java.lang.Object

org.jmol.symmetry.Symmetry

org.jmol.adapter.smarter.XtalSymmetry.FileSymmetry

All Implemented Interfaces:: SymmetryInterface

Enclosing class:: XtalSymmetry

public static class XtalSymmetry.FileSymmetry extends Symmetry

A class only used by adapter.smarter.XtalSymmetry while building the file-based model.

Field Summary

Fields inherited from class org.jmol.symmetry.Symmetry
isBio, spaceGroup, unitCell
Constructor Summary

Constructors

Constructor

Description

FileSymmetry()
Method Summary

Modifier and Type

Method

Description

void

addInversion()

boolean

addLatticeVectors(Lst<float[]> lattvecs)

String

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)

String

fcoord(T3 p)

void

getMatrixFromString(String xyz, float[] rotTransMatrix)

MMCifReader only

String

getSpaceGroupOperationCode(int iOp)

String

getSpaceGroupTitle()

Tensor

getTensor(Viewer vwr, float[] parBorU)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- FileSymmetry
  
  public FileSymmetry()
Method Details
- addLatticeVectors
  
  public boolean addLatticeVectors(Lst<float[]> lattvecs)
- addSubSystemOp
  
  public String addSubSystemOp(String code, Matrix rs, Matrix vs, Matrix sigma)
  
  Parameters:
  
  code -
  
  rs - is a full (3+d)x(3+d) array of epsilons
  
  vs - is a (3+d)x(1) array of translations
  
  sigma -
  
  Returns:
  
  Jones-Faithful representation
- checkDistance
  
  public boolean checkDistance(P3 f1, P3 f2, float distance, float dx, int iRange, int jRange, int kRange, P3 ptOffset)
- createSpaceGroup
  
  public boolean createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)
  
  Parameters:
  
  desiredSpaceGroupIndex -
  
  name -
  
  data - a Lst or Lst
  
  modDim - in [3+d] modulation dimension
  
  Returns:
  
  true if a known space group
- fcoord
  
  public String fcoord(T3 p)
- getMatrixFromString
  
  public void getMatrixFromString(String xyz, float[] rotTransMatrix)
  
  MMCifReader only
  
  Parameters:
  
  xyz -
  
  rotTransMatrix -
- getSpaceGroupOperationCode
  
  public String getSpaceGroupOperationCode(int iOp)
- getTensor
  
  public Tensor getTensor(Viewer vwr, float[] parBorU)
- getSpaceGroupTitle
  
  public String getSpaceGroupTitle()
- setPrecision
  
  public void setPrecision(float prec)
- toFractionalM
  
  public void toFractionalM(M4 m)
- toUnitCellRnd
  
  public void toUnitCellRnd(T3 pt, T3 offset)
- twelfthify
  
  public void twelfthify(P3 pt)
- addInversion
  
  public void addInversion()

Class XtalSymmetry.FileSymmetry

Field Summary

Fields inherited from class org.jmol.symmetry.Symmetry

Constructor Summary

Method Summary

Methods inherited from class org.jmol.symmetry.Symmetry

Methods inherited from class java.lang.Object

Constructor Details

FileSymmetry

Method Details

addLatticeVectors

addSubSystemOp

checkDistance

createSpaceGroup

fcoord

getMatrixFromString

getSpaceGroupOperationCode

getTensor

getSpaceGroupTitle

setPrecision

toFractionalM

toUnitCellRnd

twelfthify

addInversion