Package org.jmol.api
Interface SymmetryInterface
-
- All Known Implementing Classes:
Symmetry
public interface SymmetryInterface
-
-
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)
String
addOp(String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma)
int
addSpaceGroupOperation(String xyz, int opId)
void
calculateCIPChiralityForAtoms(Viewer vwr, javajs.util.BS bsAtoms)
String[]
calculateCIPChiralityForSmiles(Viewer vwr, 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
checkUnitCell(SymmetryInterface uc, javajs.util.P3 cell, javajs.util.P3 ptTemp, boolean isAbsolute)
boolean
createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)
String
fcoord(javajs.util.T3 p)
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(String latticeType, javajs.util.M3 primitiveToCryst)
boolean
getCoordinatesAreFractional()
javajs.util.P3
getFractionalOffset()
javajs.util.T3
getFractionalOrigin()
String
getIntTableNumber()
AtomIndexIterator
getIterator(Viewer vwr, Atom atom, Atom[] atoms, javajs.util.BS bstoms, float radius)
Object
getLatticeDesignation()
int
getLatticeOp()
String
getLatticeType()
String
getMatrixFromString(String xyz, float[] temp, boolean allowScaling, int modDim)
javajs.util.Lst<String>
getMoreInfo()
javajs.util.Matrix
getOperationRsVs(int op)
Object
getPointGroupInfo(int modelIndex, String drawID, boolean asInfo, String type, int index, float scale)
String
getPointGroupName()
javajs.util.Quat
getQuaternionRotation(String abc)
int
getSiteMultiplicity(javajs.util.P3 a)
Object
getSpaceGroup()
Map<String,Object>
getSpaceGroupInfo(ModelSet modelSet, String spaceGroup, int modelIndex, boolean isFull, float[] cellParams)
Object
getSpaceGroupInfoObj(String name, SymmetryInterface cellInfo, boolean isFull)
String
getSpaceGroupName()
javajs.util.M4
getSpaceGroupOperation(int i)
String
getSpaceGroupOperationCode(int op)
int
getSpaceGroupOperationCount()
String
getSpaceGroupXyz(int i, boolean doNormalize)
float
getSpinOp(int op)
boolean
getState(javajs.util.SB commands)
Object
getSymmetryInfoAtom(ModelSet ms, int iatom, String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type, float scaleFactor, int nth, int options)
String
getSymmetryInfoStr()
javajs.util.M4[]
getSymmetryOperations()
Tensor
getTensor(Viewer vwr, float[] anisoBorU)
SymmetryInterface
getUnitCell(javajs.util.T3[] points, boolean setRelative, String name)
float[]
getUnitCellAsArray(boolean vectorsOnly)
String
getUnitCellInfo()
Map<String,Object>
getUnitCellInfoMap()
float
getUnitCellInfoType(int infoType)
javajs.util.T3
getUnitCellMultiplier()
float[]
getUnitCellParams()
String
getUnitCellState()
javajs.util.P3[]
getUnitCellVectors()
javajs.util.P3[]
getUnitCellVerticesNoOffset()
javajs.util.T3[]
getV0abc(Object def)
boolean
haveUnitCell()
void
initializeOrientation(javajs.util.M3 matUnitCellOrientation)
boolean
isBio()
boolean
isPolymer()
boolean
isSimple()
boolean
isSlab()
boolean
isSupercell()
void
newSpaceGroupPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ, javajs.util.M4 o)
javajs.util.BS
notInCentroid(ModelSet modelSet, javajs.util.BS bsAtoms, int[] minmax)
javajs.util.V3[]
rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
void
setFinalOperations(String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, String filterSymop)
void
setLattice(int latt)
set symmetry lattice type using Hall rotationsvoid
setLatticeType(String type)
void
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
setSpaceGroupFrom(SymmetryInterface symmetry)
void
setSpaceGroupName(String name)
SymmetryInterface
setSymmetryInfo(int modelIndex, Map<String,Object> modelAuxiliaryInfo, float[] notionalCell)
void
setTimeReversal(int op, int val)
void
setUnitCell(float[] params, boolean setRelative)
void
setUnitCell(Symmetry 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)
boolean
unitCellEquals(SymmetryInterface uc2)
void
unitize(javajs.util.T3 ptFrac)
-
-
-
Method Detail
-
addBioMoleculeOperation
int addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse)
-
addLatticeVectors
boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
-
addOp
String addOp(String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma)
-
addSpaceGroupOperation
int addSpaceGroupOperation(String xyz, int opId)
-
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)
-
checkUnitCell
boolean checkUnitCell(SymmetryInterface uc, javajs.util.P3 cell, javajs.util.P3 ptTemp, boolean isAbsolute)
-
createSpaceGroup
boolean createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)
-
fcoord
String fcoord(javajs.util.T3 p)
-
getCanonicalCopy
javajs.util.P3[] getCanonicalCopy(float scale, boolean withOffset)
-
getCartesianOffset
javajs.util.P3 getCartesianOffset()
-
getCellRange
int[] getCellRange()
-
getCoordinatesAreFractional
boolean getCoordinatesAreFractional()
-
getFractionalOffset
javajs.util.P3 getFractionalOffset()
-
getLatticeDesignation
Object getLatticeDesignation()
-
getLatticeOp
int getLatticeOp()
-
getMatrixFromString
