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

History

182 lines (122 loc) · 10.6 KB

Raw

100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

<!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 Mar 11, 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.fatcat.FatCatFlexible;<a name="line.33"></a>

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

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

036import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;<a name="line.36"></a>

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

038import org.biojava.nbio.structure.align.model.AfpChainWriter;<a name="line.38"></a>

039import org.biojava.nbio.structure.align.util.AtomCache;<a name="line.39"></a>

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

041<a name="line.41"></a>

042public class CookBook<a name="line.42"></a>

043{<a name="line.43"></a>

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

045<a name="line.45"></a>

046 public static void main(String[] args){<a name="line.46"></a>

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

048 String name1="1HNG.B";<a name="line.48"></a>

049 String name2="1A64.A";<a name="line.49"></a>

050<a name="line.50"></a>

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

052 try {<a name="line.52"></a>

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

054 // for this example we are going to use the jFatCat-rigid algorithm<a name="line.54"></a>

055 StructureAlignment algorithm = StructureAlignmentFactory.getAlgorithm(FatCatFlexible.algorithmName);<a name="line.55"></a>

056<a name="line.56"></a>

057 // the cache takes care of loading the structures<a name="line.57"></a>

058 // Downloads files to a temp dir by default<a name="line.58"></a>

059 AtomCache cache = new AtomCache();<a name="line.59"></a>

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

061<a name="line.61"></a>

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

063 // no need to change anything below this line<a name="line.63"></a>

064 // ////////////////////////////<a name="line.64"></a>

065<a name="line.65"></a>

066 // load the structures<a name="line.66"></a>

067 Structure structure1 = cache.getStructure(name1);<a name="line.67"></a>

068 Structure structure2 = cache.getStructure(name2);<a name="line.68"></a>

069<a name="line.69"></a>

070 // we are only using the CA atoms in the structure for the alignment<a name="line.70"></a>

071 Atom[] ca1 = StructureTools.getAtomCAArray(structure1);<a name="line.71"></a>

072 Atom[] ca2 = StructureTools.getAtomCAArray(structure2);<a name="line.72"></a>

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

074 // do the actual alignment<a name="line.74"></a>

075 AFPChain afpChain = algorithm.align(ca1,ca2);<a name="line.75"></a>

076<a name="line.76"></a>

077 // just name the two molecules<a name="line.77"></a>

078 afpChain.setName1(name1);<a name="line.78"></a>

079 afpChain.setName2(name2);<a name="line.79"></a>

080<a name="line.80"></a>

081 // print and display results:<a name="line.81"></a>

082<a name="line.82"></a>

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

084 // flexible original results:<a name="line.84"></a>

085 System.out.println(afpChain.toFatcat(ca1,ca2));<a name="line.85"></a>

086<a name="line.86"></a>

087 // show the alignment in 3D in jmol<a name="line.87"></a>

088 StructureAlignmentJmol jmol= StructureAlignmentDisplay.display(afpChain, ca1, ca2);<a name="line.88"></a>

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

090 // set the display title for the frame<a name="line.90"></a>

091 jmol.setTitle(algorithm.getAlgorithmName() + " : " + name1 + " vs. " + name2);<a name="line.91"></a>

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

093 // here we open up the alignment - text panel that can interact with the 3D jmol display.<a name="line.93"></a>

094 DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);<a name="line.94"></a>

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

096 // we can print an XML version<a name="line.96"></a>

097 //System.out.println(AFPChainXMLConverter.toXML(afpChain, ca1, ca2));<a name="line.97"></a>

098<a name="line.98"></a>

099 // or print the same output as original FATCAT<a name="line.99"></a>

100 System.out.println(AfpChainWriter.toFatCat(afpChain, ca1, ca2));<a name="line.100"></a>

101<a name="line.101"></a>

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

103<a name="line.103"></a>

104<a name="line.104"></a>

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

106 } catch (Exception e){<a name="line.106"></a>

107 e.printStackTrace();<a name="line.107"></a>

108 }<a name="line.108"></a>

109 }<a name="line.109"></a>

110}<a name="line.110"></a>

</pre>

</div>

</body>

</html>

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

FilesExpand file tree

CookBook.html

Latest commit

History

CookBook.html

File metadata and controls