Package org.biojava.nbio.structure.contact

Class GridCell

  • public class GridCell
extends java.lang.Object
    A grid cell to be used in contact calculation via geometric hashing algorithm.
    Author:
    duarte_j

    • Constructor Summary

      Constructors 
      Constructor Description
      GridCell()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addIindex​(int serial)  
      void addJindex​(int serial)  
      java.util.List<AtomContact> getContactsToOtherCell​(GridCell otherCell, Atom[] iAtoms, Atom[] jAtoms, double cutoff)
      Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContacts
      java.util.List<AtomContact> getContactsWithinCell​(Atom[] iAtoms, Atom[] jAtoms, double cutoff)
      Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContacts
      int getNumIindices()  
      int getNumJindices()  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • GridCell

        public GridCell()

    • Method Detail

      • addIindex

        public void addIindex​(int serial)

      • addJindex

        public void addJindex​(int serial)

      • getNumIindices

        public int getNumIindices()

      • getNumJindices

        public int getNumJindices()

      • getContactsWithinCell

        public java.util.List<AtomContact> getContactsWithinCell​(Atom[] iAtoms,
                                                         Atom[] jAtoms,
                                                         double cutoff)
        Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContacts
        Parameters:
        iAtoms - the first set of atoms to which the iIndices correspond
        jAtoms - the second set of atoms to which the jIndices correspond, if null distances are within the iAtoms only
        cutoff -
        Returns:

      • getContactsToOtherCell

        public java.util.List<AtomContact> getContactsToOtherCell​(GridCell otherCell,
                                                          Atom[] iAtoms,
                                                          Atom[] jAtoms,
                                                          double cutoff)
        Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContacts
        Parameters:
        otherCell -
        iAtoms - the first set of atoms to which the iIndices correspond
        jAtoms - the second set of atoms to which the jIndices correspond, if null distances are within the iAtoms only
        cutoff -
        Returns: