

• getV0abc

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

  Specified by:

  getV0abc in interface SymmetryInterface

• getQuaternionRotation

  public Quat getQuaternionRotation(String abc)

  Specified by:

  getQuaternionRotation in interface SymmetryInterface

• getFractionalOrigin

  public P3 getFractionalOrigin()

  Specified by:

  getFractionalOrigin in interface SymmetryInterface

• getState

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

  Specified by:

  getState in interface SymmetryInterface

• getIterator

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

  Specified by:

  getIterator in interface SymmetryInterface

• toFromPrimitive

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

  Specified by:

  toFromPrimitive in interface SymmetryInterface

• generateCrystalClass

  public Lst<P3> generateCrystalClass(P3 pt00)

  Specified by:

  generateCrystalClass in interface SymmetryInterface

• calculateCIPChiralityForAtoms

  public void calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms)

  Specified by:

  calculateCIPChiralityForAtoms in interface SymmetryInterface

• calculateCIPChiralityForSmiles

  public String[] calculateCIPChiralityForSmiles(String smiles) throws Exception

  Specified by:

  calculateCIPChiralityForSmiles in interface SymmetryInterface

  Throws:

  Exception

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

  Specified by:

  findSpaceGroup in interface SymmetryInterface

• setSpaceGroupName

  public void setSpaceGroupName(String name)

  Specified by:

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

  Specified by:

  removeDuplicates in interface SymmetryInterface

• getPeriodicity

  public int getPeriodicity()

  0x1 a only frieze, rod-a 0x2 b only rod-b 0x4 c only rod-c 0x3 ab only plane, layer 0x5 ac only n/a 0x6 bc only n/a 0x7 abc all space

  Specified by:

  getPeriodicity in interface SymmetryInterface

• getDimensionality

  public int getDimensionality()

  plane 2 freize 2 layer 3 rod 3

  Specified by:

  getDimensionality in interface SymmetryInterface

• getGroupType

  public int getGroupType()

  Specified by:

  getGroupType in interface SymmetryInterface

• getEquivPoints

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

  Specified by:

  getEquivPoints in interface SymmetryInterface

  Parameters:

  pt -

  flags -

  packing -

  Returns:

  A list of equivalent points

• getEquivPointList

  public void 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.

  Specified by:

  getEquivPointList in interface SymmetryInterface

  Parameters:

  nInitial - number of initial points

  flags - indicating input/output Cartesian or fractional options

  opsCtr - centering operations for subgroup filling that are to be used rather than space group operations

  packing - if .gte. 0, the fractional packing distance around the unit cell to include

  pts - total list of initial (current) points, needed for duplication check; additional points are those to be operated on, including the identity operation

• adjustRangeMinMax

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

  Specified by:

  adjustRangeMinMax in interface SymmetryInterface

• getInvariantSymops

  public int[] getInvariantSymops(P3 pt, int[] v0)

  Specified by:

  getInvariantSymops in interface SymmetryInterface

  Returns:

  array of 1-based symmetry operation numbers for which the pt is invariant.

• getWyckoffPosition

  public Object getWyckoffPosition(P3 p, String letter)

  Specified by:

  getWyckoffPosition in interface SymmetryInterface

• getTransform

  public M4 getTransform(P3 fracA, P3 fracB, boolean best)

  Specified by:

  getTransform in interface SymmetryInterface

  Parameters:

  fracA -

  fracB -

  Returns:

  matrix

• isWithinUnitCell

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

  Specified by:

  isWithinUnitCell in interface SymmetryInterface

• checkPeriodic

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

  Specified by:

  checkPeriodic in interface SymmetryInterface

• staticConvertOperation

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

  Specified by:

  staticConvertOperation in interface SymmetryInterface

• getSubgroupJSON

  public Object getSubgroupJSON(String nameFrom, String nameTo, int i1, int i2, int flags, Map<String,Object> retMap, Lst<Object> retLst)

  Retrieve subgroup information for a space group. This method allows for recursive searching of the ITA maximal subgroup tree to find a path to a target subgroup. Returns: values are 1-based so that "0" has special meaning, "-" means ignored; "MnV" is Integer.MIN_VALUE Critical information array is: [ isub, ntrm, subIndex, idet, trType ] isub: subgroupNumber ntrm: transformation count subIndex: index of this group-subgroup relationship idet: determinant if determinant >= 1; -1/determinant if determinant invalid input: '<' 1 trType: 1 translationengeliechen, 3 klassengleichen "ct" loss of centering translation, 4 klassengleichen "eu" enlarged unit cell

  Specified by:

  getSubgroupJSON in interface SymmetryInterface

  Parameters:

  nameFrom -

  nameTo -

  i1 - for a specific index or Integer.MIN_VALUE for all itaFrom; itaTo ignored

  i2 - Integer.MIN_VALUE for all, or an index for a specific transform

  flags - what to do if we don't find a maximal subgroup; if non-zero, we will search the maximal subgroup tree for a path flags = (indexMax invalid input: '<'invalid input: '<' 24) | indexMin invalid input: '<'invalid input: '<' 16 | depthMax invalid input: '<'invalid input: '<' 8 | depthMin

  Returns:

  Map, Lst, or String with conjugation class removed (first two characters "a:......")

