Class CrystalBuilder


  • public class CrystalBuilder
    extends java.lang.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
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      StructureInterfaceList getUniqueInterfaces()
      Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
      StructureInterfaceList getUniqueInterfaces​(double cutoff)
      Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.
      void setNumCells​(int numCells)
      Set the number of neighboring crystal cells that will be used in the search for contacts
      void translate​(javax.vecmath.Matrix4d m, javax.vecmath.Vector3d translation)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • IDENTITY

        public static final javax.vecmath.Matrix4d IDENTITY
    • Constructor Detail

      • CrystalBuilder

        public CrystalBuilder​(Structure structure)
    • Method Detail

      • 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:
        DEFAULT_INTERFACE_DISTANCE_CUTOFF
      • 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)