001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.structure.cluster;
022
023/**
024 * The SubunitClustererMethod ennummerates all methods that can be used to
025 * cluster {@link Subunit} in the {@link SubunitCluster}.
026 *
027 * @author Aleix Lafita
028 * @since 5.0.0
029 *
030 */
031public enum SubunitClustererMethod {
032
033        /**
034         * The SEQUENCE clustering method uses the residue sequence of the
035         * {@link Subunit} to calculate sequence alignments.
036         * <p>
037         * Two {@link Subunit} with sufficient sequence identity and coverage are
038         * clustered together.
039         */
040        SEQUENCE,
041
042        /**
043         * The STRUCTURE clustering method uses the residue sequence and the
044         * coordinates of its Atom representatives of the {@link Subunit} to
045         * calculate sequence and structure alignments.
046         * <p>
047         * Two {@link Subunit} with sufficient structural similarity and coverage
048         * are clustered together.
049         */
050        STRUCTURE,
051        /**
052         * The SEQUENCE_STRUCTURE clustering method uses the residue sequence and the
053         * coordinates of its Atom representatives of the {@link Subunit} to
054         * calculate sequence and structure alignments.
055         * <p>
056         * Two {@link Subunit} with sufficient sequence identity and coverage are
057         * clustered together. Additionally, two {@link Subunit} with sufficient
058         * structural similarity and coverage are clustered together. If the
059         * sequence and structure clustering differ, the cluster contains
060         * pseudosymmetry (by definition).
061         */
062        SEQUENCE_STRUCTURE
063}
064