Package org.jmol.api
Interface SymmetryInterface
- All Known Implementing Classes:
Symmetry
,XtalSymmetry.FileSymmetry
public interface SymmetryInterface
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Method Summary
Modifier and TypeMethodDescriptionint
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) convertTransform
(String transform, M4 trm) findSpaceGroup
(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) boolean
fixUnitCell
(float[] unitCellParams) generateCrystalClass
(P3 pt0) M4[]
int
P3[]
getCanonicalCopy
(float scale, boolean withOffset) int[]
float
getCellWeight
(P3 pt) boolean
void
getEquivPointList
(Lst<P3> pts, int nIgnore, String flags, M4[] opsCtr) getEquivPoints
(Lst<P3> pts, P3 pt, String flags) int
int[]
getInvariantSymops
(P3 p3, int[] v0) getITASettingValue
(Viewer vwr, String itaIndex, String key) getIterator
(Viewer vwr, Atom atom, BS bstoms, float radius) int
char
getOperationRsVs
(int op) getPointGroupInfo
(int modelIndex, String drawID, boolean asInfo, String type, int index, float scale) float
int
getSpaceGroupInfo
(ModelSet modelSet, String spaceGroup, int modelIndex, boolean isFull, float[] cellParams) getSpaceGroupInfoObj
(String name, Object params, boolean isFull, boolean addNonstandard) getSpaceGroupJSON
(Viewer vwr, String name, Object data, int index) getSpaceGroupNameType
(String type) getSpaceGroupOperation
(int i) int
getSpaceGroupXyz
(int i, boolean doNormalize) int
getSpinOp
(int op) boolean
getSubgroupJSON
(Viewer vwr, int ita1, int ita2, int index1, int index2) getSymmetryInfoAtom
(ModelSet ms, int iatom, String xyz, int op, P3 translation, P3 pt, P3 pt2, String id, int type, float scaleFactor, int nth, int options, int[] oplist) M4[]
getTransform
(P3 fracA, P3 fracB, boolean debug) getUnitCell
(T3[] points, boolean setRelative, String name) float[]
getUnitCellAsArray
(boolean vectorsOnly) getUnitCellInfo
(boolean scaled) float
getUnitCellInfoType
(int infoType) float[]
P3[]
P3[]
T3[]
getWyckoffPosition
(Viewer vwr, P3 pt, String letter) boolean
void
initializeOrientation
(M3 matUnitCellOrientation) boolean
isBio()
boolean
boolean
isSimple()
boolean
isSlab()
boolean
boolean
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) notInCentroid
(ModelSet modelSet, BS bsAtoms, int[] minmax) removeDuplicates
(ModelSet ms, BS bs, boolean highPrec) 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 rotationsvoid
setOffset
(int nnn) void
setOffsetPt
(T3 pt) setPointGroup
(Viewer vwr, SymmetryInterface pointGroupPrevious, 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 spaceGroup) void
setUnitCellFromParams
(float[] params, boolean setRelative, float slop) staticConvertOperation
(String string, M4 matrix) staticGetTransformABC
(Object value, boolean normalize) staticToRationalXYZ
(P3 fPt, String sep) void
toCartesian
(T3 pt, boolean ignoreOffset) void
toFractional
(T3 pt, boolean ignoreOffset) boolean
toFromPrimitive
(boolean toPrimitive, char type, T3[] oabc, M3 primitiveToCrystal) toSupercell
(P3 fpt) void
toUnitCell
(T3 pt, T3 offset) boolean
void
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Method Details
-
addSpaceGroupOperation
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calculateCIPChiralityForAtoms
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calculateCIPChiralityForSmiles
- Throws:
Exception
-
addBioMoleculeOperation
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findSpaceGroup
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getCellRange
int[] getCellRange() -
getCoordinatesAreFractional
boolean getCoordinatesAreFractional() -
getEquivPointList
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getFractionalOffset
P3 getFractionalOffset() -
getIntTableNumber
String getIntTableNumber() -
getIntTableNumberFull
String getIntTableNumberFull() -
getLatticeOp
int getLatticeOp() -
getLatticeType
char getLatticeType() -
getMoreInfo
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getOperationRsVs
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getPointGroupName
String getPointGroupName() -
getQuaternionRotation
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getSiteMultiplicity
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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
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getSpaceGroupOperationCount
int getSpaceGroupOperationCount() -
getSpaceGroupXyz
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getSpinOp
int getSpinOp(int op) -
getState
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getSymmetryInfoStr
String getSymmetryInfoStr() -
getSymmetryOperations
M4[] getSymmetryOperations() -
getTransform
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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() -
getUnitCellParams
float[] getUnitCellParams() -
getUnitCellState
String getUnitCellState() -
getUnitCellVectors
P3[] getUnitCellVectors() -
getUnitCellVerticesNoOffset
P3[] getUnitCellVerticesNoOffset() -
getV0abc
-
haveUnitCell
boolean haveUnitCell() -
isBio
boolean isBio() -
isPolymer
boolean isPolymer() -
isSimple
boolean isSimple() -
isSlab
boolean isSlab() -
isSupercell
boolean isSupercell() -
newSpaceGroupPoint
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notInCentroid
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removeDuplicates
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rotateAxes
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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
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setSpaceGroup
void setSpaceGroup(boolean doNormalize) -
setSpaceGroupName
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setSpaceGroupTo
- Parameters:
spaceGroup
- ITA number, ITA full name ("48:1")
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setUnitCellFromParams
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setUnitCell
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toCartesian
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toFractional
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toFromPrimitive
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toUnitCell
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unitCellEquals
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unitize
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initializeOrientation
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getSymmetryInfoAtom
Object getSymmetryInfoAtom(ModelSet ms, int iatom, String xyz, int op, P3 translation, P3 pt, P3 pt2, String id, int type, float scaleFactor, int nth, int options, int[] oplist) - 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.offsetoplist
-- Returns:
- a variety of object types
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toSupercell
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getUnitCellMultiplier
T3 getUnitCellMultiplier() -
getCartesianOffset
P3 getCartesianOffset() -
getCanonicalCopy
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getLatticeCentering
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getLatticeDesignation
Object getLatticeDesignation() -
getPointGroupInfo
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setPointGroup
SymmetryInterface setPointGroup(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) -
getInvariantSymops
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getEquivPoints
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generateCrystalClass
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getFractionalOrigin
P3 getFractionalOrigin() -
getIterator
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isWithinUnitCell
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checkPeriodic
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staticConvertOperation
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getAdditionalOperationsCount
int getAdditionalOperationsCount() -
getAdditionalOperations
M4[] getAdditionalOperations() -
getWyckoffPosition
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getSpaceGroupJSON
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getCellWeight
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getPrecision
float getPrecision() -
fixUnitCell
boolean fixUnitCell(float[] unitCellParams) -
isSymmetryCell
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staticGetTransformABC
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getITASettingValue
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staticCleanTransform
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replaceTransformMatrix
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getSubgroupJSON
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getIntTableIndex
String getIntTableIndex() -
getIntTableTransform
String getIntTableTransform() -
getUnitCellDisplayName
String getUnitCellDisplayName() -
staticToRationalXYZ
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getClegId
String getClegId() -
getFinalOperationCount
int getFinalOperationCount() -
convertTransform
-