java.lang.Object

org.jmol.symmetry.Symmetry

All Implemented Interfaces:: SymmetryInterface

Direct Known Subclasses:: XtalSymmetry.FileSymmetry

public class Symmetry extends Object implements SymmetryInterface

Field Summary

Fields

Modifier and Type

Field

Description

boolean

isBio

SpaceGroup

spaceGroup

UnitCell

unitCell
Constructor Summary

Constructors

Constructor

Description

Symmetry()
Method Summary

Modifier and Type

Method

Description

int

addBioMoleculeOperation(M4 mat, boolean isReverse)

int

addSpaceGroupOperation(String xyz, int opId)

void

calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms)

String[]

calculateCIPChiralityForSmiles(Viewer vwr, String smiles)

boolean

checkPeriodic(P3 pt)

Object

convertTransform(String transform, M4 trm)

Object

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

boolean

fixUnitCell(float[] params)

String

geCIFWriterValue(String type)

Lst<P3>

generateCrystalClass(P3 pt00)

M4[]

getAdditionalOperations()

int

getAdditionalOperationsCount()

P3[]

getCanonicalCopy(float scale, boolean withOffset)

P3[]

getCanonicalCopyTrimmed(P3 frac, float scale)

P3

getCartesianOffset()

int[]

getCellRange()

float

getCellWeight(P3 pt)

boolean

getCoordinatesAreFractional()

int

getDimensionality()

void

getEquivPointList(Lst<P3> pts, int nInitial, String flags, M4[] opsCtr)

Lst<P3>

getEquivPoints(Lst<P3> pts, P3 pt, String flags)

int

getFinalOperationCount()

P3

getFractionalOffset(boolean onlyIfFractional)

P3

getFractionalOrigin()

String

getIntTableIndex()

String

getIntTableNumber()

String

getIntTableTransform()

int[]

getInvariantSymops(P3 pt, int[] v0)

Object

getITASettingValue(Viewer vwr, String itaIndex, String key)

AtomIndexIterator

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

Lst<P3>

getLatticeCentering()

Object

getLatticeDesignation()

int

getLatticeOp()

char

getLatticeType()

Lst<String>

getMoreInfo()

Matrix

getOperationRsVs(int iop)

int

getPeriodicity()

Object

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

String

getPointGroupName()

float

getPrecision()

Quat

getQuaternionRotation(String abc)

int

getSiteMultiplicity(P3 pt)

Object

getSpaceGroup()

String

getSpaceGroupClegId()

Map<String,Object>

getSpaceGroupInfo(ModelSet modelSet, String sgName, int modelIndex, boolean isFull, float[] cellParams)

Object

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

String

getSpaceGroupJmolId()

Object

getSpaceGroupJSON(Viewer vwr, String name, String data, int index)

String

getSpaceGroupName()

M4

getSpaceGroupOperation(int i)

int

getSpaceGroupOperationCount()

String

getSpaceGroupXyz(int i, boolean doNormalize)

int

getSpinOp(int op)

boolean

getState(ModelSet ms, int modelIndex, SB commands)

Object

getSubgroupJSON(Viewer vwr, int itaFrom, int itaTo, int index1, int index2)

Retrieve subgroup information for a space group.

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)

String

getSymmetryInfoStr()

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

SymmetryOperation[]

getSymmetryOperations()

String[]

getSymopList(boolean doNormalize)

M4

getTransform(P3 fracA, P3 fracB, boolean best)

SymmetryInterface

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

float[]

getUnitCellAsArray(boolean vectorsOnly)

P3

getUnitCellCenter()

String

getUnitCellDisplayName()

String

getUnitCellInfo(boolean scaled)

Map<String,Object>

getUnitCellInfoMap()

float

getUnitCellInfoType(int infoType)

SymmetryInterface

getUnitCellMultiplied()

Note, this has no origin shift.

