Package org.biojava.nbio.structure.contact

Class GridCell

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

  • Constructor Details

    • GridCell

      public GridCell()

  • Method Details

    • addIindex

      public void addIindex(int serial)

    • addJindex

      public void addJindex(int serial)

    • getNumIindices

      public int getNumIindices()

    • getNumJindices

      public int getNumJindices()

    • getContactsWithinCell

      public 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 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: