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:
Jose Duarte
  • Field Details

    • NCS_CHAINID_SUFFIX_CHAR

      public static final String NCS_CHAINID_SUFFIX_CHAR
      See Also:
    • 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, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)
      Special constructor for NCS-aware CrystalBuilder. The output list of interfaces will be pre-clustered by NCS-equivalence. Run expandNcsOps(Structure, Map, Map) first to extend the AU and get the equivalence information.
      Parameters:
      structure - NCS-extended structure
      chainOrigNames - chain names mapped to the original chain names (pre-NCS extension)
      chainNcsOps - chain names mapped to the ncs operators that was used to generate them
      Since:
      5.0.0
    • CrystalBuilder

      public CrystalBuilder(Structure structure)
  • Method Details

    • hasNcsOps

      public boolean hasNcsOps()
      Returns:
      true if this CrystalBuilder is NCS-aware.
      Since:
      5.0.0
    • 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)
    • expandNcsOps

      public static void expandNcsOps(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)
      Apply the NCS operators in the given Structure adding new chains as needed. All chains are (re)assigned ids of the form: original_chain_id+ncs_operator_index+"n".
      Parameters:
      structure - the structure to expand
      chainOrigNames - new chain names mapped to the original chain names
      chainNcsOps - new chain names mapped to the ncs operators that was used to generate them
      Since:
      5.0.0