Package org.biojava.nbio.structure.xtal

Class SpaceGroup

java.lang.Object
org.biojava.nbio.structure.xtal.SpaceGroup
All Implemented Interfaces:
Serializable
public class SpaceGroup extends Object implements Serializable
A crystallographic space group. We store the standard numeric identifier, the international short symbol and the transformations corresponding to each space group (as Matrix4ds and in algebraic notation). The information for all (protein crystallography) space groups can be parsed from the XML file in the resource directory. See: http://en.wikipedia.org/wiki/Space_group
Author:
duarte_j
See Also:

  • Field Details

  • Constructor Details

  • 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:

    • 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:

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • 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)