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 Summary

Constructors

Constructor and Description
GridCell()

Method Summary

Methods

Modifier and Type	Method and Description
void	addIindex(int serial)
void	addJindex(int serial)
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
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 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: