Package org.biojava.nbio.structure.xtal

Class CrystalBuilder

java.lang.Object
org.biojava.nbio.structure.xtal.CrystalBuilder
public class CrystalBuilder extends Object
A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators
Author:
duarte_j

  • Field Details

    • DEF_NUM_CELLS

      public static final int DEF_NUM_CELLS
      See Also:

    • DEFAULT_INTERFACE_DISTANCE_CUTOFF

      public static final double DEFAULT_INTERFACE_DISTANCE_CUTOFF
      Default maximum distance between two chains to be considered an interface.
      See Also:

    • IDENTITY

      public static final javax.vecmath.Matrix4d IDENTITY

  • Constructor Details

    • CrystalBuilder

      public CrystalBuilder(Structure structure)

  • Method Details

    • setNumCells

      public void setNumCells(int numCells)
      Set the number of neighboring crystal cells that will be used in the search for contacts
      Parameters:
      numCells -

    • getUniqueInterfaces

      public StructureInterfaceList getUniqueInterfaces()
      Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates. An interface is defined as any pair of chains that contact, i.e. for which there is at least a pair of atoms (one from each chain) within the default cutoff distance.
      Returns:
      See Also:

    • getUniqueInterfaces

      public StructureInterfaceList getUniqueInterfaces(double cutoff)
      Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates. An interface is defined as any pair of chains that contact, i.e. for which there is at least a pair of atoms (one from each chain) within the given cutoff distance.
      Parameters:
      cutoff - the distance cutoff for 2 chains to be considered in contact
      Returns:

    • translate

      public void translate(javax.vecmath.Matrix4d m, javax.vecmath.Vector3d translation)