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 demo; 022 023import org.biojava.nbio.structure.Structure; 024import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol; 025import org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory; 026import org.biojava.nbio.structure.StructureIO; 027 028public class DemoShowBiolAssembly { 029 030 public static void main(String[] args){ 031 032 try{ 033 // see also: http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html 034 // good examples: 1stp 1gav 1hv4 1hho 7dfr 3fad 1qqp 035 036 // assembly 0 ... asym Unit 037 // assembly 1 ... the first bio assembly 038 // example 1fah has 2 assemblies (two copies of the assembly in asymmetric unit) 039 040 041 // Various interesting symmetries: (see Lawson, 2008) 042 // Circular - 1TJA 043 // Dihedral - 1ei7 044 // Icosahedral - 1a34 045 // Helical - 1cgm 046 047 048 // DNA 173D .. 2 049 050 BioUnitDataProviderFactory.setBioUnitDataProvider(BioUnitDataProviderFactory.pdbProviderClassName); 051 //Structure bioAssembly = StructureIO.getBiologicalAssembly("4A1I",2); 052 053 Structure bioAssembly = StructureIO.getBiologicalAssembly("1pdr",1); 054 055 StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol(); 056 //jmolPanel.evalString("set autobond=false"); 057 jmolPanel.setStructure(bioAssembly); 058 059 // send some commands to Jmol 060 jmolPanel.evalString("select * ; color structure ; spacefill off; wireframe off; backbone off; cartoon on; select ligands ; spacefill 0.4; color cpk; model 0;"); 061 062 System.out.println("done!"); 063 064 } catch (Exception e) { 065 e.printStackTrace(); 066 } 067 } 068}