Package org.jmol.api

Interface SymmetryInterface

All Known Implementing Classes:
Symmetry, XtalSymmetry.FileSymmetry

public interface SymmetryInterface
  • Method Details

    • addSpaceGroupOperation

      int addSpaceGroupOperation(String xyz, int opId)
    • calculateCIPChiralityForAtoms

      void calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms)
    • calculateCIPChiralityForSmiles

      String[] calculateCIPChiralityForSmiles(Viewer vwr, String smiles) throws Exception
      Throws:
      Exception
    • addBioMoleculeOperation

      int addBioMoleculeOperation(M4 mat, boolean isReverse)
    • findSpaceGroup

      Object findSpaceGroup(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags)
    • getCellRange

      int[] getCellRange()
    • getCoordinatesAreFractional

      boolean getCoordinatesAreFractional()
    • getEquivPointList

      void getEquivPointList(Lst<P3> pts, int nIgnore, String flags, M4[] opsCtr)
    • getFractionalOffset

      P3 getFractionalOffset(boolean onlyIfFractional)
    • getIntTableNumber

      String getIntTableNumber()
    • getSpaceGroupJmolId

      String getSpaceGroupJmolId()
    • getLatticeOp

      int getLatticeOp()
    • getLatticeType

      char getLatticeType()
    • getMoreInfo

      Lst<String> getMoreInfo()
    • getOperationRsVs

      Matrix getOperationRsVs(int op)
    • getPointGroupName

      String getPointGroupName()
    • getQuaternionRotation

      Quat getQuaternionRotation(String abc)
    • getSiteMultiplicity

      int getSiteMultiplicity(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, Object params, boolean isFull, boolean addNonstandard)
    • getSpaceGroupName

      String getSpaceGroupName()
    • geCIFWriterValue

      String geCIFWriterValue(String type)
    • getSpaceGroupOperation

      M4 getSpaceGroupOperation(int i)
    • getSpaceGroupOperationCount

      int getSpaceGroupOperationCount()
    • getSpaceGroupXyz

      String getSpaceGroupXyz(int i, boolean doNormalize)
    • getSpinOp

      int getSpinOp(int op)
    • getState

      boolean getState(ModelSet ms, int modelIndex, SB commands)
    • getSymmetryInfoStr

      String getSymmetryInfoStr()
    • getSymmetryOperations

      M4[] getSymmetryOperations()
    • getTransform

      M4 getTransform(P3 fracA, P3 fracB, boolean debug)
    • getUnitCell

      SymmetryInterface getUnitCell(T3[] points, boolean setRelative, String name)
    • getUnitCellAsArray

      float[] getUnitCellAsArray(boolean vectorsOnly)
    • getUnitCellInfo

      String getUnitCellInfo(boolean scaled)
    • getUnitCellInfoMap

      Map<String,Object> getUnitCellInfoMap()
    • getUnitCellInfoType

      float getUnitCellInfoType(int infoType)
    • getUnitCellMultiplied

      SymmetryInterface getUnitCellMultiplied()
    • getUnitCellParams

      float[] getUnitCellParams()
    • getUnitCellState

      String getUnitCellState()
    • getUnitCellVectors

      P3[] getUnitCellVectors()
    • getUnitCellVerticesNoOffset

      P3[] getUnitCellVerticesNoOffset()
    • getV0abc

      T3[] getV0abc(Object def, M4 m)
    • haveUnitCell

      boolean haveUnitCell()
    • isBio

      boolean isBio()
    • isPolymer

      boolean isPolymer()
    • isSimple

      boolean isSimple()
    • isSlab

      boolean isSlab()
    • isSupercell

      boolean isSupercell()
    • newSpaceGroupPoint

      void newSpaceGroupPoint(P3 pt, int i, M4 o, int transX, int transY, int transZ, P3 retPoint)
    • notInCentroid

      BS notInCentroid(ModelSet modelSet, BS bsAtoms, int[] minmax)
    • removeDuplicates

      BS removeDuplicates(ModelSet ms, BS bs, boolean highPrec)
    • rotateAxes

      V3[] rotateAxes(int iop, V3[] axes, P3 ptTemp, M3 mTemp)
    • setFinalOperations

      void setFinalOperations(int dim, String name, 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(T3 pt)
    • setSpaceGroup

      void setSpaceGroup(boolean doNormalize)
    • setSpaceGroupName

      void setSpaceGroupName(String name)
    • setSpaceGroupTo

      void setSpaceGroupTo(Object spaceGroup)
      Parameters:
      spaceGroup - ITA number, ITA full name ("48:1")
    • setUnitCellFromParams

