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.symmetry.internal;
022
023import org.biojava.nbio.structure.Atom;
024import org.biojava.nbio.structure.StructureException;
025import org.biojava.nbio.structure.align.model.AFPChain;
026import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
027
028/**
029 * Interface for all symmetry refinement implementations.
030 *
031 * @author Aleix Lafita
032 * @since 4.2.0
033 *
034 */
035public interface SymmetryRefiner {
036
037        /**
038         * Returns a refined symmetry alignment, where the repeat residues are
039         * aligned consistently in a MultipleAlignment.
040         *
041         * @param selfAlignment
042         *            optimal self-alignment calculated by CeSymm
043         * @param atoms
044         *            coordinates of the structure
045         * @param order
046         *            order of symmetry to use
047         * @return MultipleAlignment refined symmetry alignment
048         * @throws RefinerFailedException
049         * @throws StructureException
050         */
051        public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms, int order)
052                        throws RefinerFailedException, StructureException;
053
054}