Package org.jmol.api
Interface SymmetryInterface
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- All Known Implementing Classes:
Symmetry
public interface SymmetryInterface
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description int
addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse)
boolean
addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
int
addSpaceGroupOperation(java.lang.String xyz, int opId)
java.lang.String
addSubSystemOp(java.lang.String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma)
void
calculateCIPChiralityForAtoms(Viewer vwr, javajs.util.BS bsAtoms)
java.lang.String[]
calculateCIPChiralityForSmiles(Viewer vwr, java.lang.String smiles)
boolean
checkDistance(javajs.util.P3 f1, javajs.util.P3 f2, float distance, float dx, int iRange, int jRange, int kRange, javajs.util.P3 ptOffset)
boolean
createSpaceGroup(int desiredSpaceGroupIndex, java.lang.String name, java.lang.Object data, int modDim)
java.lang.String
fcoord(javajs.util.T3 p)
java.lang.Object
findSpaceGroup(Viewer vwr, javajs.util.BS atoms, java.lang.String op, boolean asString)
javajs.util.Lst<javajs.util.P3>
generateCrystalClass(javajs.util.P3 pt0)
javajs.util.P3[]
getCanonicalCopy(float scale, boolean withOffset)
javajs.util.P3
getCartesianOffset()
int[]
getCellRange()
javajs.util.T3[]
getConventionalUnitCell(java.lang.String latticeType, javajs.util.M3 primitiveToCryst)
boolean
getCoordinatesAreFractional()
void
getEquivPointList(javajs.util.Lst<javajs.util.P3> pts, int nIgnore, java.lang.String flags)
javajs.util.Lst<javajs.util.P3>
getEquivPoints(javajs.util.Lst<javajs.util.P3> pts, javajs.util.P3 pt, java.lang.String flags)
javajs.util.P3
getFractionalOffset()
javajs.util.T3
getFractionalOrigin()
java.lang.String
getIntTableNumber()
int[]
getInvariantSymops(javajs.util.P3 p3, int[] v0)
AtomIndexIterator
getIterator(Viewer vwr, Atom atom, javajs.util.BS bstoms, float radius)
javajs.util.Lst<javajs.util.P3>
getLatticeCentering()
java.lang.Object
getLatticeDesignation()
int
getLatticeOp()
char
getLatticeType()
java.lang.String
getMatrixFromString(java.lang.String xyz, float[] temp, boolean allowScaling, int modDim)
javajs.util.Lst<java.lang.String>
getMoreInfo()
javajs.util.Matrix
getOperationRsVs(int op)
java.lang.Object
getPointGroupInfo(int modelIndex, java.lang.String drawID, boolean asInfo, java.lang.String type, int index, float scale)
java.lang.String
getPointGroupName()
javajs.util.Quat
getQuaternionRotation(java.lang.String abc)
int
getSiteMultiplicity(javajs.util.P3 a)
java.lang.Object
getSpaceGroup()
java.util.Map<java.lang.String,java.lang.Object>
getSpaceGroupInfo(ModelSet modelSet, java.lang.String spaceGroup, int modelIndex, boolean isFull, float[] cellParams)
java.lang.Object
getSpaceGroupInfoObj(java.lang.String name, SymmetryInterface cellInfo, boolean isFull, boolean addNonstandard)
java.lang.String
getSpaceGroupName()
java.lang.String
getSpaceGroupNameType(java.lang.String type)
javajs.util.M4
getSpaceGroupOperation(int i)
java.lang.String
getSpaceGroupOperationCode(int op)
int
getSpaceGroupOperationCount()
javajs.util.M4
getSpaceGroupOperationRaw(int i)
java.lang.String
getSpaceGroupXyz(int i, boolean doNormalize)
float
getSpinOp(int op)
boolean
getState(ModelSet ms, int modelIndex, javajs.util.SB commands)
java.lang.Object
getSymmetryInfoAtom(ModelSet ms, 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)
java.lang.String
getSymmetryInfoStr()
javajs.util.M4[]
getSymmetryOperations()
Tensor
getTensor(Viewer vwr, float[] anisoBorU)
javajs.util.M4
getTransform(javajs.util.P3 fracA, javajs.util.P3 fracB, boolean debug)
SymmetryInterface
getUnitCell(javajs.util.T3[] points, boolean setRelative, java.lang.String name)
float[]
getUnitCellAsArray(boolean vectorsOnly)
java.lang.String
getUnitCellInfo(boolean scaled)
java.util.Map<java.lang.String,java.lang.Object>
getUnitCellInfoMap()
float
getUnitCellInfoType(int infoType)
SymmetryInterface
getUnitCellMultiplied()
javajs.util.T3
getUnitCellMultiplier()
float[]
getUnitCellParams()
java.lang.String
getUnitCellState()
javajs.util.P3[]
getUnitCellVectors()
javajs.util.P3[]
getUnitCellVerticesNoOffset()
javajs.util.T3[]
getV0abc(java.lang.Object def)
boolean
haveUnitCell()
void
initializeOrientation(javajs.util.M3 matUnitCellOrientation)
boolean
isBio()
boolean
isPolymer()
boolean
isSimple()
boolean
isSlab()
boolean
isSupercell()
void
newSpaceGroupPoint(javajs.util.P3 pt, int i, javajs.util.M4 o, int transX, int transY, int transZ, javajs.util.P3 retPoint)
javajs.util.BS
notInCentroid(ModelSet modelSet, javajs.util.BS bsAtoms, int[] minmax)
javajs.util.BS
removeDuplicates(ModelSet ms, javajs.util.BS bs)
javajs.util.V3[]
rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
void
