Package org.jmol.adapter.smarter
Class XtalSymmetry.FileSymmetry
java.lang.Object
org.jmol.symmetry.Symmetry
org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry
- All Implemented Interfaces:
SymmetryInterface
- Enclosing class:
XtalSymmetry
A class only used by adapter.smarter.XtalSymmetry while building the
file-based model.
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Field Summary
Fields inherited from class org.jmol.symmetry.Symmetry
isBio, spaceGroup, unitCell
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
boolean
addLatticeVectors
(Lst<float[]> lattvecs) addSubSystemOp
(String code, Matrix rs, Matrix vs, Matrix sigma) boolean
checkDistance
(P3 f1, P3 f2, float distance, float dx, int iRange, int jRange, int kRange, P3 ptOffset) boolean
createSpaceGroup
(int desiredSpaceGroupIndex, String name, Object data, int modDim) void
getMatrixFromString
(String xyz, float[] rotTransMatrix) MMCifReader onlygetSpaceGroupOperationCode
(int iOp) void
setPrecision
(float prec) void
toFractionalM
(M4 m) void
toUnitCellRnd
(T3 pt, T3 offset) void
twelfthify
(P3 pt) Methods inherited from class org.jmol.symmetry.Symmetry
addBioMoleculeOperation, addSpaceGroupOperation, calculateCIPChiralityForAtoms, calculateCIPChiralityForSmiles, checkPeriodic, convertTransform, findSpaceGroup, fixUnitCell, geCIFWriterValue, generateCrystalClass, getAdditionalOperations, getAdditionalOperationsCount, getCanonicalCopy, getCanonicalCopyTrimmed, getCartesianOffset, getCellRange, getCellWeight, getCoordinatesAreFractional, getDimensionality, getEquivPointList, getEquivPoints, getFinalOperationCount, getFractionalOffset, getFractionalOrigin, getIntTableIndex, getIntTableNumber, getIntTableTransform, getInvariantSymops, getITASettingValue, getIterator, getLatticeCentering, getLatticeDesignation, getLatticeOp, getLatticeType, getMoreInfo, getOperationRsVs, getPeriodicity, getPointGroupInfo, getPointGroupName, getPrecision, getQuaternionRotation, getSiteMultiplicity, getSpaceGroup, getSpaceGroupClegId, getSpaceGroupInfo, getSpaceGroupInfoObj, getSpaceGroupJmolId, getSpaceGroupJSON, getSpaceGroupName, getSpaceGroupOperation, getSpaceGroupOperationCount, getSpaceGroupXyz, getSpinOp, getState, getSubgroupJSON, getSymmetryInfoAtom, getSymmetryInfoStr, getSymmetryOperations, getSymopList, getTransform, getUnitCell, getUnitCellAsArray, getUnitCellCenter, getUnitCellDisplayName, getUnitCellInfo, getUnitCellInfoMap, getUnitCellInfoType, getUnitCellMultiplied, getUnitCellMultiplier, getUnitCellParams, getUnitCellState, getUnitCellVectors, getUnitCellVerticesNoOffset, getV0abc, getWyckoffPosition, haveUnitCell, initializeOrientation, isBio, isPolymer, isSimple, isSlab, isSupercell, isSymmetryCell, isWithinUnitCell, newSpaceGroupPoint, notInCentroid, removeDuplicates, replaceTransformMatrix, rotateAxes, setFinalOperations, setLattice, setOffset, setOffsetPt, setPointGroup, setSpaceGroup, setSpaceGroupName, setSpaceGroupTo, setSymmetryInfoFromFile, setUnitCell, setUnitCellFromParams, setViewer, staticCleanTransform, staticConvertOperation, staticGetMatrixTransform, staticGetTransformABC, staticToRationalXYZ, staticTransformSpaceGroup, toCartesian, toFractional, toFromPrimitive, toSupercell, toUnitCell, transformUnitCell, unitCellEquals, unitize
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Constructor Details
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FileSymmetry
public FileSymmetry()
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Method Details
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addLatticeVectors
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addSubSystemOp
- Parameters:
code
-rs
- is a full (3+d)x(3+d) array of epsilonsvs
- is a (3+d)x(1) array of translationssigma
-- Returns:
- Jones-Faithful representation
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checkDistance
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createSpaceGroup
- Parameters:
desiredSpaceGroupIndex
-name
-data
- a Lstor Lst modDim
- in [3+d] modulation dimension- Returns:
- true if a known space group
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fcoord
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getMatrixFromString
MMCifReader only- Parameters:
xyz
-rotTransMatrix
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getSpaceGroupOperationCode
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getTensor
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getSpaceGroupTitle
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setPrecision
public void setPrecision(float prec) -
toFractionalM
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toUnitCellRnd
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twelfthify
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addInversion
public void addInversion()
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