T3

getUnitCellMultiplier()

float[]

getUnitCellParams()

String

getUnitCellState()

P3[]

getUnitCellVectors()

P3[]

getUnitCellVerticesNoOffset()

T3[]

getV0abc(Object def, M4 retMatrix)

Object

getWyckoffPosition(Viewer vwr, P3 p, String letter)

boolean

haveUnitCell()

void

initializeOrientation(M3 mat)

boolean

isBio()

boolean

isPolymer()

boolean

isSimple()

boolean

isSlab()

boolean

isSupercell()

boolean

isSymmetryCell(SymmetryInterface sym)

boolean

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

void

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

BS

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

BS

removeDuplicates(ModelSet ms, BS bs, boolean highPrec)

M4

replaceTransformMatrix(M4 trm)

V3[]

rotateAxes(int iop, V3[] axes, P3 ptTemp, M3 mTemp)

void

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

void

setLattice(int latt)

set symmetry lattice type using Hall rotations

void

setOffset(int nnn)

void

setOffsetPt(T3 pt)

SymmetryInterface

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

void

setSpaceGroup(boolean doNormalize)

void

setSpaceGroupName(String name)

void

setSpaceGroupTo(Object sg)

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.

void

setUnitCell(SymmetryInterface uc)

SymmetryInterface

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

SymmetryInterface

setViewer(Viewer vwr)

for the vwr.getSymTemp() only

String

staticCleanTransform(String tr)

Object

staticConvertOperation(String xyz, M4 matrix)

M4

staticGetMatrixTransform(String cleg)

String

staticGetTransformABC(Object transform, boolean normalize)

String

staticToRationalXYZ(P3 fPt, String sep)

String

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

void

toCartesian(T3 pt, boolean ignoreOffset)

void

toFractional(T3 pt, boolean ignoreOffset)

boolean

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

P3

toSupercell(P3 fpt)

void

toUnitCell(T3 pt, T3 offset)

void

transformUnitCell(M4 trm)

boolean

unitCellEquals(SymmetryInterface uc2)

void

unitize(T3 ptFrac)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- spaceGroup
  
  public SpaceGroup spaceGroup
- unitCell
  
  public UnitCell unitCell
- isBio
  
  public boolean isBio
Constructor Details
- Symmetry
  
  public 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
- getSpaceGroupXyz
  
  public String getSpaceGroupXyz(int i, boolean doNormalize)
  
  Specified by:
  
  getSpaceGroupXyz 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
- rotateAxes
  
  public V3[] rotateAxes(int iop, V3[] axes, P3 ptTemp, M3 mTemp)
  
  Specified by:
  
  rotateAxes 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)
  
  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
- getCanonicalCopyTrimmed
  
  public P3[] getCanonicalCopyTrimmed(P3 frac, float scale)
  
  Specified by:
  
  getCanonicalCopyTrimmed 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
- 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(Viewer vwr, 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(Viewer vwr, 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
- getEquivPoints
  
  public Lst<P3> getEquivPoints(Lst<P3> pts, P3 pt, String flags)
  
  Specified by:
  
  getEquivPoints in interface SymmetryInterface
- getPeriodicity
  
  public int getPeriodicity()
  
  Specified by:
  
  getPeriodicity in interface SymmetryInterface
- getDimensionality
  
  public int getDimensionality()
  
  Specified by:
  
  getDimensionality in interface SymmetryInterface
- getEquivPointList
  
  public void getEquivPointList(Lst<P3> pts, int nInitial, String flags, M4[] opsCtr)
  
  Specified by:
  
  getEquivPointList in interface SymmetryInterface
- getInvariantSymops
  
  public int[] getInvariantSymops(P3 pt, int[] v0)
  
  Specified by:
  
  getInvariantSymops in interface SymmetryInterface
- getWyckoffPosition
  
  public Object getWyckoffPosition(Viewer vwr, 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)
  
  Specified by:
  
  isWithinUnitCell in interface SymmetryInterface
- checkPeriodic
  
  public boolean checkPeriodic(P3 pt)
  
  Specified by:
  
  checkPeriodic in interface SymmetryInterface
- staticConvertOperation
  
  public Object staticConvertOperation(String xyz, M4 matrix)
  
