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 * Created on May 17, 2010 021 * Author: Andreas Prlic 022 * 023 */ 024 025package demo; 026 027import org.biojava.nbio.structure.*; 028import org.biojava.nbio.structure.align.util.AtomCache; 029import org.biojava.nbio.structure.io.MMCIFFileReader; 030import org.biojava.nbio.structure.io.StructureProvider; 031 032import java.util.List; 033 034/** An example of how to read MMcif files 035 * 036 * @author Andreas Prlic 037 * 038 */ 039public class DemoMMCIFReader 040{ 041 042 public static void main(String[] args){ 043 044 DemoMMCIFReader demo = new DemoMMCIFReader(); 045 046 demo.loadSimple(); 047 048 demo.loadFromDirectAccess(); 049 050 } 051 052 /** 053 * A basic example how to load an mmCif file and get a Structure object 054 * 055 */ 056 public void loadSimple(){ 057 String pdbId = "4hhb"; 058 059 AtomCache cache = new AtomCache(); 060 cache.setUseMmCif(true); 061 062 StructureIO.setAtomCache(cache); 063 064 try { 065 Structure s = StructureIO.getStructure(pdbId); 066 067 System.out.println(pdbId + " has nr atoms: " + StructureTools.getNrAtoms(s)); 068 069 } catch (Exception e){ 070 e.printStackTrace(); 071 } 072 } 073 074 075 /** 076 * An example demonstrating how to directly use the mmCif file parsing classes. This could potentially be used 077 * to use the parser to populate a data-structure that is different from the biojava-structure data model. 078 * 079 */ 080 public void loadFromDirectAccess(){ 081 String pdbId = "1A4W"; 082 083 StructureProvider pdbreader = new MMCIFFileReader(); 084 085 try { 086 Structure s = pdbreader.getStructureById(pdbId); 087 088 System.out.println("Getting chain H of 1A4W"); 089 090 List<Chain> hs = s.getNonPolyChainsByPDB("H"); 091 092 Chain h = hs.get(0); 093 List<Group> ligands = h.getAtomGroups(); 094 095 System.out.println("These ligands have been found in chain " + h.getName()); 096 097 for (Group l:ligands){ 098 System.out.println(l); 099 } 100 101 System.out.println("Accessing QWE directly: "); 102 Group qwe = s.getNonPolyChainsByPDB("H").get(2).getGroupByPDB(new ResidueNumber("H",373,null)); 103 104 System.out.println(qwe.getChemComp()); 105 106 System.out.println(h.getSeqResSequence()); 107 System.out.println(h.getAtomSequence()); 108 System.out.println(h.getAtomGroups(GroupType.HETATM)); 109 110 System.out.println("Entities: " + s.getEntityInfos()); 111 112 } catch (Exception e) { 113 e.printStackTrace(); 114 } 115 116 117 } 118}