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The protein structure modules of BioJava.

There is a newer version: 7.1.3

/*
 *                    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.align.model;

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

import java.io.Serializable;

/**
 * A class to represent a FATCAT aligned fragment pair (AFP)
 *
 * @author Andreas Prlic
 *
 */
public class AFP implements Serializable {

	private static final long serialVersionUID = 3901209995477111829L;

	private int p1;
	private int p2;
	private int fragLen;
	private double rmsd;
	private Matrix m;
	private double[] t;
	private double score;

	private long id;

	@Override
	public String toString(){

		// we use the metric of
		// Manfred J. Sippl
		// On Distance and Similarity in Fold Space
		// Bioinformatics, 24, pp. 872-873  (2008)

		StringBuffer buf = new StringBuffer();
		buf.append("AFP: p1:");
		buf.append(p1);
		buf.append(" p2: ");
		buf.append(p2);
		buf.append(" len " );
		buf.append(fragLen);
		buf.append(" rmsd ");
		buf.append(rmsd);
		buf.append(" score ");
		buf.append(score);
		return buf.toString();
	}


	public long getId()
	{
		return id;
	}

	public void setId(long id)
	{
		this.id = id;
	}

	public int getP1() {
		return p1;
	}
	public void setP1(int p1) {
		this.p1 = p1;
	}
	public int getP2() {
		return p2;
	}
	public void setP2(int p2) {
		this.p2 = p2;
	}
	public int getFragLen() {
		return fragLen;
	}
	public void setFragLen(int fragLen) {
		this.fragLen = fragLen;
	}
	public double getRmsd() {
		return rmsd;
	}
	public void setRmsd(double rmsd) {
		this.rmsd = rmsd;
	}
	public Matrix getM() {
		return m;
	}
	public void setM(Matrix m) {
		this.m = m;
	}
	public double[] getT() {
		return t;
	}
	public void setT(double[] t) {
		this.t = t;
	}
	public double getScore() {
		return score;
	}
	public void setScore(double score) {
		this.score = score;
	}

}