biojava.github.io/docs/api5.0.0/src-html/demo/DemoSCOP.html at master · biojava/biojava.github.io

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">

<head>

<title>Source code</title>

</head>

<body>

002 * BioJava development code<a name="line.2"></a>

003 *<a name="line.3"></a>

004 * This code may be freely distributed and modified under the<a name="line.4"></a>

005 * terms of the GNU Lesser General Public Licence. This should<a name="line.5"></a>

006 * be distributed with the code. If you do not have a copy,<a name="line.6"></a>

007 * see:<a name="line.7"></a>

008 *<a name="line.8"></a>

009 * http://www.gnu.org/copyleft/lesser.html<a name="line.9"></a>

010 *<a name="line.10"></a>

011 * Copyright for this code is held jointly by the individual<a name="line.11"></a>

012 * authors. These should be listed in @author doc comments.<a name="line.12"></a>

013 *<a name="line.13"></a>

014 * For more information on the BioJava project and its aims,<a name="line.14"></a>

015 * or to join the biojava-l mailing list, visit the home page<a name="line.15"></a>

016 * at:<a name="line.16"></a>

017 *<a name="line.17"></a>

018 * http://www.biojava.org/<a name="line.18"></a>

019 *<a name="line.19"></a>

020 * Created on Jun 30, 2010<a name="line.20"></a>

021 * Author: Andreas Prlic<a name="line.21"></a>

022 *<a name="line.22"></a>

023 */<a name="line.23"></a>

024<a name="line.24"></a>

025package demo;<a name="line.25"></a>

026<a name="line.26"></a>

027<a name="line.27"></a>

028import org.biojava.nbio.structure.Atom;<a name="line.28"></a>

029import org.biojava.nbio.structure.Structure;<a name="line.29"></a>

030import org.biojava.nbio.structure.StructureTools;<a name="line.30"></a>

031import org.biojava.nbio.structure.align.StructureAlignment;<a name="line.31"></a>

032import org.biojava.nbio.structure.align.StructureAlignmentFactory;<a name="line.32"></a>

033import org.biojava.nbio.structure.align.ce.CeMain;<a name="line.33"></a>

034import org.biojava.nbio.structure.align.model.AFPChain;<a name="line.34"></a>

035import org.biojava.nbio.structure.align.model.AfpChainWriter;<a name="line.35"></a>

036import org.biojava.nbio.structure.align.util.AFPChainScorer;<a name="line.36"></a>

037import org.biojava.nbio.structure.align.util.AtomCache;<a name="line.37"></a>

038import org.biojava.nbio.structure.io.FileParsingParameters;<a name="line.38"></a>

039import org.biojava.nbio.structure.scop.*;<a name="line.39"></a>

040<a name="line.40"></a>

041import java.util.List;<a name="line.41"></a>

042<a name="line.42"></a>

043/** A class demonstrating the use of the SCOP parsing tools<a name="line.43"></a>

044 *<a name="line.44"></a>

045 * @author Andreas Prlic<a name="line.45"></a>

046 *<a name="line.46"></a>

047 */<a name="line.47"></a>

048public class DemoSCOP<a name="line.48"></a>

049{<a name="line.49"></a>

050 public static void main(String[] args){<a name="line.50"></a>

051<a name="line.51"></a>

052 DemoSCOP demo = new DemoSCOP();<a name="line.52"></a>

053<a name="line.53"></a>

054<a name="line.54"></a>

055 // this creates a local copy of SCOP<a name="line.55"></a>

056 ScopDatabase scop = new ScopInstallation();<a name="line.56"></a>

057<a name="line.57"></a>

058 // an alternative would be this one, which fetches data dynamically<a name="line.58"></a>

