Package org.jmol.api
Interface SymmetryInterface
- All Known Implementing Classes:
Symmetry
public interface SymmetryInterface
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Method Summary
Modifier and TypeMethodDescriptionint
addBioMoleculeOperation
(javajs.util.M4 mat, boolean isReverse) boolean
addLatticeVectors
(javajs.util.Lst<float[]> lattvecs) int
addSpaceGroupOperation
(String xyz, int opId) addSubSystemOp
(String code, javajs.util.Matrix rs, javajs.util.Matrix vs, javajs.util.Matrix sigma) 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
createSpaceGroup
(int desiredSpaceGroupIndex, String name, Object data, int modDim) fcoord
(javajs.util.T3 p) findSpaceGroup
(Viewer vwr, javajs.util.BS atoms, String xyzList, float[] unitcellParams, boolean asString, boolean isAssign) javajs.util.Lst<javajs.util.P3>
generateCrystalClass
(javajs.util.P3 pt0) javajs.util.P3[]
getCanonicalCopy
(float scale, boolean withOffset) javajs.util.P3
int[]
javajs.util.T3[]
getConventionalUnitCell
(String latticeType, javajs.util.M3 primitiveToCryst) boolean
void
getEquivPointList
(javajs.util.Lst<javajs.util.P3> pts, int nIgnore, String flags) javajs.util.Lst<javajs.util.P3>
getEquivPoints
(javajs.util.Lst<javajs.util.P3> pts, javajs.util.P3 pt, String flags) javajs.util.P3
javajs.util.T3
int[]
getInvariantSymops
(javajs.util.P3 p3, int[] v0) getIterator
(Viewer vwr, Atom atom, javajs.util.BS bstoms, float radius) javajs.util.Lst<javajs.util.P3>
int
char
getMatrixFromString
(String xyz, float[] temp, boolean allowScaling, int modDim) javajs.util.Lst<String>
javajs.util.Matrix
getOperationRsVs
(int op) getPointGroupInfo
(int modelIndex, String drawID, boolean asInfo, String type, int index, float scale) javajs.util.Quat
int
getSiteMultiplicity
(javajs.util.P3 a) getSpaceGroupInfo
(ModelSet modelSet, String spaceGroup, int modelIndex, boolean isFull, float[] cellParams) getSpaceGroupInfoObj
(String name, float[] params, boolean isFull, boolean addNonstandard) getSpaceGroupNameType
(String type) javajs.util.M4
getSpaceGroupOperation
(int i) getSpaceGroupOperationCode
(int op) int
getSpaceGroupXyz
(int i, boolean doNormalize) float
getSpinOp
(int op) boolean
getSymmetryInfoAtom
(ModelSet ms, int iatom, String xyz, int op, javajs.util.P3 translation, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type, float scaleFactor, int nth, int options) javajs.util.M4[]
javajs.util.M4
getTransform
(javajs.util.P3 fracA, javajs.util.P3 fracB, boolean debug) getUnitCell
(javajs.util.T3[] points, boolean setRelative, String name) float[]
getUnitCellAsArray
(boolean vectorsOnly) getUnitCellInfo
(boolean scaled) float
getUnitCellInfoType
(int infoType) javajs.util.T3
float[]
javajs.util.P3[]
javajs.util.P3[]
javajs.util.T3[]
boolean
void
initializeOrientation
(javajs.util.M3 matUnitCellOrientation) boolean
isBio()
boolean
boolean
isSimple()
boolean
isSlab()
boolean
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, boolean highPrec) javajs.util.V3[]
rotateAxes
(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp) void
setFinalOperations
(int dim, 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
setOffset
(int nnn) void
setOffsetPt
(javajs.util.T3 pt) setPointGroup
(SymmetryInterface pointGroupPrevious, javajs.util.T3 center, javajs.util.T3[] atomset, javajs.util.BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) void
setSpaceGroup
(boolean doNormalize) void
setSpaceGroupName
(String name) void
setSpaceGroupTo
(Object spaceGroup) setSymmetryInfo
(int modelIndex, Map<String, Object> modelAuxiliaryInfo, float[] notionalCell) void
setTimeReversal
(int op, int val) setUnitCell
(float[] params, boolean setRelative) void
void
toCartesian
(javajs.util.T3 pt, boolean ignoreOffset) void
toFractional
(javajs.util.T3 pt, boolean ignoreOffset) 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
void
unitize
(javajs.util.T3 ptFrac)
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Method Details
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addBioMoleculeOperation
int addBioMoleculeOperation(javajs.util.M4 mat, boolean isReverse) -
addLatticeVectors
boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs) -
addSpaceGroupOperation
-
addSubSystemOp
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calculateCIPChiralityForAtoms
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calculateCIPChiralityForSmiles
- Throws:
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) -
createSpaceGroup
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fcoord
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findSpaceGroup
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generateCrystalClass
javajs.util.Lst<javajs.util.P3> generateCrystalClass(javajs.util.P3 pt0) -
getCanonicalCopy
javajs.util.P3[] getCanonicalCopy(float scale, boolean withOffset) -
getCartesianOffset
javajs.util.P3 getCartesianOffset() -
getCellRange
int[] getCellRange() -
getConventionalUnitCell
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getCoordinatesAreFractional
boolean getCoordinatesAreFractional() -
getEquivPointList
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getEquivPoints
