Package org.jmol.symmetry

Class SpaceGroup

java.lang.Object
org.jmol.symmetry.SpaceGroup
All Implemented Interfaces:
Cloneable, HallInfo.HallReceiver
Direct Known Subclasses:
SpecialGroup
public class SpaceGroup extends Object implements Cloneable, HallInfo.HallReceiver
A general class to deal with Hermann-Mauguin or Hall names Bob Hanson 9/2006 references: International Tables for Crystallography Vol. A. (2002) http://www.iucr.org/iucr-top/cif/cifdic_html/1/cif_core.dic/Ispace_group_symop_operation_xyz.html http://www.iucr.org/iucr-top/cif/cifdic_html/1/cif_core.dic/Isymmetry_equiv_pos_as_xyz.html Hall symbols: https://cci.lbl.gov/sginfo/hall_symbols.html and https://cci.lbl.gov/cctbx/explore_symmetry.html (-)L [N_A^T_1] [N_A^T_2] ... [N_A^T_P] V(Nx Ny Nz) lattice types S and T are not supported here data table is from Syd Hall, private email, 9/4/2006, amended using * to indicate nonstandard H-M symbols or full names amended 2024.03.24 to add several ITA settings; full set of ITA settings are now encoded. NEVER ACCESS THESE METHODS DIRECTLY! ONLY THROUGH CLASS Symmetry

  • Field Details

    • PREFIX_FRIEZE

      public static final String PREFIX_FRIEZE
      See Also:

    • PREFIX_ROD

      public static final String PREFIX_ROD
      See Also:

    • PREFIX_LAYER

      public static final String PREFIX_LAYER
      See Also:

    • PREFIX_PLANE

      public static final String PREFIX_PLANE
      See Also:

    • PREFIX_SPACE

      public static final String PREFIX_SPACE
      See Also:

    • TYPE_FRIEZE

      public static final int TYPE_FRIEZE
      See Also:

    • TYPE_ROD

      public static final int TYPE_ROD
      See Also:

    • TYPE_LAYER

      public static final int TYPE_LAYER
      See Also:

    • TYPE_PLANE

      public static final int TYPE_PLANE
      See Also:

    • TYPE_SPACE

      public static final int TYPE_SPACE
      See Also:

    • TYPE_INVALID

      public static final int TYPE_INVALID
      See Also:

    • specialPrefix

      protected String specialPrefix

    • displayName

      public String displayName

    • NEW_NO_HALL_GROUP

      protected static final String NEW_NO_HALL_GROUP
      See Also:

    • groupType

      public int groupType

    • symmetryOperations

      public SymmetryOperation[] symmetryOperations

    • itaNumber

      protected String itaNumber

    • itaNo

      public int itaNo
      X in X.n or X:a... for SpaceGroupFinder sorting

    • setNo

      public int setNo
      n in X.n or 9 for X:a... (152_2 and 154_2 only)

    • sfIndex

      public transient int sfIndex
      just while SpaceGroupFinder is sorting

    • itaIndex

      protected String itaIndex
      index in cleg_settings.tab; "-" if in Jmol's list but not at ITA -- 152:_2 and 154:_2

    • nDim

      protected int nDim
      number of dimesions -- 2 (plane, frieze) or 3 (layer, rod, space)

    • periodicity

      protected int periodicity

    • isSSG

      public boolean isSSG

  • Constructor Details

    • SpaceGroup

      protected SpaceGroup(int index, String strData, boolean doInit)

  • Method Details

    • getSpecialPrefix

      public String getSpecialPrefix()
      Returns:
      [p/ | f/ | l/ | r/ | ""]

    • getNull

      public static SpaceGroup getNull(boolean doInit, boolean doNormalize, boolean doFinalize)

    • createSpaceGroup

      public static SpaceGroup createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)

    • getItaIndex

      public String getItaIndex()

    • getIndex

      public int getIndex()

    • setClegId

      public void setClegId(String cleg)

    • getClegId

      public String getClegId()

    • addSymmetry

      public int addSymmetry(String xyz, int opId, boolean allowScaling)
      Parameters:
      xyz -
      opId - generally 0; -1 for subsystems
      allowScaling - generally false; true for subsystems
      Returns:
      index

    • setFinalOperationsSafely

      public void setFinalOperationsSafely()

