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.geometry;
022
023import javax.vecmath.Matrix4d;
024import javax.vecmath.Point3d;
025
026/**
027 * SuperPositions is a Class that provides static helper methods and an easy
028 * access to the whole family of {@link SuperPosition} algorithms.
029 * <p>
030 * It defines a static SuperPosition object and uses it for calculation.
031 *
032 * @author Aleix Lafita
033 * @since 5.0.0
034 *
035 */
036public class SuperPositions {
037
038        private static SuperPositionAbstract superposer = new SuperPositionQuat(
039                        false);
040
041        /** Prevent instantiation */
042        private SuperPositions(){}
043
044        /**
045         * Use the {@link SuperPosition#superpose(Point3d[], Point3d[])} method of
046         * the default static SuperPosition algorithm contained in this Class.
047         */
048        public static Matrix4d superpose(Point3d[] fixed, Point3d[] moved) {
049                superposer.setCentered(false);
050                return superposer.superpose(fixed, moved);
051        }
052
053        /**
054         * Use the {@link SuperPosition#superpose(Point3d[], Point3d[])} method of
055         * the default static SuperPosition algorithm contained in this Class,
056         * assuming that the point arrays are centered at the origin.
057         */
058        public static Matrix4d superposeAtOrigin(Point3d[] fixed, Point3d[] moved) {
059                superposer.setCentered(true);
060                return superposer.superpose(fixed, moved);
061        }
062
063        /**
064         * Use the {@link SuperPosition#superposeAndTransform(Point3d[], Point3d[])}
065         * method of the default static SuperPosition algorithm contained in this
066         * Class.
067         */
068        public static Matrix4d superposeAndTransform(Point3d[] fixed,
069                        Point3d[] moved) {
070                superposer.setCentered(false);
071                return superposer.superposeAndTransform(fixed, moved);
072        }
073
074        /**
075         * Use the {@link SuperPosition#superposeAndTransform(Point3d[], Point3d[])}
076         * method of the default static SuperPosition algorithm contained in this
077         * Class, assuming that the point arrays are centered at the origin.
078         */
079        public static Matrix4d superposeAndTransformAtOrigin(Point3d[] fixed,
080                        Point3d[] moved) {
081                superposer.setCentered(true);
082                return superposer.superposeAndTransform(fixed, moved);
083        }
084
085        /**
086         * Use the {@link SuperPosition#getRmsd(Point3d[], Point3d[])} method of the
087         * default static SuperPosition algorithm contained in this Class.
088         */
089        public static double getRmsd(Point3d[] fixed, Point3d[] moved) {
090                superposer.setCentered(false);
091                return superposer.getRmsd(fixed, moved);
092        }
093
094        /**
095         * Use the {@link SuperPosition#getRmsd(Point3d[], Point3d[])} method of the
096         * default static SuperPosition algorithm contained in this Class, assuming
097         * that the point arrays are centered at the origin.
098         */
099        public static double getRmsdAtOrigin(Point3d[] fixed, Point3d[] moved) {
100                superposer.setCentered(true);
101                return superposer.getRmsd(fixed, moved);
102        }
103
104        public static void setDefaultSuperPosition(SuperPositionAbstract defaultAlgorithm) {
105                superposer = defaultAlgorithm;
106        }
107}