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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/
 *
 * Created on Jan 7, 2006
 *
 */
package org.biojava.nbio.structure.align.pairwise;


import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.AtomImpl;
import org.biojava.nbio.structure.jama.Matrix;


/** a pair of fragments of two protein structures
 *
 * @author Andreas Prlic
 * @since 1.5
 * @version %I% %G%
 */
public class FragmentPair {


	int length;
	int pos1;
	int pos2;

	// parameter below may be used in different approaches

	int contacts;
	int cluster;
	double rms;
	int used;
	int covered;

	//filled if fragments are superimposed
	Matrix rot;
	Atom trans;

	//this unit vector indicates the rotation of j onto i
	Atom unitv;

	Atom center1;
	Atom center2;


	public FragmentPair(int length, int p1, int p2) {
		super();
		this.length = length ;
		 pos1 = p1;
		 pos2 = p2;

		 contacts = 0;
		 cluster = 0;
		 rms = 0.0;
		 used = 0;
		 covered = 0;

		 unitv = new AtomImpl();
		 unitv.setX(0);
		 unitv.setY(0);
		 unitv.setZ(1);
		 rot = null;
		 trans = new AtomImpl();
		 center1 = new AtomImpl();
		 center2 = new AtomImpl();

	}
	@Override
	public Object clone(){

		FragmentPair n = new FragmentPair(length,pos1,pos2);
		if ( center1 !=null)
			n.setCenter1((Atom)center1.clone());

		if ( center2 != null)
			n.setCenter2((Atom)center2.clone());

		n.setCluster(cluster);
		n.setContacts(contacts);
		n.setCovered(covered);
		n.setRms(rms);
		n.setLength(length);
		n.setRot((Matrix)rot.clone());
		n.setUnitv((Atom)unitv.clone());

		return n;
	}
	public int getCluster() {
		return cluster;
	}

	public void setCluster(int cluster) {
		this.cluster = cluster;
	}

	public int getContacts() {
		return contacts;
	}

	public void setContacts(int contacts) {
		this.contacts = contacts;
	}

	public int getCovered() {
		return covered;
	}

	public void setCovered(int covered) {
		this.covered = covered;
	}

	public int getLength() {
		return length;
	}

	public void setLength(int length) {
		this.length = length;
	}

	public int getPos1() {
		return pos1;
	}

	public void setPos1(int pos1) {
		this.pos1 = pos1;
	}

	public int getPos2() {
		return pos2;
	}

	public void setPos2(int pos2) {
		this.pos2 = pos2;
	}

	public double getRms() {
		return rms;
	}

	public void setRms(double rms) {
		this.rms = rms;
	}

	public Matrix getRot() {
		return rot;
	}

	public void setRot(Matrix rot) {
		this.rot = rot;
	}

	public Atom getTrans() {
		return trans;
	}

	public void setTrans(Atom trans) {
		this.trans = trans;
	}

	public Atom getUnitv() {
		return unitv;
	}

	public void setUnitv(Atom unitv) {
		this.unitv = unitv;
	}

	public int getUsed() {
		return used;
	}

	public void setUsed(int used) {
		this.used = used;
	}

	public Atom getCenter1() {
		return center1;
	}

	public void setCenter1(Atom center1) {
		this.center1 = center1;
	}

	public Atom getCenter2() {
		return center2;
	}

	public void setCenter2(Atom center2) {
		this.center2 = center2;
	}

	@Override
	public String toString() {
		return String.format("Fragment (%d,%d) len %d", pos1, pos2, length);
	}
}