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.*;
024import org.biojava.nbio.structure.align.util.AtomCache;
025import org.biojava.nbio.structure.contact.AtomContact;
026import org.biojava.nbio.structure.contact.AtomContactSet;
027import org.biojava.nbio.structure.contact.GroupContactSet;
028import org.biojava.nbio.structure.io.StructureFiletype;
029
030import java.io.IOException;
031
032
033public class DemoContacts {
034
035
036        public static void main(String[] args) throws IOException, StructureException {
037
038                String pdbCode = "1smt";
039
040                demoContacts(pdbCode);
041        }
042
043        private static void demoContacts(String pdbCode) throws IOException, StructureException {
044
045                AtomCache cache = new AtomCache();
046                cache.setFiletype(StructureFiletype.CIF);
047
048                StructureIO.setAtomCache(cache);
049
050                Structure structure = StructureIO.getStructure(pdbCode);
051
052                Chain chain = structure.getPolyChainByPDB("A");
053
054                String[] atoms = {"CA"};
055                AtomContactSet contacts = StructureTools.getAtomsInContact(chain, atoms, 8.0);
056
057                System.out.println("Contacting residues (on CA atoms)");
058
059                for (AtomContact contact:contacts) {
060                        Atom atom1 = contact.getPair().getFirst();
061                        Atom atom2 = contact.getPair().getSecond();
062
063                        System.out.printf(" %3s-%3s %3s-%3s : %5.2f\n",
064                                        atom1.getGroup().getResidueNumber(),
065                                        atom1.getGroup().getPDBName(),
066                                        atom2.getGroup().getResidueNumber(),
067                                        atom2.getGroup().getPDBName(),
068                                        contact.getDistance());
069                }
070
071                System.out.println("Total number of atom contacts: "+contacts.size());
072
073                GroupContactSet groupContacts = new GroupContactSet(contacts);
074//              for (GroupContact groupContact:groupContacts) {
075//                      Group g1 = groupContact.getPair().getFirst();
076//                      Group g2 = groupContact.getPair().getSecond();
077//
078//                      System.out.printf(" %3s-%3s %3s-%3s : %5.2f\n",
079//                                      g1.getResidueNumber(),
080//                                      g1.getPDBName(),
081//                                      g2.getResidueNumber(),
082//                                      g2.getPDBName(),
083//                                      groupContact.getMinDistance());
084//              }
085                System.out.println("Total number of residue contacts: "+groupContacts.size());
086
087
088                contacts = StructureTools.getAtomsInContact(structure.getChainByIndex(0),structure.getChainByIndex(1),5.5, false);
089
090                System.out.println("Contacting residues between 2 first chains (all non-H non-hetatoms)");
091
092                for (AtomContact contact:contacts) {
093                        Atom atom1 = contact.getPair().getFirst();
094                        Atom atom2 = contact.getPair().getSecond();
095
096                        System.out.printf(" %3s:%1s-%3s-%3s || %3s:%1s-%3s-%3s : %5.2f\n",
097                                        atom1.getGroup().getResidueNumber(),
098                                        atom1.getGroup().getChainId(),
099                                        atom1.getGroup().getPDBName(),
100                                        atom1.getName(),
101                                        atom2.getGroup().getResidueNumber(),
102                                        atom2.getGroup().getChainId(),
103                                        atom2.getGroup().getPDBName(),
104                                        atom2.getName(),
105                                        contact.getDistance());
106                }
107
108                System.out.println("Total number of atom contacts: "+contacts.size());
109
110                groupContacts = new GroupContactSet(contacts);
111                System.out.println("Total number of residue contacts: "+groupContacts.size());
112
113        }
114
115
116}