  Specified by:
  
  staticConvertOperation in interface SymmetryInterface
- getSubgroupJSON
  
  public Object getSubgroupJSON(Viewer vwr, int itaFrom, int itaTo, int index1, int index2)
  Retrieve subgroup information for a space group. Returns:
  values are 1-based so that "0" has special meaning, "-" means ignored; "MnV" is Integer.MIN_VALUE itaFrom itaTo index1 index2 n MnV - - return map for group n, contents of sub_n.json n 0 0 0 return int[][] of critical information n 0 m MnV return map map.subgroups[m] n 0 MnV - return int[] array of list of valid super>>sub n 0 m t return string transform map.subgroups[m].trm[t] n1 n2 MnV - return list map.subgroups.select("WHERE subgroup=n2") n1 n2 m MnV return map map.subgroups.select("WHERE subgroup=n2")[m] n1 n2 m t return string transform map.subgroups.select("WHERE subgroup=n2")[m].trm[t]
  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:
  
  vwr -
  
  itaFrom - group ITA number
  
  itaTo - subgroup ITA number
  
  index1 - for a specific index or Integer.MIN_VALUE for all itaFrom; itaTo ignored
  
  index2 - Integer.MIN_VALUE for all, or an index for a specific transform
  
  Returns:
  
  Map, List, or String with conjugation class removed (first two characters "a:......")
- getSpaceGroupJSON
  
  public Object getSpaceGroupJSON(Viewer vwr, 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(Object 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)
- getITASettingValue
  
  public Object getITASettingValue(Viewer vwr, String itaIndex, String key)
  
  Specified by:
  
  getITASettingValue in interface SymmetryInterface
- staticCleanTransform
  
  public String staticCleanTransform(String tr)
  
  Specified by:
  
  staticCleanTransform in interface SymmetryInterface
- replaceTransformMatrix
  
  public M4 replaceTransformMatrix(M4 trm)
  
  Specified by:
  
  replaceTransformMatrix 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)
  
  Specified by:
  
  convertTransform in interface SymmetryInterface
- staticGetMatrixTransform
  
  public M4 staticGetMatrixTransform(String cleg)
  
  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 SymmetryInterface setViewer(Viewer vwr)
  
  for the vwr.getSymTemp() only
  
  Specified by:
  
  setViewer in interface SymmetryInterface
  
  Parameters:
  
  vwr -
  
  Returns:
  
  this
- getUnitCellCenter
  
  public P3 getUnitCellCenter()
  
  Specified by:
  
  getUnitCellCenter in interface SymmetryInterface

Class Symmetry

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

spaceGroup

unitCell

isBio

Constructor Details

Symmetry

Method Details

getSymopList

isBio

setPointGroup

getPointGroupName

getPointGroupInfo

setSpaceGroup

addSpaceGroupOperation

addBioMoleculeOperation

setLattice

getSpaceGroup

getSpaceGroupInfoObj

getLatticeDesignation

setFinalOperations

getSpaceGroupOperation

getSpaceGroupXyz

newSpaceGroupPoint

rotateAxes

getSpinOp

getLatticeOp

getLatticeCentering

getOperationRsVs

getSiteMultiplicity

getSpaceGroupName

geCIFWriterValue

getLatticeType

getIntTableNumber

getIntTableIndex

getIntTableTransform

getSpaceGroupClegId

getSpaceGroupJmolId

getCoordinatesAreFractional

getCellRange

getSymmetryInfoStr

getSpaceGroupOperationCount

getSymmetryOperations

getAdditionalOperationsCount

getAdditionalOperations

isSimple

haveUnitCell

setUnitCellFromParams

unitCellEquals

isSymmetryCell

getUnitCellState

getMoreInfo

initializeOrientation

unitize

toUnitCell

toSupercell

toFractional

toCartesian

getUnitCellParams

getUnitCellAsArray

getUnitCellVerticesNoOffset

getCartesianOffset

getFractionalOffset

setOffsetPt

setOffset

getUnitCellMultiplier

getUnitCellMultiplied

getCanonicalCopy

getCanonicalCopyTrimmed

getUnitCellInfoType

getUnitCellInfo

isSlab

isPolymer

getUnitCellVectors

getUnitCell

isSupercell