Class 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 Detail

      • NeighborList

        public NeighborList​(IAtom[] atoms,
                            double radius)
    • Method Detail

      • 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