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; 022 023 024import org.biojava.nbio.structure.Structure; 025import org.biojava.nbio.structure.align.util.AtomCache; 026import org.biojava.nbio.structure.domain.LocalProteinDomainParser; 027import org.biojava.nbio.structure.domain.pdp.Domain; 028import org.biojava.nbio.structure.domain.pdp.Segment; 029import org.biojava.nbio.structure.io.FileParsingParameters; 030 031import java.util.List; 032 033public class DemoDomainsplit { 034 035 public static void main(String[] args){ 036 037 DemoDomainsplit split = new DemoDomainsplit(); 038 039 //String pdbId = "3gly"; 040 String pdbId = "4hhb"; 041 042 split.basicLoad(pdbId); 043 044 } 045 046 public void basicLoad(String pdbId){ 047 048 try { 049 050 // This utility class can automatically download missing PDB files. 051 AtomCache cache = new AtomCache(); 052 053 // 054 // configure the parameters of file parsing (optional) 055 056 FileParsingParameters params = new FileParsingParameters(); 057 058 // should the ATOM and SEQRES residues be aligned when creating the internal data model? 059 params.setAlignSeqRes(true); 060 // should secondary structure get parsed from the file 061 params.setParseSecStruc(false); 062 063 // and set the params in the cache. 064 cache.setFileParsingParams(params); 065 066 // end of optional part 067 068 Structure struc = cache.getStructure(pdbId); 069 070 System.out.println("structure loaded: " + struc); 071 072 List<Domain> domains = LocalProteinDomainParser.suggestDomains(struc); 073 074 System.out.println("RESULTS: ====="); 075 for ( Domain dom : domains){ 076 System.out.println("DOMAIN:" + dom.getSize() + " " + dom.getScore()); 077 List<Segment> segments = dom.getSegments(); 078 for ( Segment s : segments){ 079 System.out.println(" Segment: " + s); 080 } 081 } 082 } catch (Exception e){ 083 e.printStackTrace(); 084 } 085 086 } 087}