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<!DOCTYPE HTML>

<head>

<title>Source code</title>

</head>

<pre>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 Jun 30, 2010

021 * Author: Andreas Prlic

022 *

023 */

024

025package demo;

026

027

028import org.biojava.nbio.structure.Atom;

029import org.biojava.nbio.structure.Structure;

030import org.biojava.nbio.structure.StructureTools;

031import org.biojava.nbio.structure.align.StructureAlignment;

032import org.biojava.nbio.structure.align.StructureAlignmentFactory;

033import org.biojava.nbio.structure.align.ce.CeMain;

034import org.biojava.nbio.structure.align.model.AFPChain;

035import org.biojava.nbio.structure.align.model.AfpChainWriter;

036import org.biojava.nbio.structure.align.util.AFPChainScorer;

037import org.biojava.nbio.structure.align.util.AtomCache;

038import org.biojava.nbio.structure.io.FileParsingParameters;

039import org.biojava.nbio.structure.scop.*;

040

041import java.util.List;

042

043/** A class demonstrating the use of the SCOP parsing tools

044 *

045 * @author Andreas Prlic

046 *

047 */

048public class DemoSCOP

049{

050 public static void main(String[] args){

051

052 DemoSCOP demo = new DemoSCOP();

053

054

055 // this creates a local copy of SCOP

056 ScopDatabase scop = new ScopInstallation();

057

058 // an alternative would be this one, which fetches data dynamically

059 //ScopDatabase scop = new RemoteScopInstallation();

060

061 ScopFactory.setScopDatabase(scop);

062

063 demo.getCategories();

064 demo.printDomainsForPDB();

065 demo.traverseHierarchy();

066 demo.alignSuperfamily();

067 }

068

069 /** Traverse throught the SCOP hierarchy

070 *

071 */

072 public void traverseHierarchy()

073 {

074 String pdbId = "4HHB";

075 // download SCOP if required and load into memory

076 ScopDatabase scop = ScopFactory.getSCOP();

077

078 List<ScopDomain> domains = scop.getDomainsForPDB(pdbId);

079

080 // show the hierachy for the first domain:

081

082 ScopNode node = scop.getScopNode(domains.get(0).getSunid());

083

084 while (node != null){

085

086 System.out.println("This node: sunid:" + node.getSunid() );

087 System.out.println(scop.getScopDescriptionBySunid(node.getSunid()));

088 node = scop.getScopNode(node.getParentSunid());

089 }

090

091 }

092

093 /** Get various categories

094 *

095 */

096 public void getCategories(){

097 // download SCOP if required and load into memory

098 ScopDatabase scop = ScopFactory.getSCOP();

099 List<ScopDescription> superfams = scop.getByCategory(ScopCategory.Superfamily);

100

101 System.out.println("Total nr. of superfamilies:" + superfams.size());

102

103 List<ScopDescription> folds = scop.getByCategory(ScopCategory.Fold);

104 System.out.println("Total nr. of folds:" + folds.size());

105

106 }

107

108 public void alignSuperfamily(){

109 // download SCOP if required and load into memory

110 ScopDatabase scop = ScopFactory.getSCOP();

111 List<ScopDescription> superfams = scop.getByCategory(ScopCategory.Superfamily);

112

113 System.out.println("Total nr. of superfamilies:" + superfams.size());

114

115

116 // configure where to load PDB files from and

117 // what information to load

118 AtomCache cache = new AtomCache();

119 FileParsingParameters fileparams = new FileParsingParameters() ;

120 fileparams.setAlignSeqRes(false);

121 fileparams.setParseSecStruc(false);

122 cache.setFileParsingParams(fileparams);

123

124 // get tge first superfamily

125 ScopDescription superfam1 = superfams.get(0);

126 System.out.println("First superfamily: " + superfam1);

127

128 ScopNode node = scop.getScopNode(superfam1.getSunID());

129 System.out.println("scopNode for first superfamily:" + node);

130

131 List<ScopDomain> doms4superfam1 = scop.getScopDomainsBySunid(superfam1.getSunID());

132 ScopDomain dom1 = doms4superfam1.get(0);

133

134 // align the first domain against all others members of this superfamily

135 for ( int i = 1 ; i < doms4superfam1.size() ; i ++){

136

137 ScopDomain dom2 = doms4superfam1.get(i);

138

139 try {

140 Structure s1 = cache.getStructureForDomain(dom1);

141 Structure s2 = cache.getStructureForDomain(dom2);

142

143 Atom[] ca1 = StructureTools.getAtomCAArray(s1);

144 Atom[] ca2 = StructureTools.getAtomCAArray(s2);

145 StructureAlignment ce = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);

146 AFPChain afpChain = ce.align(ca1, ca2);

147

148 //System.out.println(afpChain.toCE(ca1, ca2));

149

150 //StructureAlignmentDisplay.display(afpChain, ca1, ca2);

151

152 System.out.println(dom1.getScopId() + " vs. " + dom2.getScopId()+ " :" + afpChain.getProbability());

153 double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2);

154 afpChain.setTMScore(tmScore);

155 System.out.println(AfpChainWriter.toScoresList(afpChain));

156

157 } catch (Exception e){

158 e.printStackTrace();

159 }

160 }

161

162 }

163

164 public void printDomainsForPDB(){

165 String pdbId = "4HHB";

166

167 // download SCOP if required and load into memory

168 ScopDatabase scop = ScopFactory.getSCOP();

169

170 List<ScopDomain> domains = scop.getDomainsForPDB(pdbId);

171

172 System.out.println(domains);

173

174 }

175

176

177}

</pre>

</div>

</main>

</body>

</html>

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