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The protein structure modules of BioJava.
There is a newer version: 7.2.2
/* This class is based on the original FATCAT implementation by
 *  * Yuzhen Ye & Adam Godzik (2003)
 * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
 * Bioinformatics vol.19 suppl. 2. ii246-ii255.
 * http://www.ncbi.nlm.nih.gov/pubmed/14534198
 * 
 *
 * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this 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.
 *
 *
 * Created on Jun 17, 2009
 * Created by Andreas Prlic - RCSB PDB
 *
 */

package org.biojava.nbio.structure.align.fatcat;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner;
import org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.ConfigurationException;


public class FatCat
{

	/**
	 *  version history:
	 *  1.1 - Added more parameters to the command line
	 *  1.0 - Initial version
	 */
	public static final String VERSION = "1.1";

	public static String newline = System.getProperty("line.separator");

	FatCatAligner aligner;

	public static final String algorithmName = "jFatCat";


	/** See demo/FatCatDemo.java for an example how to run.
	 *
	 * Launch FatCat from command line.
	 *
	 * Parameters are:
	 *
	 * @param argv
	 */
	public static void main(String[] argv) throws ConfigurationException {
		FatCatUserArgumentProcessor processor = new FatCatUserArgumentProcessor();
		processor.process(argv);
	}

	@Override
	public String toString(){
		return "JFatCat v. " + VERSION;
	}


	public AFPChain alignRigid(Atom[] ca1, Atom[] ca2) throws StructureException{
		StructureAlignment fatCat = new FatCatRigid();
		return fatCat.align(ca1,ca2);
	}

	public AFPChain alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params) throws StructureException{

		AFPChain afpChain = align(ca1,ca2,params,true);
		afpChain.setAlgorithmName(FatCatRigid.algorithmName);
		afpChain.setVersion(VERSION+"");
		return afpChain;
	}

	public AFPChain alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params) throws StructureException{

		AFPChain afpChain = align(ca1,ca2,params,false);
		afpChain.setAlgorithmName(FatCatFlexible.algorithmName);
		afpChain.setVersion(VERSION+"");
		return afpChain;
	}


	protected AFPChain align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid) throws StructureException{

		aligner = new FatCatAligner();

		aligner.align(ca1, ca2, doRigid, params);

		return aligner.getAfpChain();


	}

	public FatCatAligner getFatCatAligner(){
		if ( aligner == null)
			aligner = new FatCatAligner();
		return aligner;
	}

}