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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/
 *
 */
package demo;


import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.io.StructureFiletype;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.contact.*;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.xtal.CrystalBuilder;
import org.biojava.nbio.structure.xtal.CrystalTransform;
import org.biojava.nbio.structure.xtal.SpaceGroup;
import org.biojava.nbio.structure.StructureIO;

import javax.vecmath.AxisAngle4d;
import javax.vecmath.Vector3d;
import java.util.List;



public class DemoCrystalInterfaces {


	private static final double BSATOASA_CUTOFF = 0.95;
	private static final double MIN_ASA_FOR_SURFACE = 5;
	private static final int CONSIDER_COFACTORS = 40; // minimum number of atoms for a cofactor to be considered, if -1 all ignored


	private static final double CUTOFF = 5.5;

	private static final int N_SPHERE_POINTS = 3000;

	private static final double MIN_AREA_TO_KEEP = 35;

	private static final int NTHREADS = Runtime.getRuntime().availableProcessors();

	private static final double CLASH_DISTANCE = 1.5;


	/**
	 * @param args
	 */
	public static void main(String[] args) throws Exception {
		String pdbCode = "1smt";

		AtomCache cache = new AtomCache();
		cache.setFiletype(StructureFiletype.CIF);

		FileParsingParameters params = new FileParsingParameters();
		params.setAlignSeqRes(true);
		cache.setFileParsingParams(params);

		StructureIO.setAtomCache(cache);

		Structure structure = StructureIO.getStructure(pdbCode);


		System.out.println(structure.getPDBCode());


		SpaceGroup sg = structure.getCrystallographicInfo().getSpaceGroup();

		if (sg!=null) {
			System.out.println(sg.getShortSymbol()+" ("+sg.getId()+")");
			System.out.println("Symmetry operators: "+sg.getNumOperators());
		}
		System.out.println("Calculating possible interfaces... (using "+NTHREADS+" CPUs for ASA calculation)");
		long start = System.currentTimeMillis();

		CrystalBuilder cb = new CrystalBuilder(structure);


		StructureInterfaceList interfaces = cb.getUniqueInterfaces(CUTOFF);
		interfaces.calcAsas(N_SPHERE_POINTS, NTHREADS, CONSIDER_COFACTORS);
		interfaces.removeInterfacesBelowArea(MIN_AREA_TO_KEEP);
		List clusters = interfaces.getClusters();


		//interfaces.initialiseClusters(pdb, CLUSTERING_CUTOFF, MINATOMS_CLUSTERING, "CA");

		long end = System.currentTimeMillis();
		long total = (end-start)/1000;
		System.out.println("Total time for interface calculation: "+total+"s");

		System.out.println("Total number of interfaces found: "+interfaces.size());

		for (int i=0;i clashing = interf.getContacts().getContactsWithinDistance(CLASH_DISTANCE);
			if (clashing.size()>10)
				System.out.println(clashing.size()+" CLASHES!!!");

			CrystalTransform transf1 = interf.getTransforms().getFirst();
			CrystalTransform transf2 = interf.getTransforms().getSecond();

			System.out.println("Transf1: "+SpaceGroup.getAlgebraicFromMatrix(transf1.getMatTransform())+
					". Transf2: "+SpaceGroup.getAlgebraicFromMatrix(transf2.getMatTransform()));


			String screwStr = "";
			if (transf2.getTransformType().isScrew()) {
				Vector3d screwTransl =
						transf2.getTranslScrewComponent();
				screwStr = " -- "+transf2.getTransformType().getShortName()+" with translation "+
				String.format("(%5.2f,%5.2f,%5.2f)",screwTransl.x,screwTransl.y,screwTransl.z);

			}

			if (structure.isCrystallographic()) {
				int foldType = sg.getAxisFoldType(transf2.getTransformId());
				AxisAngle4d axisAngle = sg.getRotAxisAngle(transf2.getTransformId());

				System.out.println(" "+foldType+"-fold on axis "+String.format("(%5.2f,%5.2f,%5.2f)",axisAngle.x,axisAngle.y,axisAngle.z)+screwStr);
			}

			System.out.println("Number of contacts: "+interf.getContacts().size());
			//System.out.println("Number of contacting atoms (from both molecules): "+interf.getNumAtomsInContact());
			Pair> cores = interf.getCoreResidues(BSATOASA_CUTOFF, MIN_ASA_FOR_SURFACE);
			System.out.println("Number of core residues at "+String.format("%4.2f", BSATOASA_CUTOFF)+
					" bsa to asa cutoff: "+
					cores.getFirst().size()+" "+
					cores.getSecond().size());
			System.out.printf("Interface area: %8.2f\n",interf.getTotalArea());

			if (interf.isIsologous()) {
				System.out.println("Isologous");
			} else {
				System.out.println("Heterologous");
			}

		}

		System.out.println("Interface clusters (one per line): ");
		for (StructureInterfaceCluster cluster:clusters) {
			System.out.print(cluster.getId()+": ");
			for (StructureInterface member:cluster.getMembers()) {
				System.out.print(member.getId()+" ");
			}
			System.out.println();
		}

	}

}