/*
* 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.align.util.AtomCache;
import org.biojava.nbio.structure.scop.ScopDatabase;
import org.biojava.nbio.structure.scop.ScopFactory;
/** A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
*
* @author andreas
* @since 3.0.4
*
*/
public class DemoBerkeleyScop {
public static void main(String[]args){
//ScopDatabase berkeley = new BerkeleyScopInstallation();
//ScopFactory.setScopDatabase(berkeley);
AtomCache cache = new AtomCache();
// whenever you want to get access to SCOP now request it like this:
ScopDatabase scop = ScopFactory.getSCOP("1.75");
ScopFactory.setScopDatabase(scop);
System.out.println(cache.getPath());
System.out.println(cache.getCachePath());
// ... and do something with it
// eg. you can run all the demos that work for the UK - SCOP (currently at version 1.75)
// this demo no automatically picks up the Berkeley version (currently 1.75A)
DemoSCOP scopDemo = new DemoSCOP();
scopDemo.getCategories();
scopDemo.printDomainsForPDB();
scopDemo.traverseHierarchy();
scopDemo.alignSuperfamily();
}
}