String getMatrixFromString(String xyz, float[] temp, boolean allowScaling, int modDim)
-
getMoreInfo
javajs.util.Lst<String> getMoreInfo()
-
getUnitCellParams
float[] getUnitCellParams()
-
getOperationRsVs
javajs.util.Matrix getOperationRsVs(int op)
-
getPointGroupInfo
Object getPointGroupInfo(int modelIndex, String drawID, boolean asInfo, String type, int index, float scale)
-
getPointGroupName
String getPointGroupName()
-
getSiteMultiplicity
int getSiteMultiplicity(javajs.util.P3 a)
-
getSpaceGroup
Object getSpaceGroup()
-
getSpaceGroupInfo
Map<String,Object> getSpaceGroupInfo(ModelSet modelSet, String spaceGroup, int modelIndex, boolean isFull, float[] cellParams)
-
getSpaceGroupInfoObj
Object getSpaceGroupInfoObj(String name, SymmetryInterface cellInfo, boolean isFull)
-
getSpaceGroupName
String getSpaceGroupName()
-
setSpaceGroupName
void setSpaceGroupName(String name)
-
getSpaceGroupOperation
javajs.util.M4 getSpaceGroupOperation(int i)
-
getSpaceGroupOperationCode
String getSpaceGroupOperationCode(int op)
-
getSpaceGroupOperationCount
int getSpaceGroupOperationCount()
-
getSpaceGroupXyz
String getSpaceGroupXyz(int i, boolean doNormalize)
-
getSymmetryInfoStr
String getSymmetryInfoStr()
-
getSymmetryOperations
javajs.util.M4[] getSymmetryOperations()
-
getSpinOp
float getSpinOp(int op)
-
getUnitCell
SymmetryInterface getUnitCell(javajs.util.T3[] points, boolean setRelative, String name)
-
getUnitCellAsArray
float[] getUnitCellAsArray(boolean vectorsOnly)
-
getUnitCellInfo
String getUnitCellInfo()
-
getUnitCellInfoType
float getUnitCellInfoType(int infoType)
-
getUnitCellMultiplier
javajs.util.T3 getUnitCellMultiplier()
-
getUnitCellState
String getUnitCellState()
-
getUnitCellVectors
javajs.util.P3[] getUnitCellVectors()
-
getUnitCellVerticesNoOffset
javajs.util.P3[] getUnitCellVerticesNoOffset()
-
haveUnitCell
boolean haveUnitCell()
-
isBio
boolean isBio()
-
isSimple
boolean isSimple()
-
isPolymer
boolean isPolymer()
-
isSlab
boolean isSlab()
-
isSupercell
boolean isSupercell()
-
newSpaceGroupPoint
void newSpaceGroupPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ, javajs.util.M4 o)
-
notInCentroid
javajs.util.BS notInCentroid(ModelSet modelSet, javajs.util.BS bsAtoms, int[] minmax)
-
rotateAxes
javajs.util.V3[] rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp)
-
setFinalOperations
void setFinalOperations(String name, javajs.util.P3[] atoms, int iAtomFirst, int noSymmetryCount, boolean doNormalize, String filterSymop)
-
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
-
setOffset
void setOffset(int nnn)
-
setOffsetPt
void setOffsetPt(javajs.util.T3 pt)
-
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)
-
setSpaceGroup
void setSpaceGroup(boolean doNormalize)
-
setSpaceGroupFrom
void setSpaceGroupFrom(SymmetryInterface symmetry)
-
setSymmetryInfo
SymmetryInterface setSymmetryInfo(int modelIndex, Map<String,Object> modelAuxiliaryInfo, float[] notionalCell)
-
getSymmetryInfoAtom
Object getSymmetryInfoAtom(ModelSet ms, int iatom, String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type, float scaleFactor, int nth, int options)
- Parameters:
ms
-iatom
-xyz
-op
-pt
-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
-
setTimeReversal
void setTimeReversal(int op, int val)
-
setUnitCell
void setUnitCell(float[] params, boolean setRelative)
-
initializeOrientation
void initializeOrientation(javajs.util.M3 matUnitCellOrientation)
-
toCartesian
void toCartesian(javajs.util.T3 pt, boolean asAbsolute)
-
toFractional
void toFractional(javajs.util.T3 pt, boolean asAbsolute)
-
toSupercell
javajs.util.P3 toSupercell(javajs.util.P3 fpt)
-
toUnitCell
void toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset)
-
unitCellEquals
boolean unitCellEquals(SymmetryInterface uc2)
-
unitize
void unitize(javajs.util.T3 ptFrac)
-
getV0abc
javajs.util.T3[] getV0abc(Object def)
-
getQuaternionRotation
javajs.util.Quat getQuaternionRotation(String abc)
-
getFractionalOrigin
javajs.util.T3 getFractionalOrigin()
-
getState
boolean getState(javajs.util.SB commands)
-
getIterator
AtomIndexIterator getIterator(Viewer vwr, Atom atom, Atom[] atoms, javajs.util.BS bstoms, float radius)
-
toFromPrimitive
boolean toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] oabc, javajs.util.M3 primitiveToCrystal)
-
getLatticeType
String getLatticeType()
-
setLatticeType
void setLatticeType(String type)
-
getIntTableNumber
String getIntTableNumber()
-
generateCrystalClass
javajs.util.Lst<javajs.util.P3> generateCrystalClass(javajs.util.P3 pt0)
-
toFractionalM
void toFractionalM(javajs.util.M4 m)
-
calculateCIPChiralityForAtoms
void calculateCIPChiralityForAtoms(Viewer vwr, javajs.util.BS bsAtoms)
-
calculateCIPChiralityForSmiles
String[] calculateCIPChiralityForSmiles(Viewer vwr, String smiles) throws Exception
- Throws:
Exception
-
getConventionalUnitCell
javajs.util.T3[] getConventionalUnitCell(String latticeType, javajs.util.M3 primitiveToCryst)
-
setUnitCell
void setUnitCell(Symmetry uc)
-
-