Class SpaceGroup

Method Details

• parseSpaceGroup

  public static SpaceGroup parseSpaceGroup(String shortName)

  Get the space group for the given international short name, using the PDB format, e.g. 'P 21 21 21' or 'C 1 c 1'

  Parameters:

  shortName -

  Returns:

  the SpaceGroup or null if the shortName is not valid

  See Also:

  • SymoplibParser.getSpaceGroup(String)

• addTransformation

  public void addTransformation(String transfAlgebraic)

• initializeCellTranslations

  protected void initializeCellTranslations()

• getMultiplicity

  public int getMultiplicity()

• getPrimitiveMultiplicity

  public int getPrimitiveMultiplicity()

• getCellTranslations

  public javax.vecmath.Vector3d[] getCellTranslations()

• getCellTranslation

  public javax.vecmath.Vector3d getCellTranslation(int i)

• getMatrixFromAlgebraic

  public static javax.vecmath.Matrix4d getMatrixFromAlgebraic(String transfAlgebraic)

• getId

  public int getId()

  Gets the standard numeric identifier for the space group. See for example http://en.wikipedia.org/wiki/Space_group or the IUCr crystallographic tables

  Returns:

• getShortSymbol

  public String getShortSymbol()

  Gets the international short name (as used in PDB), e.g. "P 21 21 21" or "C 1 c 1"

  Returns:

• getAltShortSymbol

  public String getAltShortSymbol()

  Gets the alternative international short name (as sometimes used in PDB), e.g. "I 1 2 1" instead of "I 2"

  Returns:

• getTransformations

  public List<javax.vecmath.Matrix4d> getTransformations()

  Gets all transformations except for the identity in crystal axes basis.

  Returns:

• getRotAxisAngle

  public javax.vecmath.AxisAngle4d getRotAxisAngle(int transformId)

• areInSameAxis

  public boolean areInSameAxis(int tId1, int tId2)

  Returns true if both given transform ids belong to the same crystallographic axis (a, b or c) For two non-rotation transformations (i.e. identity operators) it returns true

  Parameters:

  tId1 -

  tId2 -

  Returns:

• getAxisFoldType

  public int getAxisFoldType(int transformId)

  Given a transformId returns the type of axis of rotation: 1 (no rotation), 2, 3, 4 or 6 -fold and for improper rotations: -1, -2, -3, -4 and -6

  Parameters:

  transformId -

  Returns:

• getTransformation

  public javax.vecmath.Matrix4d getTransformation(int i)

  Gets a transformation by index expressed in crystal axes basis. Index 0 corresponds always to the identity transformation. Beware the returned Matrix4d is not a copy but it stays linked to the one stored in this SpaceGroup object

  Parameters:

  i -

  Returns:

• getTransfAlgebraic

  public String getTransfAlgebraic(int i)

  Gets a transformation algebraic string given its index. Index 0 corresponds always to the identity transformation.

  Parameters:

  i -

  Returns:

• equals

  public boolean equals(Object o)

  Overrides:

  equals in class Object

• getNumOperators

  public int getNumOperators()

  Gets the number of symmetry operators corresponding to this SpaceGroup (counting the identity operator)

  Returns:

• getAlgebraicFromMatrix

  public static String getAlgebraicFromMatrix(javax.vecmath.Matrix4d m)

• deltaComp

  protected static boolean deltaComp(double d1, double d2, double delta)

• getBravLattice

  public BravaisLattice getBravLattice()

• isEnantiomorphic

  public boolean isEnantiomorphic()

• getRotAxisAndAngle

  public static javax.vecmath.AxisAngle4d getRotAxisAndAngle(javax.vecmath.Matrix3d m)

  Given a rotation matrix calculates the rotation axis and angle for it. The angle is calculated from the trace, the axis from the eigenvalue decomposition. If given matrix is improper rotation or identity matrix then axis (0,0,0) and angle 0 are returned.

  Parameters:

  m -

  Returns:

  Throws:

  IllegalArgumentException - if given matrix is not a rotation matrix (determinant not 1 or -1)

• getRotAxisType

  public static int getRotAxisType(javax.vecmath.Matrix4d m)

  Given a transformation matrix containing a rotation returns the type of rotation: 1 for identity, 2 for 2-fold rotation, 3 for 3-fold rotation, 4 for 4-fold rotation, 6 for 6-fold rotation, -1 for inversions, -2 for mirror planes, -3 for 3-fold improper rotation, -4 for 4-fold improper rotation and -6 for 6-fold improper rotation

  Parameters:

  m -

  Returns:

• toString

  public String toString()

  Overrides:

  toString in class Object

• toXML

  public String toXML()

• getTransfAlgebraic

  public List<String> getTransfAlgebraic()

• setTransfAlgebraic

  public void setTransfAlgebraic(List<String> transfAlgebraic)

• getAxisTypes

  public int[] getAxisTypes()

• setAxisTypes

  public void setAxisTypes(int[] axisTypes)

• getSerialversionuid

  public static long getSerialversionuid()

• getSplitpat1

  public static Pattern getSplitpat1()

• getSplitpat2

  public static Pattern getSplitpat2()

• getCoordpat

  public static Pattern getCoordpat()

• getTranscoefpat

  public static Pattern getTranscoefpat()

• getNonenantpat

  public static Pattern getNonenantpat()

• getDelta

  public static double getDelta()

• setId

  public void setId(int id)

• setMultiplicity

  public void setMultiplicity(int multiplicity)

• setPrimitiveMultiplicity

  public void setPrimitiveMultiplicity(int primitiveMultiplicity)

• setShortSymbol

  public void setShortSymbol(String shortSymbol)

• setAltShortSymbol

  public void setAltShortSymbol(String altShortSymbol)

• setBravLattice

  public void setBravLattice(BravaisLattice bravLattice)