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 java.io.IOException;
024import java.util.List;
025
026import org.biojava.nbio.structure.Structure;
027import org.biojava.nbio.structure.StructureException;
028import org.biojava.nbio.structure.align.util.AtomCache;
029import org.biojava.nbio.structure.io.FileParsingParameters;
030import org.biojava.nbio.structure.secstruc.DSSPParser;
031import org.biojava.nbio.structure.secstruc.SecStrucCalc;
032import org.biojava.nbio.structure.secstruc.SecStrucInfo;
033import org.biojava.nbio.structure.secstruc.SecStrucTools;
034
035/**
036 * Demonstration of how to load a Structure with the SS information, either from
037 * the PDB file annotation (Author's assignment) or from the DSSP file in the
038 * PDB servers (DSSP assignment).
039 *
040 * @author Aleix Lafita
041 *
042 */
043public class DemoLoadSecStruc {
044
045        public static void main(String[] args) throws IOException,
046                        StructureException {
047
048                String pdbID = "5pti";
049
050                // Only change needed to the DEFAULT Structure loading
051                FileParsingParameters params = new FileParsingParameters();
052                params.setParseSecStruc(true);
053
054                AtomCache cache = new AtomCache();
055                cache.setFileParsingParams(params);
056
057                // Use PDB format, because SS cannot be parsed from mmCIF yet
058                cache.setUseMmCif(false);
059
060                // The loaded Structure contains the SS assigned by Author (simple)
061                Structure s = cache.getStructure(pdbID);
062
063                // Print the Author's assignment (from PDB file)
064                System.out.println("Author's assignment: ");
065                printSecStruc(s);
066
067                // If the more detailed DSSP prediction is required call this
068                DSSPParser.fetch(pdbID, s, true);
069
070                // Print the assignment residue by residue
071                System.out.println("DSSP assignment: ");
072                printSecStruc(s);
073
074                // finally use BioJava's built in DSSP-like secondary structure assigner
075                SecStrucCalc secStrucCalc = new SecStrucCalc();
076
077                // calculate and assign
078                secStrucCalc.calculate(s,true);
079                printSecStruc(s);
080
081        }
082
083        public static void printSecStruc(Structure s){
084                List<SecStrucInfo> ssi = SecStrucTools.getSecStrucInfo(s);
085                for (SecStrucInfo ss : ssi) {
086                        System.out.println(ss.getGroup().getChain().getName() + " "
087                                        + ss.getGroup().getResidueNumber() + " "
088                                        + ss.getGroup().getPDBName() + " -> " + ss.toString());
089                }
090        }
091}