CookBook.java example

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biojava-master
/*
 *                    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 Mar 11, 2010
 * Author: Andreas Prlic
 *
 */

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.fatcat.FatCatFlexible;
import org.biojava.nbio.structure.align.gui.DisplayAFP;
import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.model.AfpChainWriter;
import org.biojava.nbio.structure.align.util.AtomCache;


public class CookBook
{


	public static void main(String[] args){

		String name1="1HNG.B";
		String name2="1A64.A";


		try {

			// for this example we are going to use the jFatCat-rigid algorithm
			StructureAlignment algorithm = StructureAlignmentFactory.getAlgorithm(FatCatFlexible.algorithmName);

			// the cache takes care of loading the structures
			// Downloads files to a temp dir by default
			AtomCache cache = new AtomCache();


			//////////////////////////////
			// no need to change anything below this line
			// ////////////////////////////

			// load the structures
			Structure structure1 = cache.getStructure(name1);
			Structure structure2 = cache.getStructure(name2);

			// we are only using the CA atoms in the structure for the alignment
			Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
			Atom[] ca2 = StructureTools.getAtomCAArray(structure2);

			// do the actual alignment
			AFPChain afpChain = algorithm.align(ca1,ca2);

			// just name the two molecules
			afpChain.setName1(name1);
			afpChain.setName2(name2);

			// print and display results:


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

			// show the alignment in 3D in jmol
			StructureAlignmentJmol jmol= StructureAlignmentDisplay.display(afpChain, ca1, ca2);

			// set the display title for the frame
			jmol.setTitle(algorithm.getAlgorithmName() + " : " + name1 + " vs. " + name2);

			// here we open up the alignment - text panel that can interact with the 3D jmol display.
			DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);

			// we can print an XML version
			//System.out.println(AFPChainXMLConverter.toXML(afpChain, ca1, ca2));

			// or print the same output as original FATCAT
			System.out.println(AfpChainWriter.toFatCat(afpChain, ca1, ca2));





		} catch (Exception e){
			e.printStackTrace();
		}
	}
}