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The protein structure modules of BioJava.
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/*
 *                    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 21, 2010
 *
 */
package demo;


import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.StructureAlignmentFactory;
import org.biojava.nbio.structure.align.ce.CeMain;
import org.biojava.nbio.structure.align.ce.CeParameters;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AFPChainScorer;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;


/** Example of how to run a structure alignment using the CE algorithm.
 *
 * @author Andreas Prlic
 *
 */
public class DemoCE {

	public static void main(String[] args){

		//String name1 = "4hhb.A";
		//String name2 = "4hhb.B";

		String name1 = "1cdg.A";
		String name2 = "1tim.B";



		AtomCache cache = new AtomCache();

		Structure structure1 = null;
		Structure structure2 = null;

		try {

		   StructureAlignment algorithm  = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);

			structure1 = cache.getStructure(name1);
			structure2 = cache.getStructure(name2);

			Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
			Atom[] ca2 = StructureTools.getAtomCAArray(structure2);

			// get default parameters
			CeParameters params = new CeParameters();

			// add more print
			params.setShowAFPRanges(true);

			// set the maximum gap size to unlimited
			params.setMaxGapSize(-1);

			AFPChain afpChain = algorithm.align(ca1,ca2,params);

			afpChain.setName1(name1);
			afpChain.setName2(name2);

			// flexible original results:
			System.out.println(afpChain.toFatcat(ca1,ca2));

			System.out.println(afpChain.toRotMat());
			//System.out.println(afpChain.toCE(ca1, ca2));

			System.out.println(AFPChainXMLConverter.toXML(afpChain,ca1,ca2));

			double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2);
			afpChain.setTMScore(tmScore);

			//System.out.println(AfpChainWriter.toWebSiteDisplay(afpChain, ca1, ca2));

			printScores(afpChain);
		} catch (Exception e) {
			e.printStackTrace();
			return;
		}
	}

	private static void printScores(AFPChain afpChain) {
		System.out.println("=====================");
		System.out.println("The main scores for the alignment:");

		System.out.println("EQR       :\t" + afpChain.getNrEQR() + "\t The number of residues on structurally equivalent positions.")  ;
		System.out.println("RMSD      :\t" + String.format("%.2f",afpChain.getTotalRmsdOpt() )+ "\t The RMSD of the alignment");
		System.out.println("Z-score   :\t" + afpChain.getProbability() + "\t The Z-score of the alignment (CE)");
		System.out.println("TM-score  :\t" + String.format("%.2f",afpChain.getTMScore()) + "\t The TM-score of the alignment.");
		System.out.println("");
		System.out.println("Other scores:");
		System.out.println("Identity  :\t" + String.format("%.2f",afpChain.getIdentity())   + "\t The percent of residues that are sequence-identical in the alignment.");
		System.out.println("Similarity:\t" + String.format("%.2f",afpChain.getSimilarity()) + "\t The percent of residues in the alignment that are sequence-similar.");
		System.out.println("Coverage1 :\t" + afpChain.getCoverage1() + " %\t Percent of protein 1 that is covered with the alignment.");
		System.out.println("Coverage2 :\t" + afpChain.getCoverage2() + " %\t Percent of protein 2 that is covered with the alignment.");
		int dab = afpChain.getCa1Length()+afpChain.getCa2Length() - 2 * afpChain.getNrEQR();
		System.out.println("Distance  :\t" + dab + "\t Distance between folds a,b ");
		double sab = 2 * afpChain.getNrEQR() / (double)( afpChain.getCa1Length() + afpChain.getCa2Length());
		System.out.println("Rel. Sim. :\t" + String.format("%.2f",sab) + "\t Relative similarity");



	}
}