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. and Lijnzaad, P. and Argos, P. and Sander, C. and Scharf, M. , The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contourin gof Molecular Assemblies, Journal of Computational Chemistry, 1995, 16:273-284] 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:

master

Belongs to CDK module:

qsarmolecular

Created on:

2005-05-09

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
int[]	getNeighbors(int ii)
int	getNumberOfNeighbors(int i)

Methods inherited from class java.lang.Object

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

Constructor Detail

NeighborList

public NeighborList(IAtom[] atoms,
            double radius)

Method Detail

getNumberOfNeighbors

public int getNumberOfNeighbors(int i)

getNeighbors

public int[] getNeighbors(int ii)