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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.*;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.contact.AtomContact;
import org.biojava.nbio.structure.contact.AtomContactSet;
import org.biojava.nbio.structure.contact.GroupContactSet;
import org.biojava.nbio.structure.io.StructureFiletype;

import java.io.IOException;


public class DemoContacts {


	public static void main(String[] args) throws IOException, StructureException {

		String pdbCode = "1smt";

		demoContacts(pdbCode);
	}

	private static void demoContacts(String pdbCode) throws IOException, StructureException {

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

		StructureIO.setAtomCache(cache);

		Structure structure = StructureIO.getStructure(pdbCode);

		Chain chain = structure.getPolyChainByPDB("A");

		String[] atoms = {"CA"};
		AtomContactSet contacts = StructureTools.getAtomsInContact(chain, atoms, 8.0);

		System.out.println("Contacting residues (on CA atoms)");

		for (AtomContact contact:contacts) {
			Atom atom1 = contact.getPair().getFirst();
			Atom atom2 = contact.getPair().getSecond();

			System.out.printf(" %3s-%3s %3s-%3s : %5.2f\n",
					atom1.getGroup().getResidueNumber(),
					atom1.getGroup().getPDBName(),
					atom2.getGroup().getResidueNumber(),
					atom2.getGroup().getPDBName(),
					contact.getDistance());
		}

		System.out.println("Total number of atom contacts: "+contacts.size());

		GroupContactSet groupContacts = new GroupContactSet(contacts);
//		for (GroupContact groupContact:groupContacts) {
//			Group g1 = groupContact.getPair().getFirst();
//			Group g2 = groupContact.getPair().getSecond();
//
//			System.out.printf(" %3s-%3s %3s-%3s : %5.2f\n",
//					g1.getResidueNumber(),
//					g1.getPDBName(),
//					g2.getResidueNumber(),
//					g2.getPDBName(),
//					groupContact.getMinDistance());
//		}
		System.out.println("Total number of residue contacts: "+groupContacts.size());


		contacts = StructureTools.getAtomsInContact(structure.getChainByIndex(0),structure.getChainByIndex(1),5.5, false);

		System.out.println("Contacting residues between 2 first chains (all non-H non-hetatoms)");

		for (AtomContact contact:contacts) {
			Atom atom1 = contact.getPair().getFirst();
			Atom atom2 = contact.getPair().getSecond();

			System.out.printf(" %3s:%1s-%3s-%3s || %3s:%1s-%3s-%3s : %5.2f\n",
					atom1.getGroup().getResidueNumber(),
					atom1.getGroup().getChainId(),
					atom1.getGroup().getPDBName(),
					atom1.getName(),
					atom2.getGroup().getResidueNumber(),
					atom2.getGroup().getChainId(),
					atom2.getGroup().getPDBName(),
					atom2.getName(),
					contact.getDistance());
		}

		System.out.println("Total number of atom contacts: "+contacts.size());

		groupContacts = new GroupContactSet(contacts);
		System.out.println("Total number of residue contacts: "+groupContacts.size());

	}


}