Package org.openscience.cdk.geometry.surface

Class NeighborList

java.lang.Object

org.openscience.cdk.geometry.surface.NeighborList

public class NeighborList
extends Object

Creates a list of atoms neighboring each atom in the molecule.

The routine is a simplified version of the neighbor list described in [Eisenhaber, F. et. al.. Journal of Computational Chemistry. 1995. 16] and is based on the implementation by Peter McCluskey. Due to the fact that it divides the cube into a fixed number of sub cubes, some accuracy may be lost.

Author:

Rajarshi Guha

Source code:

main

Belongs to CDK module:

qsarmolecular

Created on:

2005-05-09

Constructor Summary

Constructors

Constructor	Description
NeighborList(IAtom[] atoms, double radius)

Method Summary

Modifier and Type	Method	Description
int[]	getNeighbors(int i)	Get the neighbors that are with the given radius of atom i.
int	getNumberOfNeighbors(int i)

Methods inherited from class java.lang.Object

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

Constructor Details

NeighborList

public NeighborList(IAtom[] atoms,
 double radius)

Method Details

getNumberOfNeighbors

public int getNumberOfNeighbors(int i)

getNeighbors

public int[] getNeighbors(int i)

Get the neighbors that are with the given radius of atom i.

Parameters:

i - atom index

Returns:

atom indexs within that radius