      SymmetryInterface setUnitCellFromParams(float[] params, boolean setRelative, float slop)
    • setUnitCell

      void setUnitCell(SymmetryInterface uc)
    • toCartesian

      void toCartesian(T3 pt, boolean ignoreOffset)
    • toFractional

      void toFractional(T3 pt, boolean ignoreOffset)
    • toFromPrimitive

      boolean toFromPrimitive(boolean toPrimitive, char type, T3[] oabc, M3 primitiveToCrystal)
    • toUnitCell

      void toUnitCell(T3 pt, T3 offset)
    • unitCellEquals

      boolean unitCellEquals(SymmetryInterface uc2)
    • unitize

      void unitize(T3 ptFrac)
    • initializeOrientation

      void initializeOrientation(M3 matUnitCellOrientation)
    • 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 - TODO
      pt -
      pt2 - a second point or an offset
      id -
      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.center
      scaleFactor -
      nth - TODO
      options - could be T.offset
      oplist -
      Returns:
      a variety of object types
    • toSupercell

      P3 toSupercell(P3 fpt)
    • getUnitCellMultiplier

      T3 getUnitCellMultiplier()
    • getCartesianOffset

      P3 getCartesianOffset()
    • getCanonicalCopy

      P3[] getCanonicalCopy(float scale, boolean withOffset)
    • getCanonicalCopyTrimmed

      P3[] getCanonicalCopyTrimmed(P3 frac, float scale)
    • getLatticeCentering

      Lst<P3> getLatticeCentering()
    • getLatticeDesignation

      Object getLatticeDesignation()
    • getPointGroupInfo

      Object getPointGroupInfo(int modelIndex, String drawID, boolean asInfo, String type, int index, float scale)
    • setPointGroup

      SymmetryInterface setPointGroup(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly)
    • getInvariantSymops

      int[] getInvariantSymops(P3 p3, int[] v0)
    • getEquivPoints

      Lst<P3> getEquivPoints(Lst<P3> pts, P3 pt, String flags)
    • generateCrystalClass

      Lst<P3> generateCrystalClass(P3 pt0)
    • getFractionalOrigin

      P3 getFractionalOrigin()
    • getIterator

      AtomIndexIterator getIterator(Viewer vwr, Atom atom, BS bstoms, float radius)
    • isWithinUnitCell

      boolean isWithinUnitCell(P3 pt, float x, float y, float z)
    • checkPeriodic

      boolean checkPeriodic(P3 pt)
    • staticConvertOperation

      Object staticConvertOperation(String string, M4 matrix)
    • getAdditionalOperationsCount

      int getAdditionalOperationsCount()
    • getAdditionalOperations

      M4[] getAdditionalOperations()
    • getWyckoffPosition

      Object getWyckoffPosition(Viewer vwr, P3 pt, String letter)
    • getSpaceGroupJSON

      Object getSpaceGroupJSON(Viewer vwr, String name, String data, int index)
    • getCellWeight

      float getCellWeight(P3 pt)
    • getPrecision

      float getPrecision()
    • fixUnitCell

      boolean fixUnitCell(float[] unitCellParams)
    • isSymmetryCell

      boolean isSymmetryCell(SymmetryInterface sym)
    • staticGetTransformABC

      String staticGetTransformABC(Object value, boolean normalize)
    • getITASettingValue

      Object getITASettingValue(Viewer vwr, String itaIndex, String key)
    • staticCleanTransform

      String staticCleanTransform(String tr)
    • replaceTransformMatrix

      M4 replaceTransformMatrix(M4 trm)
    • getSubgroupJSON

      Object getSubgroupJSON(Viewer vwr, int ita1, int ita2, int index1, int index2)
    • getIntTableIndex

      String getIntTableIndex()
    • getIntTableTransform

      String getIntTableTransform()
    • getUnitCellDisplayName

      String getUnitCellDisplayName()
    • staticToRationalXYZ

      String staticToRationalXYZ(P3 fPt, String sep)
    • getSpaceGroupClegId

      String getSpaceGroupClegId()
    • getFinalOperationCount

      int getFinalOperationCount()
    • convertTransform

      Object convertTransform(String transform, M4 trm)
    • getSymopList

      String[] getSymopList(boolean normalize)
    • setViewer

      SymmetryInterface setViewer(Viewer vwr)
      for Viewer.getSymStatic only
      Parameters:
      vwr -
      Returns:
      this
    • staticGetMatrixTransform

      M4 staticGetMatrixTransform(String cleg)
    • staticTransformSpaceGroup

      String staticTransformSpaceGroup(BS bs, String cleg, Object paramsOrUC, SB sb)
    • getPeriodicity

      int getPeriodicity()
    • getDimensionality

      int getDimensionality()
    • getUnitCellCenter

      P3 getUnitCellCenter()