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

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The protein structure modules of BioJava.
There is a newer version: 7.1.3
/*
 *                    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 org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.ResidueNumber;

import java.io.Serializable;
import java.util.HashMap;
import java.util.Iterator;

/**
 * A set of residue-residue contacts.
 * Relies on residue indices (based on SEQRES and starting with 1) to store the pairs
 * and thus to match contacts.
 *
 * @author duarte_j
 * @see ResidueIdentifier
 */
public class GroupContactSet implements Serializable, Iterable{

	private static final long serialVersionUID = 1L;

	private HashMap, GroupContact> contacts;

	public GroupContactSet() {
		contacts = new HashMap<>();
	}

	/**
	 * Constructs a GroupContactSet by collapsing the given AtomContactSet into
	 * residue-residue (group-group) contacts.
	 * @param atomContacts
	 */
	public GroupContactSet(AtomContactSet atomContacts) {
		contacts = new HashMap<>();
		atoms2groups(atomContacts);
	}

	private void atoms2groups(AtomContactSet atomContacts) {


		for (AtomContact atomContact:atomContacts) {

			Pair atomPair = atomContact.getPair();

			Group iResidue = atomPair.getFirst().getGroup();
			Group jResidue = atomPair.getSecond().getGroup();

			// we skip the self-residue contacts
			if (iResidue.equals(jResidue)) continue;

			Pair residuePair = new Pair<> (iResidue, jResidue);
			Pair pair = new Pair<>(new ResidueIdentifier(iResidue), new ResidueIdentifier(jResidue));

			if (!contacts.containsKey(pair)) {

				GroupContact groupContact = new GroupContact();
				groupContact.setPair(residuePair);
				groupContact.addAtomContact(atomContact);

				contacts.put(pair, groupContact);

			} else {

				GroupContact groupContact = contacts.get(pair);

				groupContact.addAtomContact(atomContact);

			}

		}
	}

	public void add(GroupContact groupContact) {
		contacts.put(getResIdPairFromContact(groupContact),groupContact);
	}

	/**
	 * Tell whether the given group pair is a contact in this GroupContactSet,
	 * the comparison is done by matching residue numbers and chain identifiers
	 * @param group1
	 * @param group2
	 * @return
	 */
	public boolean hasContact(Group group1, Group group2) {
		return hasContact(group1.getResidueNumber(),group2.getResidueNumber());
	}

	/**
	 * Tell whether the given pair is a contact in this GroupContactSet,
	 * the comparison is done by matching residue numbers and chain identifiers
	 * @param resNumber1
	 * @param resNumber2
	 * @return
	 */
	public boolean hasContact(ResidueNumber resNumber1, ResidueNumber resNumber2) {
		return contacts.containsKey(new Pair(resNumber1, resNumber2));
	}

	/**
	 * Tell whether the given pair is a contact in this GroupContactSet,
	 * in a chain-identifier independent way: contacts happening between different copies of
	 * the same Compound(Entity) will be considered equal as long as they have the same
	 * residue numbers.
	 * @param resId1
	 * @param resId2
	 * @return
	 */
	public boolean hasContact(ResidueIdentifier resId1, ResidueIdentifier resId2) {

		return contacts.containsKey(new Pair(resId1, resId2));
	}

	/**
	 * Returns the corresponding GroupContact or null if no contact exists between the 2 given groups
	 * @param group1
	 * @param group2
	 * @return
	 */
	public GroupContact getContact(Group group1, Group group2) {
		return contacts.get(
				new Pair(group1.getResidueNumber(),group2.getResidueNumber()));
	}

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

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

	private Pair getResIdPairFromContact(GroupContact groupContact) {
		return new Pair<>(
				new ResidueIdentifier(groupContact.getPair().getFirst()),
				new ResidueIdentifier(groupContact.getPair().getSecond()) );

	}
}