javajs.util.Lst<javajs.util.P3> getEquivPoints(javajs.util.Lst<javajs.util.P3> pts, javajs.util.P3 pt, String flags) -
getFractionalOffset
javajs.util.P3 getFractionalOffset() -
getFractionalOrigin
javajs.util.T3 getFractionalOrigin() -
getIntTableNumber
String getIntTableNumber() -
getInvariantSymops
int[] getInvariantSymops(javajs.util.P3 p3, int[] v0) -
getIterator
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getLatticeCentering
javajs.util.Lst<javajs.util.P3> getLatticeCentering() -
getLatticeDesignation
Object getLatticeDesignation() -
getLatticeOp
int getLatticeOp() -
getLatticeType
char getLatticeType() -
getMatrixFromString
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getMoreInfo
javajs.util.Lst<String> getMoreInfo() -
getOperationRsVs
javajs.util.Matrix getOperationRsVs(int op) -
getPointGroupInfo
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getPointGroupName
String getPointGroupName() -
getQuaternionRotation
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getSiteMultiplicity
int getSiteMultiplicity(javajs.util.P3 a) -
getSpaceGroup
Object getSpaceGroup() -
getSpaceGroupInfo
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getSpaceGroupInfoObj
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getSpaceGroupName
String getSpaceGroupName() -
getSpaceGroupNameType
- Parameters:
type
- "Hall" or "HM" or "ITA"- Returns:
- type or null
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getSpaceGroupOperation
javajs.util.M4 getSpaceGroupOperation(int i) -
getSpaceGroupOperationCode
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getSpaceGroupOperationCount
int getSpaceGroupOperationCount() -
getSpaceGroupXyz
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getSpinOp
float getSpinOp(int op) -
getState
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getSymmetryInfoAtom
Object getSymmetryInfoAtom(ModelSet ms, int iatom, String xyz, int op, javajs.util.P3 translation, javajs.util.P3 pt, javajs.util.P3 pt2, 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
String getSymmetryInfoStr() -
getSymmetryOperations
javajs.util.M4[] getSymmetryOperations() -
getTensor
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getTransform
javajs.util.M4 getTransform(javajs.util.P3 fracA, javajs.util.P3 fracB, boolean debug) -
getUnitCell
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getUnitCellAsArray
float[] getUnitCellAsArray(boolean vectorsOnly) -
getUnitCellInfo
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getUnitCellInfoMap
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getUnitCellInfoType
float getUnitCellInfoType(int infoType) -
getUnitCellMultiplied
SymmetryInterface getUnitCellMultiplied() -
getUnitCellMultiplier
javajs.util.T3 getUnitCellMultiplier() -
getUnitCellParams
float[] getUnitCellParams() -
getUnitCellState
String getUnitCellState() -
getUnitCellVectors
javajs.util.P3[] getUnitCellVectors() -
getUnitCellVerticesNoOffset
javajs.util.P3[] getUnitCellVerticesNoOffset() -
getV0abc
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haveUnitCell
boolean haveUnitCell() -
initializeOrientation
void initializeOrientation(javajs.util.M3 matUnitCellOrientation) -
isBio
boolean isBio() -
isPolymer
boolean isPolymer() -
isSimple
boolean isSimple() -
isSlab
boolean isSlab() -
isSupercell
boolean isSupercell() -
newSpaceGroupPoint
void newSpaceGroupPoint(javajs.util.P3 pt, int i, javajs.util.M4 o, int transX, int transY, int transZ, javajs.util.P3 retPoint) -
notInCentroid
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removeDuplicates
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rotateAxes
javajs.util.V3[] rotateAxes(int iop, javajs.util.V3[] axes, javajs.util.P3 ptTemp, javajs.util.M3 mTemp) -
setFinalOperations
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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) -
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, int maxAtoms, boolean localEnvOnly) -
setSpaceGroup
void setSpaceGroup(boolean doNormalize) -
setSpaceGroupName
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setSpaceGroupTo
- Parameters:
spaceGroup
- ITA number, ITA full name ("48:1")
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setSymmetryInfo
SymmetryInterface setSymmetryInfo(int modelIndex, Map<String, Object> modelAuxiliaryInfo, float[] notionalCell) -
setTimeReversal
void setTimeReversal(int op, int val) -
setUnitCell
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setUnitCell
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toCartesian
void toCartesian(javajs.util.T3 pt, boolean ignoreOffset) -
toFractional
void toFractional(javajs.util.T3 pt, boolean ignoreOffset) -
toFractionalM
void toFractionalM(javajs.util.M4 m) -
toFromPrimitive
boolean toFromPrimitive(boolean toPrimitive, char type, javajs.util.T3[] oabc, javajs.util.M3 primitiveToCrystal) -
toSupercell
javajs.util.P3 toSupercell(javajs.util.P3 fpt) -
toUnitCell
void toUnitCell(javajs.util.T3 pt, javajs.util.T3 offset) -
toUnitCellRnd
void toUnitCellRnd(javajs.util.T3 pt, javajs.util.T3 offset) -
unitCellEquals
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unitize
void unitize(javajs.util.T3 ptFrac)
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