org.biojava.nbio.structure.contact

Class Grid

java.lang.Object

org.biojava.nbio.structure.contact.Grid

public class Grid
extends Object

A grid to be used for calculating atom contacts through geometric hashing algorithm. The grid is composed of cells of size of the cutoff so that the distances that need to be calculated are reduced to those within each cell and to the neighbouring cells.

Author:

duarte_j

Constructor Summary

Constructors

Constructor and Description
Grid(double cutoff) Creates a Grid, the cutoff is in Angstroms and can be specified to a precision of 0.01A

Method Summary

Modifier and Type	Method and Description
void	addAtoms(Atom[] atoms) Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
void	addAtoms(Atom[] iAtoms, Atom[] jAtoms) Adds the i and j atoms and fills the grid.
void	addAtoms(Atom[] atoms, BoundingBox bounds) Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
void	addAtoms(Atom[] iAtoms, BoundingBox icoordbounds, Atom[] jAtoms, BoundingBox jcoordbounds) Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
AtomContactSet	getContacts() Returns all contacts, i.e.
double	getCutoff()
boolean	isNoOverlap() Tells whether (after having added atoms to grid) the i and j grids are not overlapping.

Methods inherited from class java.lang.Object

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

Constructor Detail

Grid

public Grid(double cutoff)

Creates a Grid, the cutoff is in Angstroms and can be specified to a precision of 0.01A

Parameters:

cutoff -

Method Detail

addAtoms

public void addAtoms(Atom[] iAtoms,
                     Atom[] jAtoms)

Adds the i and j atoms and fills the grid. Their bounds will be computed.

Parameters:

iAtoms -

jAtoms -

addAtoms

public void addAtoms(Atom[] iAtoms,
                     BoundingBox icoordbounds,
                     Atom[] jAtoms,
                     BoundingBox jcoordbounds)

Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.

Parameters:

iAtoms -

icoordbounds -

jAtoms -

jcoordbounds -

addAtoms

public void addAtoms(Atom[] atoms)

Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts. The bounding box of the atoms will be computed based on input array

Parameters:

atoms -

addAtoms

public void addAtoms(Atom[] atoms,
                     BoundingBox bounds)

Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts. The bounds calculated elsewhere can be passed, or if null they are computed.

Parameters:

atoms -

bounds -

getContacts

public AtomContactSet getContacts()

Returns all contacts, i.e. all atoms that are within the cutoff distance. If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms, if jAtoms is null, then contacts are within the iAtoms.

Returns:

getCutoff

public double getCutoff()

isNoOverlap

public boolean isNoOverlap()

Tells whether (after having added atoms to grid) the i and j grids are not overlapping. Overlap is defined as enclosing bounds of the 2 grids being no more than one cell size apart.

Returns:

true if the 2 grids don't overlap, false if they do