• getSpaceGroupJSON

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

  Specified by:

  getSpaceGroupJSON in interface SymmetryInterface

• getCellWeight

  public float getCellWeight(P3 pt)

  Specified by:

  getCellWeight in interface SymmetryInterface

• getPrecision

  public float getPrecision()

  Specified by:

  getPrecision in interface SymmetryInterface

• fixUnitCell

  public boolean fixUnitCell(float[] params)

  Specified by:

  fixUnitCell in interface SymmetryInterface

• staticGetTransformABC

  public String staticGetTransformABC(M4 transform, boolean normalize)

  Specified by:

  staticGetTransformABC in interface SymmetryInterface

• setSymmetryInfoFromFile

  public void setSymmetryInfoFromFile(ModelSet ms, int modelIndex, float[] unitCellParams)

  Set space group and unit cell from the auxiliary info generated by XtalSymmetry specific to a given model. Only called by ModelLoader.

  Parameters:

  ms -

  modelIndex -

  unitCellParams -

• transformUnitCell

  public void transformUnitCell(M4 trm)

  Transform the unit cell based on the calculated transformation matrix. From SpaceGroupFinder only.

  Parameters:

  trm -

• staticCleanTransform

  public String staticCleanTransform(String tr)

  Normalize the transform, changing for instance a+1/2,b,c to "a,b,c;1/2,0,0" From SpaceGroupFinder only.

  Specified by:

  staticCleanTransform in interface SymmetryInterface

• saveOrRetrieveTransformMatrix

  public M4 saveOrRetrieveTransformMatrix(M4 trm)

  Saved by CLEG.assignSpaceGroup; retrieved by SpaceGroupFinder. One-time save/retrieve a transformation matrix. Just a way for CLEG to pass a transform matrix off to SpaceGroupFinder.

  Specified by:

  saveOrRetrieveTransformMatrix in interface SymmetryInterface

• getUnitCellDisplayName

  public String getUnitCellDisplayName()

  Specified by:

  getUnitCellDisplayName in interface SymmetryInterface

• staticToRationalXYZ

  public String staticToRationalXYZ(P3 fPt, String sep)

  Specified by:

  staticToRationalXYZ in interface SymmetryInterface

• getFinalOperationCount

  public int getFinalOperationCount()

  Specified by:

  getFinalOperationCount in interface SymmetryInterface

• convertTransform

  public Object convertTransform(String transform, M4 trm)

  A general method to handle converstions between string-based and matrix-based representations of transformations. When the transform is non-null and other than the string "xyz", the trm matrix is filled with the matrix representation corresponding to the given string, which is expected to be in the form specified for the Bilbao Crystallographic Server/International Table of Crystallography "Pp" format (if containing "a", "b", and "c") for basis transformtions. For example, "a+b,-a+b,c;0,0,1/2". The method includes support for expressions that contain reciprocal lattice descriptions "a*", "b*", and "c*", but only when this Symmetry object has a non-null unitCell field. When involving "x", "y", or "z", then the string is expected to have the form for space group operations, for example: "x+y,-x+y,z+1/2"

  Specified by:

  convertTransform in interface SymmetryInterface

  Parameters:

  transform - the string form to be converted to matrix format; if this string involves abc, a 4x4 column matrix is returned; if xyz, a 4x4 row matrix is returned. For example, "a+b,-a+b,c;0,0,1/2" will fill trm as

  [
  [1 -1 0 0  ]
  [1  1 0 0  ] 
  [0  0 1 0.5]
  [0  0 0 1  ]
  ]
         

  while"x+y,-x+y,z+1/2" will fill trm as

  [
  [ 1 1 0 0  ]
  [-1 1 0 0  ] 
  [ 0 0 1 0.5]
  [ 0 0 0 1  ]
  ]
         

  trm -

  Returns:

  if transform is null, the abc-string equivalent to trm; if transform is "xyz", the xyz-string equivalent to the operation matrix trm; otherwise, the 4x4 matrix representing this transform or operation.

• staticGetMatrixTransform

  public M4 staticGetMatrixTransform(String cleg, Object retLstOrMap)

  Specified by:

  staticGetMatrixTransform in interface SymmetryInterface

• staticTransformSpaceGroup

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

  Specified by:

  staticTransformSpaceGroup in interface SymmetryInterface

• setViewer

  public Symmetry setViewer(Viewer vwr, String id)

  Description copied from interface: SymmetryInterface

  for Viewer.getSymStatic only

  Specified by:

  setViewer in interface SymmetryInterface

  Parameters:

  vwr -

  id - TODO

  Returns:

  this

• getUnitCellCenter

  public P3 getUnitCellCenter()

  Specified by:

  getUnitCellCenter in interface SymmetryInterface

• getConstrainableEquivAtom

  public Atom getConstrainableEquivAtom(Atom a)

  This atom is usually the atom being moved, but in some cases we need to switch to a different atom in order to avoid the special case where a screw axis (SG 224 Wyckoff i) or glide (plane group 12 Wyckoff c) creates a stationary point. In such a case, we can't do a projection the way we can with an axis or plane.

  Specified by:

  getConstrainableEquivAtom in interface SymmetryInterface

• setSpinAxisAngle

  public void setSpinAxisAngle(A4 aa)

  Specified by:

  setSpinAxisAngle in interface SymmetryInterface

• getSpinIndex

  public int getSpinIndex(int op)

  Specified by:

  getSpinIndex in interface SymmetryInterface

• getSpinSym

  public SymmetryInterface getSpinSym()

  Specified by:

  getSpinSym in interface SymmetryInterface

• updatePointGroup

  public String updatePointGroup()

  Specified by:

  updatePointGroup in interface SymmetryInterface

• toFractionalSpin

  public void toFractionalSpin(T3 v)

  Specified by:

  toFractionalSpin in interface SymmetryInterface

• toCartesianSpin

  public void toCartesianSpin(T3 v)

  Specified by:

  toCartesianSpin in interface SymmetryInterface