setFinalOperations(int dim, java.lang.String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, java.lang.String filterSymop)
void
setLattice(int latt)
set symmetry lattice type using Hall rotationsvoid
setOffset(int nnn)
void
setOffsetPt(javajs.util.T3 pt)
SymmetryInterface
setPointGroup(SymmetryInterface pointGroupPrevious, javajs.util.T3 center, javajs.util.T3[] atomset, javajs.util.BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, boolean localEnvOnly)
void
setSpaceGroup(boolean doNormalize)
void
setSpaceGroupName(java.lang.String name)
void
setSpaceGroupTo(java.lang.Object spaceGroup)
SymmetryInterface
setSymmetryInfo(int modelIndex, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo, float[] notionalCell)
void
setTimeReversal(int op, int val)
SymmetryInterface
setUnitCell(float[] params, boolean setRelative)
void
setUnitCell(SymmetryInterface uc)
void
toCartesian(javajs.util.T3 pt, boolean asAbsolute)
void
toFractional(javajs.util.T3 pt, boolean asAbsolute)
void
toFractionalM(javajs.util.M4 m)
boolean
toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] oabc, javajs.util.M3 primitiveToCrystal)
javajs.util.P3
toSupercell(javajs.util.P3 fpt)
void
toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset)
void
toUnitCellRnd(javajs.util.T3 pt, javajs.util.T3 offset)
boolean
unitCellEquals(SymmetryInterface uc2)
void
unitize(javajs.util.T3 ptFrac)
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Method Detail
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addBioMoleculeOperation
int addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse)
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addLatticeVectors
boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
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addSpaceGroupOperation
int addSpaceGroupOperation(java.lang.String xyz, int opId)
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addSubSystemOp
java.lang.String addSubSystemOp(java.lang.String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma)
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calculateCIPChiralityForAtoms
void calculateCIPChiralityForAtoms(Viewer vwr, javajs.util.BS bsAtoms)
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calculateCIPChiralityForSmiles
java.lang.String[] calculateCIPChiralityForSmiles(Viewer vwr, java.lang.String smiles) throws java.lang.Exception
- Throws:
java.lang.Exception
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checkDistance
boolean checkDistance(javajs.util.P3 f1, javajs.util.P3 f2, float distance, float dx, int iRange, int jRange, int kRange, javajs.util.P3 ptOffset)
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createSpaceGroup
boolean createSpaceGroup(int desiredSpaceGroupIndex, java.lang.String name, java.lang.Object data, int modDim)
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fcoord
java.lang.String fcoord(javajs.util.T3 p)
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findSpaceGroup
java.lang.Object findSpaceGroup(Viewer vwr, javajs.util.BS atoms, java.lang.String op, boolean asString)
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generateCrystalClass
javajs.util.Lst<javajs.util.P3> generateCrystalClass(javajs.util.P3 pt0)
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getCanonicalCopy
javajs.util.P3[] getCanonicalCopy(float scale, boolean withOffset)
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getCartesianOffset
javajs.util.P3 getCartesianOffset()
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getCellRange
int[] getCellRange()
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getConventionalUnitCell
javajs.util.T3[] getConventionalUnitCell(java.lang.String latticeType, javajs.util.M3 primitiveToCryst)
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getCoordinatesAreFractional
boolean getCoordinatesAreFractional()
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getEquivPointList
void getEquivPointList(javajs.util.Lst<javajs.util.P3> pts, int nIgnore, java.lang.String flags)
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getEquivPoints
javajs.util.Lst<javajs.util.P3> getEquivPoints(javajs.util.Lst<javajs.util.P3> pts, javajs.util.P3 pt, java.lang.String flags)
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getFractionalOffset
javajs.util.P3 getFractionalOffset()
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getFractionalOrigin
javajs.util.T3 getFractionalOrigin()
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getIntTableNumber
java.lang.String getIntTableNumber()
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getInvariantSymops
int[] getInvariantSymops(javajs.util.P3 p3, int[] v0)
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getIterator
