DemoShowBiolAssembly.java

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package demo;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.StructureIO;

public class DemoShowBiolAssembly {

	public static void main(String[] args){

		try{
			// see also: http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html
			// good examples: 1stp 1gav 1hv4 1hho 7dfr 3fad  1qqp

			// assembly 0 ... asym Unit
			// assembly 1 ... the first bio assembly
			// example 1fah has  2 assemblies (two copies of the assembly in asymmetric unit)


			// Various interesting symmetries: (see Lawson, 2008)
			// Circular    - 1TJA
			// Dihedral    - 1ei7
			// Icosahedral - 1a34
			// Helical     - 1cgm


			// DNA 173D .. 2

			//Structure bioAssembly = StructureIO.getBiologicalAssembly("4A1I",2);

			Structure bioAssembly = StructureIO.getBiologicalAssembly("1pdr",1);

			StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();
			//jmolPanel.evalString("set autobond=false");
			jmolPanel.setStructure(bioAssembly);

			// send some commands to Jmol
			jmolPanel.evalString("select * ; color structure ; spacefill off; wireframe off; backbone off; cartoon on; select ligands ; spacefill 0.4; color cpk; model 0;");

			System.out.println("done!");

		} catch (Exception e) {
			e.printStackTrace();
		}
	}
}