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.align.util.AtomCache; 024import org.biojava.nbio.structure.scop.ScopDatabase; 025import org.biojava.nbio.structure.scop.ScopFactory; 026 027/** A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP 028 * 029 * @author andreas 030 * @since 3.0.4 031 * 032 */ 033public class DemoBerkeleyScop { 034 035 public static void main(String[]args){ 036 037 038 //ScopDatabase berkeley = new BerkeleyScopInstallation(); 039 040 //ScopFactory.setScopDatabase(berkeley); 041 042 AtomCache cache = new AtomCache(); 043 // whenever you want to get access to SCOP now request it like this: 044 ScopDatabase scop = ScopFactory.getSCOP("1.75"); 045 ScopFactory.setScopDatabase(scop); 046 047 048 System.out.println(cache.getPath()); 049 System.out.println(cache.getCachePath()); 050 // ... and do something with it 051 052 053 // eg. you can run all the demos that work for the UK - SCOP (currently at version 1.75) 054 // this demo no automatically picks up the Berkeley version (currently 1.75A) 055 DemoSCOP scopDemo = new DemoSCOP(); 056 057 scopDemo.getCategories(); 058 scopDemo.printDomainsForPDB(); 059 scopDemo.traverseHierarchy(); 060 scopDemo.alignSuperfamily(); 061 062 063 } 064}