AtomIndexIterator getIterator(Viewer vwr, Atom atom, javajs.util.BS bstoms, float radius)
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getLatticeCentering
javajs.util.Lst<javajs.util.P3> getLatticeCentering()
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getLatticeDesignation
java.lang.Object getLatticeDesignation()
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getLatticeOp
int getLatticeOp()
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getLatticeType
char getLatticeType()
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getMatrixFromString
java.lang.String getMatrixFromString(java.lang.String xyz, float[] temp, boolean allowScaling, int modDim)
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getMoreInfo
javajs.util.Lst<java.lang.String> getMoreInfo()
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getOperationRsVs
javajs.util.Matrix getOperationRsVs(int op)
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getPointGroupInfo
java.lang.Object getPointGroupInfo(int modelIndex, java.lang.String drawID, boolean asInfo, java.lang.String type, int index, float scale)
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getPointGroupName
java.lang.String getPointGroupName()
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getQuaternionRotation
javajs.util.Quat getQuaternionRotation(java.lang.String abc)
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getSiteMultiplicity
int getSiteMultiplicity(javajs.util.P3 a)
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getSpaceGroup
java.lang.Object getSpaceGroup()
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getSpaceGroupInfo
java.util.Map<java.lang.String,java.lang.Object> getSpaceGroupInfo(ModelSet modelSet, java.lang.String spaceGroup, int modelIndex, boolean isFull, float[] cellParams)
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getSpaceGroupInfoObj
java.lang.Object getSpaceGroupInfoObj(java.lang.String name, SymmetryInterface cellInfo, boolean isFull, boolean addNonstandard)
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getSpaceGroupName
java.lang.String getSpaceGroupName()
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getSpaceGroupNameType
java.lang.String getSpaceGroupNameType(java.lang.String type)
- Parameters:
type
- "Hall" or "HM" or "ITA"- Returns:
- type or null
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getSpaceGroupOperation
javajs.util.M4 getSpaceGroupOperation(int i)
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getSpaceGroupOperationCode
java.lang.String getSpaceGroupOperationCode(int op)
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getSpaceGroupOperationCount
int getSpaceGroupOperationCount()
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getSpaceGroupOperationRaw
javajs.util.M4 getSpaceGroupOperationRaw(int i)
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getSpaceGroupXyz
java.lang.String getSpaceGroupXyz(int i, boolean doNormalize)
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getSpinOp
float getSpinOp(int op)
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getState
boolean getState(ModelSet ms, int modelIndex, javajs.util.SB commands)
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getSymmetryInfoAtom
java.lang.Object getSymmetryInfoAtom(ModelSet ms, 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)
- Parameters:
ms
-iatom
-xyz
-op
-translation
- TODOpt
-pt2
- a second point or an offsetid
-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.centerscaleFactor
-nth
- TODOoptions
- could be T.offset- Returns:
- a variety of object types
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getSymmetryInfoStr
java.lang.String getSymmetryInfoStr()
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getSymmetryOperations
javajs.util.M4[] getSymmetryOperations()
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getTransform
javajs.util.M4 getTransform(javajs.util.P3 fracA, javajs.util.P3 fracB, boolean debug)
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getUnitCell
SymmetryInterface getUnitCell(javajs.util.T3[] points, boolean setRelative, java.lang.String name)
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getUnitCellAsArray
float[] getUnitCellAsArray(boolean vectorsOnly)
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getUnitCellInfo
java.lang.String getUnitCellInfo(boolean scaled)
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getUnitCellInfoMap
java.util.Map<java.lang.String,java.lang.Object> getUnitCellInfoMap()
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getUnitCellInfoType
float getUnitCellInfoType(int infoType)
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getUnitCellMultiplied
SymmetryInterface getUnitCellMultiplied()
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getUnitCellMultiplier
