demo.DemoShowBiolAssembly Maven / Gradle / Ivy
/*
* 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();
}
}
}