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| 1 | +/* |
| 2 | + * BioJava development code |
| 3 | + * |
| 4 | + * This code may be freely distributed and modified under the |
| 5 | + * terms of the GNU Lesser General Public Licence. This should |
| 6 | + * be distributed with the code. If you do not have a copy, |
| 7 | + * see: |
| 8 | + * |
| 9 | + * http://www.gnu.org/copyleft/lesser.html |
| 10 | + * |
| 11 | + * Copyright for this code is held jointly by the individual |
| 12 | + * authors. These should be listed in @author doc comments. |
| 13 | + * |
| 14 | + * For more information on the BioJava project and its aims, |
| 15 | + * or to join the biojava-l mailing list, visit the home page |
| 16 | + * at: |
| 17 | + * |
| 18 | + * http://www.biojava.org/ |
| 19 | + * |
| 20 | + */ |
| 21 | +package demo; |
| 22 | + |
| 23 | +import org.biojava.nbio.structure.Structure; |
| 24 | +import org.biojava.nbio.structure.StructureException; |
| 25 | +import org.biojava.nbio.structure.align.util.AtomCache; |
| 26 | +import org.biojava.nbio.structure.cluster.SubunitClustererMethod; |
| 27 | +import org.biojava.nbio.structure.cluster.SubunitClustererParameters; |
| 28 | +import org.biojava.nbio.structure.gui.BiojavaJmol; |
| 29 | +import org.biojava.nbio.structure.symmetry.axis.AxisAligner; |
| 30 | +import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector; |
| 31 | +import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters; |
| 32 | +import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults; |
| 33 | +import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator; |
| 34 | +import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup; |
| 35 | + |
| 36 | +import java.io.IOException; |
| 37 | +import java.util.List; |
| 38 | + |
| 39 | +/** |
| 40 | + * This demo shows how to display the {@link QuatSymmetryResults} of a |
| 41 | + * structure. |
| 42 | + * <p> |
| 43 | + * Examples: 4HHB, 4AQ5, 1LTI, 1STP, 4F88, 2W6E, 2LXC, 3OE7, 4INU, 4D8s, 4EAR, |
| 44 | + * 4IYQ, 3ZKR |
| 45 | + * <p> |
| 46 | + * Local symmetry: 2WPD (2 local symmetries), 4F88 (local C8), 1LTI (local C5), |
| 47 | + * 2W6E (local C3), 2LXC (local C2), 3OE7 (local C3) |
| 48 | + * <p> |
| 49 | + * Local Pseudosymmetry: 3ZDY, 3ZDX |
| 50 | + * <p> |
| 51 | + * Helical: 1B47 |
| 52 | + * <p> |
| 53 | + * With internal symmetry: 4E3E, 1VYM |
| 54 | + * |
| 55 | + * @author Peter Rose |
| 56 | + * @author Aleix Lafita |
| 57 | + * |
| 58 | + */ |
| 59 | +public class DemoQuatSymmetryJmol { |
| 60 | + |
| 61 | + public static void main(String[] args) throws IOException, |
| 62 | + StructureException { |
| 63 | + |
| 64 | + String name = "4hhb"; |
| 65 | + |
| 66 | + // Download the biological assembly |
| 67 | + AtomCache cache = new AtomCache(); |
| 68 | + cache.setUseMmCif(true); |
| 69 | + Structure structure = cache.getStructure("BIO:" + name + ":1"); |
| 70 | + |
| 71 | + QuatSymmetryParameters sp = new QuatSymmetryParameters(); |
| 72 | + SubunitClustererParameters cp = new SubunitClustererParameters(); |
| 73 | + cp.setClustererMethod(SubunitClustererMethod.SEQUENCE); // normal |
| 74 | + // cp.setClustererMethod(SubunitClustererMethod.STRUCTURE); // pseudo |
| 75 | + // cp.setClustererMethod(SubunitClustererMethod.INTERNAL_SYMMETRY); |
| 76 | + cp.setCoverageThreshold(0.9); |
| 77 | + |
| 78 | + // Calculate and display the global symmetry |
| 79 | + QuatSymmetryResults globalSymmetry = QuatSymmetryDetector |
| 80 | + .calcGlobalSymmetry(structure, sp, cp); |
| 81 | + showResults(structure, name, globalSymmetry); |
| 82 | + |
| 83 | + // Calculate and displaythe local symmetry |
| 84 | + List<QuatSymmetryResults> localSymmetry = QuatSymmetryDetector |
| 85 | + .calcLocalSymmetries(structure, sp, cp); |
| 86 | + |
| 87 | + for (QuatSymmetryResults result : localSymmetry) |
| 88 | + showResults(structure, name, result); |
| 89 | + |
| 90 | + } |
| 91 | + |
| 92 | + private static void showResults(Structure s, String name, |
| 93 | + QuatSymmetryResults results) { |
| 94 | + |
| 95 | + String title = name + ": " + results.getSubunits().getStoichiometry() |
| 96 | + + ", " + results.getSymmetry(); |
| 97 | + |
| 98 | + if (results.getSubunits().isPseudoSymmetric()) |
| 99 | + title += ", pseudosymmetric"; |
| 100 | + |
| 101 | + if (results.isLocal()) |
| 102 | + title += ", local"; |
| 103 | + |
| 104 | + String script = "set defaultStructureDSSP true; set measurementUnits ANGSTROMS; select all; spacefill off; wireframe off; " |
| 105 | + + "backbone off; cartoon on; color cartoon structure; color structure; select ligand;wireframe 0.16;spacefill 0.5; " |
| 106 | + + "color cpk ; select all; model 0;set antialiasDisplay true; autobond=false;save STATE state_1;"; |
| 107 | + |
| 108 | + AxisAligner aligner = AxisAligner.getInstance(results); |
| 109 | + |
| 110 | + JmolSymmetryScriptGenerator scriptGenerator = JmolSymmetryScriptGeneratorPointGroup |
| 111 | + .getInstance(aligner, "g"); |
| 112 | + |
| 113 | + script += scriptGenerator.getOrientationWithZoom(0); |
| 114 | + script += scriptGenerator.drawPolyhedron(); |
| 115 | + script += scriptGenerator.drawAxes(); |
| 116 | + script += scriptGenerator.colorBySymmetry(); |
| 117 | + |
| 118 | + title += ", method: " + results.getMethod(); |
| 119 | + |
| 120 | + script += "draw axes* on; draw poly* on;"; |
| 121 | + |
| 122 | + BiojavaJmol jmol = new BiojavaJmol(); |
| 123 | + jmol.setStructure(s); |
| 124 | + |
| 125 | + jmol.setTitle(title); |
| 126 | + jmol.evalString(script); |
| 127 | + |
| 128 | + } |
| 129 | +} |
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