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 spatial hashing algorithm.

Author:

Jose Duarte

Constructor Summary

Constructors

Constructor	Description
GridCell(Grid parent)

Method Summary

Modifier and Type	Method	Description
void	addIindex(int serial)
void	addJindex(int serial)
List<Contact>	getContactsToOtherCell(GridCell otherCell)	Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
List<Contact>	getContactsWithinCell()	Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
int	getNumIindices()
int	getNumJindices()
boolean	hasContactToAtom(javax.vecmath.Point3d[] iAtoms, javax.vecmath.Point3d[] jAtoms, javax.vecmath.Point3d query, double cutoff)	Tests whether any atom in this cell has a contact with the specified query atom
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GridCell

public GridCell(Grid parent)

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<Contact> getContactsWithinCell()

Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance. If Grid.getJAtoms() is null, distances are within the iAtoms only

Returns:

getContactsToOtherCell

public List<Contact> getContactsToOtherCell(GridCell otherCell)

Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.

Parameters:

otherCell -

iAtoms - the first set of atom coordinates to which the iIndices correspond

jAtoms - the second set of atom coordinates to which the jIndices correspond, if null distances are within the iAtoms only

cutoff -

Returns:

hasContactToAtom

public boolean hasContactToAtom(javax.vecmath.Point3d[] iAtoms,
                                javax.vecmath.Point3d[] jAtoms,
                                javax.vecmath.Point3d query,
                                double cutoff)

Tests whether any atom in this cell has a contact with the specified query atom

Parameters:

iAtoms - the first set of atoms to which the iIndices correspond

jAtoms - the second set of atoms to which the jIndices correspond, or null

query - test point

cutoff -

Returns:

toString

public String toString()

Overrides:

toString in class Object