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 */
021/**
022 *
023 */
024package org.biojava.nbio.structure.symmetry.jmolScript;
025
026import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
027import org.biojava.nbio.structure.symmetry.geometry.Prism;
028import org.biojava.nbio.structure.symmetry.geometry.RectangularPrism;
029
030
031/**
032 * @author Peter
033 *
034 */
035public class JmolSymmetryScriptGeneratorCn extends JmolSymmetryScriptGeneratorPointGroup {
036
037        public JmolSymmetryScriptGeneratorCn(RotationAxisAligner axisTransformation, String name) {
038                super(axisTransformation, name);
039                if (axisTransformation.getRotationGroup().getPointGroup().equals("C2")) {
040                        setPolyhedron(new RectangularPrism(axisTransformation.getDimension().z*2, axisTransformation.getDimension().x*2, axisTransformation.getDimension().y*2));
041                } else {
042                        Prism p = new Prism(axisTransformation.getRotationGroup().getRotation(0).getFold());
043                        p.setHeight(axisTransformation.getDimension().z*2);
044                        p.setInscribedRadius(axisTransformation.getRadius());
045                        setPolyhedron(p);
046                }
047        }
048
049        @Override
050        public int getZoom() {
051                // find maximum extension of structure
052                double maxExtension = getMaxExtension();
053                // find maximum extension of polyhedron
054                RotationAxisAligner at = getAxisTransformation();
055                double polyhedronExtension = Math.max(getPolyhedron().getCirumscribedRadius(), at.getDimension().z);
056
057                int zoom = Math.round((float)(maxExtension/polyhedronExtension * 110));
058                if (zoom > 100) {
059                        zoom = 100;
060                }
061                return zoom;
062        }
063
064        @Override
065        public int getOrientationCount() {
066                //  the last two views (top, bottom) are not that interesting.
067                if (getAxisTransformation().getRotationGroup().getPointGroup().equals("C2")) {
068                    return getPolyhedron().getViewCount()-2;
069                }
070                return getPolyhedron().getViewCount();
071        }
072
073        /**
074         * Returns the name of a specific orientation
075         * @param index orientation index
076         * @return name of orientation
077         */
078        @Override
079        public String getOrientationName(int index) {
080                if (getAxisTransformation().getRotationGroup().getPointGroup().equals("C2")) {
081                        if (index == 0) {
082                                return "Front C2 axis";
083                        } else if (index == 2) {
084                                return "Back C2 axis";
085                        }
086                }
087                return getPolyhedron().getViewName(index);
088        }
089}