javajs.util.T3 getUnitCellMultiplier()
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getUnitCellParams
float[] getUnitCellParams()
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getUnitCellState
java.lang.String getUnitCellState()
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getUnitCellVectors
javajs.util.P3[] getUnitCellVectors()
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getUnitCellVerticesNoOffset
javajs.util.P3[] getUnitCellVerticesNoOffset()
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getV0abc
javajs.util.T3[] getV0abc(java.lang.Object def)
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haveUnitCell
boolean haveUnitCell()
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initializeOrientation
void initializeOrientation(javajs.util.M3 matUnitCellOrientation)
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isBio
boolean isBio()
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isPolymer
boolean isPolymer()
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isSimple
boolean isSimple()
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isSlab
boolean isSlab()
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isSupercell
boolean isSupercell()
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newSpaceGroupPoint
void newSpaceGroupPoint(javajs.util.P3 pt, int i, javajs.util.M4 o, int transX, int transY, int transZ, javajs.util.P3 retPoint)
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notInCentroid
javajs.util.BS notInCentroid(ModelSet modelSet, javajs.util.BS bsAtoms, int[] minmax)
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removeDuplicates
javajs.util.BS removeDuplicates(ModelSet ms, javajs.util.BS bs)
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rotateAxes
javajs.util.V3[] rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
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setFinalOperations
void setFinalOperations(int dim, java.lang.String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, java.lang.String filterSymop)
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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
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setOffset
void setOffset(int nnn)
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setOffsetPt
void setOffsetPt(javajs.util.T3 pt)
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setPointGroup
SymmetryInterface setPointGroup(SymmetryInterface pointGroupPrevious, javajs.util.T3 center, javajs.util.T3[] atomset, javajs.util.BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, boolean localEnvOnly)
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setSpaceGroup
void setSpaceGroup(boolean doNormalize)
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setSpaceGroupName
void setSpaceGroupName(java.lang.String name)
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setSpaceGroupTo
void setSpaceGroupTo(java.lang.Object spaceGroup)
- Parameters:
spaceGroup
- ITA number, ITA full name ("48:1")
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setSymmetryInfo
SymmetryInterface setSymmetryInfo(int modelIndex, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo, float[] notionalCell)
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setTimeReversal
void setTimeReversal(int op, int val)
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setUnitCell
SymmetryInterface setUnitCell(float[] params, boolean setRelative)
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setUnitCell
void setUnitCell(SymmetryInterface uc)
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toCartesian
void toCartesian(javajs.util.T3 pt, boolean asAbsolute)
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toFractional
void toFractional(javajs.util.T3 pt, boolean asAbsolute)
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toFractionalM
void toFractionalM(javajs.util.M4 m)
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toFromPrimitive
boolean toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] oabc, javajs.util.M3 primitiveToCrystal)
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toSupercell
javajs.util.P3 toSupercell(javajs.util.P3 fpt)
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toUnitCell
void toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset)
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toUnitCellRnd
void toUnitCellRnd(javajs.util.T3 pt, javajs.util.T3 offset)
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unitCellEquals
boolean unitCellEquals(SymmetryInterface uc2)
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unitize
void unitize(javajs.util.T3 ptFrac)
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