org.biojava.nbio.structure.contact.AtomContactSet Maven / Gradle / Ivy

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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 org.biojava.nbio.structure.contact;

import org.biojava.nbio.structure.Atom;

import java.io.Serializable;
import java.util.*;


/**
 * A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
 *
 * @author duarte_j
 *
 */
public class AtomContactSet implements Serializable, Iterable {


	private static final long serialVersionUID = 1L;

	private HashMap, AtomContact> contacts;
	private double cutoff;

	public AtomContactSet(double cutoff) {
		this.cutoff = cutoff;
		this.contacts = new HashMap,AtomContact>();
	}

	public void add(AtomContact contact) {
		this.contacts.put(getAtomIdPairFromContact(contact), contact);
	}

	public void addAll(Collection list) {
		for (AtomContact contact:list) {
			this.contacts.put(getAtomIdPairFromContact(contact), contact);
		}
	}

	public boolean hasContact(Atom atom1, Atom atom2) {
		return hasContact(
					new AtomIdentifier(atom1.getPDBserial(),atom1.getGroup().getChainId()),
					new AtomIdentifier(atom2.getPDBserial(),atom2.getGroup().getChainId()) );
	}

	public boolean hasContact(AtomIdentifier atomId1, AtomIdentifier atomId2) {
		return contacts.containsKey(new Pair(atomId1,atomId2));
	}

	/**
	 * Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms
	 * @param atom1
	 * @param atom2
	 * @return
	 */
	public AtomContact getContact(Atom atom1, Atom atom2) {
		return contacts.get(new Pair(
				new AtomIdentifier(atom1.getPDBserial(),atom1.getGroup().getChainId()),
				new AtomIdentifier(atom2.getPDBserial(),atom2.getGroup().getChainId()) ));
	}

	public int size() {
		return contacts.size();
	}

	@Override
	public Iterator iterator() {
		return contacts.values().iterator();
	}

	private Pair getAtomIdPairFromContact(AtomContact contact) {
		Pair pair = new Pair(
				new AtomIdentifier(contact.getPair().getFirst().getPDBserial(),contact.getPair().getFirst().getGroup().getChainId()),
				new AtomIdentifier(contact.getPair().getSecond().getPDBserial(),contact.getPair().getSecond().getGroup().getChainId()));

		return pair;
	}

	/**
	 * Returns true if at least 1 contact from this set is within the given distance.
	 * Note that if the distance given is larger than the distance cutoff used to
	 * calculate the contacts then nothing will be found.
	 * @param distance
	 * @return
	 * @throws IllegalArgumentException if given distance is larger than distance cutoff
	 * used for calculation of contacts
	 */
	public boolean hasContactsWithinDistance(double distance) {

		if (distance>=cutoff)
			throw new IllegalArgumentException("Given distance "+
					String.format("%.2f", distance)+" is larger than contacts' distance cutoff "+
					String.format("%.2f", cutoff));

		for (AtomContact contact:this.contacts.values()) {
			if (contact.getDistance() getContactsWithinDistance(double distance) {

		if (distance>=cutoff)
			throw new IllegalArgumentException("Given distance "+
					String.format("%.2f", distance)+" is larger than contacts' distance cutoff "+
					String.format("%.2f", cutoff));

		List list = new ArrayList();
		for (AtomContact contact:this.contacts.values()) {
			if (contact.getDistance()