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The protein structure modules of BioJava.
There is a newer version: 7.2.2
/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure.contact;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Calc;

import java.util.ArrayList;
import java.util.List;


/**
 * A grid cell to be used in contact calculation via geometric hashing algorithm.
 *
 * @author duarte_j
 *
 */
public class GridCell {


	private ArrayList iIndices;
	private ArrayList jIndices;

	public GridCell(){
		iIndices = new ArrayList();
		jIndices = new ArrayList();
	}

	public void addIindex(int serial){
		iIndices.add(serial);
	}

	public void addJindex(int serial){
		jIndices.add(serial);
	}

	public int getNumIindices() {
		return iIndices.size();
	}

	public int getNumJindices() {
		return jIndices.size();
	}

	/**
	 * Calculates all distances of atoms within this cell returning those that are within the given cutoff
	 * as a list of AtomContacts
	 * @param iAtoms the first set of atoms to which the iIndices correspond
	 * @param jAtoms the second set of atoms to which the jIndices correspond, if null distances are within the iAtoms only
	 * @param cutoff
	 * @return
	 */
	public List getContactsWithinCell(Atom[] iAtoms, Atom[] jAtoms, double cutoff){

		List contacts = new ArrayList();

		if (jAtoms==null) {
			for (int i:iIndices) {
				for (int j:iIndices) {
					if (j>i) {
						double distance = Calc.getDistance(iAtoms[i], iAtoms[j]);
						if (distance(iAtoms[i],iAtoms[j]),distance));
					}
				}
			}

		} else {
			for (int i:iIndices) {
				for (int j:jIndices) {
					double distance = Calc.getDistance(iAtoms[i], jAtoms[j]);
					if (distance(iAtoms[i],jAtoms[j]),distance));
				}
			}
		}

		return contacts;
	}

	/**
	 * Calculates all distances of atoms between this cell and the given cell returning those that are
	 * within the given cutoff as a list of AtomContacts
	 * @param otherCell
	 * @param iAtoms the first set of atoms to which the iIndices correspond
	 * @param jAtoms the second set of atoms to which the jIndices correspond, if null distances are within the iAtoms only
	 * @param cutoff
	 * @return
	 */
	public List getContactsToOtherCell(GridCell otherCell , Atom[] iAtoms, Atom[] jAtoms, double cutoff){

		List contacts = new ArrayList();

		if (jAtoms==null) {

			for (int i:iIndices) {
				for (int j:otherCell.iIndices) {
					if (j>i) {
						double distance = Calc.getDistance(iAtoms[i], iAtoms[j]);
						if (distance(iAtoms[i],iAtoms[j]),distance));
					}
				}
			}

		} else {

			for (int i:iIndices) {
				for (int j:otherCell.jIndices) {
					double distance = Calc.getDistance(iAtoms[i], jAtoms[j]);
					if (distance(iAtoms[i],jAtoms[j]),distance));
				}
			}

		}

		return contacts;
	}

}