059 //ScopDatabase scop = new RemoteScopInstallation();<a name="line.59"></a>

060<a name="line.60"></a>

061 ScopFactory.setScopDatabase(scop);<a name="line.61"></a>

062<a name="line.62"></a>

063 demo.getCategories();<a name="line.63"></a>

064 demo.printDomainsForPDB();<a name="line.64"></a>

065 demo.traverseHierarchy();<a name="line.65"></a>

066 demo.alignSuperfamily();<a name="line.66"></a>

067 }<a name="line.67"></a>

068<a name="line.68"></a>

069 /** Traverse throught the SCOP hierarchy<a name="line.69"></a>

070 *<a name="line.70"></a>

071 */<a name="line.71"></a>

072 public void traverseHierarchy()<a name="line.72"></a>

073 {<a name="line.73"></a>

074 String pdbId = "4HHB";<a name="line.74"></a>

075 // download SCOP if required and load into memory<a name="line.75"></a>

076 ScopDatabase scop = ScopFactory.getSCOP();<a name="line.76"></a>

077<a name="line.77"></a>

078 List<ScopDomain> domains = scop.getDomainsForPDB(pdbId);<a name="line.78"></a>

079<a name="line.79"></a>

080 // show the hierachy for the first domain:<a name="line.80"></a>

081<a name="line.81"></a>

082 ScopNode node = scop.getScopNode(domains.get(0).getSunid());<a name="line.82"></a>

083<a name="line.83"></a>

084 while (node != null){<a name="line.84"></a>

085<a name="line.85"></a>

086 System.out.println("This node: sunid:" + node.getSunid() );<a name="line.86"></a>

087 System.out.println(scop.getScopDescriptionBySunid(node.getSunid()));<a name="line.87"></a>

088 node = scop.getScopNode(node.getParentSunid());<a name="line.88"></a>

089 }<a name="line.89"></a>

090<a name="line.90"></a>

091 }<a name="line.91"></a>

092<a name="line.92"></a>

093 /** Get various categories<a name="line.93"></a>

094 *<a name="line.94"></a>

095 */<a name="line.95"></a>

096 public void getCategories(){<a name="line.96"></a>

097 // download SCOP if required and load into memory<a name="line.97"></a>

098 ScopDatabase scop = ScopFactory.getSCOP();<a name="line.98"></a>

099 List<ScopDescription> superfams = scop.getByCategory(ScopCategory.Superfamily);<a name="line.99"></a>

100<a name="line.100"></a>

101 System.out.println("Total nr. of superfamilies:" + superfams.size());<a name="line.101"></a>

102<a name="line.102"></a>

103 List<ScopDescription> folds = scop.getByCategory(ScopCategory.Fold);<a name="line.103"></a>

104 System.out.println("Total nr. of folds:" + folds.size());<a name="line.104"></a>

105<a name="line.105"></a>

106 }<a name="line.106"></a>

107<a name="line.107"></a>

108 public void alignSuperfamily(){<a name="line.108"></a>

109 // download SCOP if required and load into memory<a name="line.109"></a>

110 ScopDatabase scop = ScopFactory.getSCOP();<a name="line.110"></a>

111 List<ScopDescription> superfams = scop.getByCategory(ScopCategory.Superfamily);<a name="line.111"></a>

112<a name="line.112"></a>

113 System.out.println("Total nr. of superfamilies:" + superfams.size());<a name="line.113"></a>

114<a name="line.114"></a>

115<a name="line.115"></a>

116 // configure where to load PDB files from and<a name="line.116"></a>

117 // what information to load<a name="line.117"></a>

118 AtomCache cache = new AtomCache();<a name="line.118"></a>

119 FileParsingParameters fileparams = new FileParsingParameters() ;<a name="line.119"></a>

120 fileparams.setAlignSeqRes(false);<a name="line.120"></a>

121 fileparams.setParseSecStruc(false);<a name="line.121"></a>

122 cache.setFileParsingParams(fileparams);<a name="line.122"></a>

123<a name="line.123"></a>

124 // get tge first superfamily<a name="line.124"></a>

125 ScopDescription superfam1 = superfams.get(0);<a name="line.125"></a>

126 System.out.println("First superfamily: " + superfam1);<a name="line.126"></a>

127<a name="line.127"></a>

128 ScopNode node = scop.getScopNode(superfam1.getSunID());<a name="line.128"></a>

129 System.out.println("scopNode for first superfamily:" + node);<a name="line.129"></a>

130<a name="line.130"></a>

131 List<ScopDomain> doms4superfam1 = scop.getScopDomainsBySunid(superfam1.getSunID());<a name="line.131"></a>

132 ScopDomain dom1 = doms4superfam1.get(0);<a name="line.132"></a>

133<a name="line.133"></a>

134 // align the first domain against all others members of this superfamily<a name="line.134"></a>

135 for ( int i = 1 ; i < doms4superfam1.size() ; i ++){<a name="line.135"></a>

136<a name="line.136"></a>

137 ScopDomain dom2 = doms4superfam1.get(i);<a name="line.137"></a>

138<a name="line.138"></a>

139 try {<a name="line.139"></a>

140 Structure s1 = cache.getStructureForDomain(dom1);<a name="line.140"></a>

141 Structure s2 = cache.getStructureForDomain(dom2);<a name="line.141"></a>

142<a name="line.142"></a>

143 Atom[] ca1 = StructureTools.getAtomCAArray(s1);<a name="line.143"></a>

144 Atom[] ca2 = StructureTools.getAtomCAArray(s2);<a name="line.144"></a>

145 StructureAlignment ce = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);<a name="line.145"></a>

146 AFPChain afpChain = ce.align(ca1, ca2);<a name="line.146"></a>

147<a name="line.147"></a>

148 //System.out.println(afpChain.toCE(ca1, ca2));<a name="line.148"></a>

149<a name="line.149"></a>

150 //StructureAlignmentDisplay.display(afpChain, ca1, ca2);<a name="line.150"></a>

151<a name="line.151"></a>

152 System.out.println(dom1.getScopId() + " vs. " + dom2.getScopId()+ " :" + afpChain.getProbability());<a name="line.152"></a>

153 double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2);<a name="line.153"></a>

154 afpChain.setTMScore(tmScore);<a name="line.154"></a>

155 System.out.println(AfpChainWriter.toScoresList(afpChain));<a name="line.155"></a>

156<a name="line.156"></a>

157 } catch (Exception e){<a name="line.157"></a>

158 e.printStackTrace();<a name="line.158"></a>

159 }<a name="line.159"></a>

160 }<a name="line.160"></a>

161<a name="line.161"></a>

162 }<a name="line.162"></a>

163<a name="line.163"></a>

164 public void printDomainsForPDB(){<a name="line.164"></a>

165 String pdbId = "4HHB";<a name="line.165"></a>

166<a name="line.166"></a>

167 // download SCOP if required and load into memory<a name="line.167"></a>

168 ScopDatabase scop = ScopFactory.getSCOP();<a name="line.168"></a>

169<a name="line.169"></a>

170 List<ScopDomain> domains = scop.getDomainsForPDB(pdbId);<a name="line.170"></a>

171<a name="line.171"></a>

172 System.out.println(domains);<a name="line.172"></a>

173<a name="line.173"></a>

174 }<a name="line.174"></a>

175<a name="line.175"></a>

176<a name="line.176"></a>

177}<a name="line.177"></a>

</pre>

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