/*

* 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");

}

}