    • setFinalOperations

      protected void setFinalOperations()

    • findSpaceGroupFromXYZ

      public static SpaceGroup findSpaceGroupFromXYZ(String xyzList)

    • dumpInfo

      public String dumpInfo()
      Returns:
      detailed information

    • addOperation

      protected int addOperation(String xyz0, int opId, boolean allowScaling)

    • addOp

      protected int addOp(SymmetryOperation op, String xyz0, boolean isSpecial)

    • determineSpaceGroupNS

      public static SpaceGroup determineSpaceGroupNS(String name, SpaceGroup sg)

    • determineSpaceGroupNA

      public static SpaceGroup determineSpaceGroupNA(String name, float[] unitCellParams)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • asString

      public String asString()

    • getDisplayName

      public String getDisplayName()

    • addMagLatticeVectors

      public boolean addMagLatticeVectors(Lst<float[]> lattvecs)
      Parameters:
      lattvecs - could be magnetic centering, in which case there is an additional lattice parameter that is time reversal
      Returns:
      true if successful

    • addSpinLattice

      public void addSpinLattice(Lst<String> lstSpinFrames, Map<String,String> mapSpinIdToUVW)
      spin space groups only
      Parameters:
      lstSpinFrames -
      mapSpinIdToUVW -

    • getMatrixOperation

      public M4 getMatrixOperation(int i)
      Description copied from interface: HallInfo.HallReceiver
      Get the 4x4 matrix for the kth operation. Translations must be in 12ths.
      Specified by:
      getMatrixOperation in interface HallInfo.HallReceiver
      Parameters:
      i -
      Returns:
      4x4 matrix, translations in integer 12ths

    • getMatrixOperationCount

      public int getMatrixOperationCount()
      Description copied from interface: HallInfo.HallReceiver
      Get the receiver's current operation count.
      Specified by:
      getMatrixOperationCount in interface HallInfo.HallReceiver
      Returns:
      number of operations

    • addHallOperationCheckDuplicates

      public boolean addHallOperationCheckDuplicates(M4 operation)
      Description copied from interface: HallInfo.HallReceiver
      Add a (possibly) new operation, checking for duplicates.
      Specified by:
      addHallOperationCheckDuplicates in interface HallInfo.HallReceiver
      Parameters:
      operation -
      Returns:
      true if added, false if duplicate

    • canonicalizeCleg

      public static String canonicalizeCleg(String t)
      adds :a,b,c;0,0,0 or ;0,0,0; does NOT change :h or :r
      Parameters:
      t -
      Returns:
      full CLEG

    • getHMName

      public String getHMName()

    • getHMNameShort

      public Object getHMNameShort()

    • getITNo

      public static int getITNo(String name, int n)

    • isInRange

      public static boolean isInRange(float itno, int groupType, boolean allowSetIndex, boolean allow300)

    • getMax

      public static int getMax(int groupType)

    • getGroupTypePrefix

      public static String getGroupTypePrefix(int itno)

    • getExplicitSpecialGroupType

      public static int getExplicitSpecialGroupType(String name)

    • getSpecialGroupName

      public static String getSpecialGroupName(int type)

    • getImplicitSpecialGroupType

      public static int getImplicitSpecialGroupType(int itno)

    • hmMatches

      public static boolean hmMatches(String hm, String name, int specialType)
      Matches Hermann-Mauguin names for special types by ignoring spaces and some special treatment for plane groups.
      Parameters:
      hm - the standard name, generally with x/ if special
      name - the name to check, maybe abbreviated, no spaces, no x/
      specialType -
      Returns:
      true if matching

    • createCompatibleUnitCell

      public boolean createCompatibleUnitCell(float[] params, float[] newParams, boolean allowSame)
      Create a unit cell compatible with
      Parameters:
      params -
      newParams -
      allowSame - true to allow same-distance a,b,c for lower-symmetry sg
      Returns:
      true if changes have occurred

    • isHexagonalSG

      public boolean isHexagonalSG(int n, float[] params)

    • mapSpins

      public void mapSpins(Map<String,String> mapSpinIdToUVW)

    • setMatrixOperationCount

      public void setMatrixOperationCount(int nOps)

    • setSpinList

      public Lst<String> setSpinList(String configuration)