biojava.github.io/docs/api7.1.4/src-html/demo/DemoAsa.html at master · biojava/biojava.github.io

History

187 lines (127 loc) · 11.1 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

183

184

185

186

187

<!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 */

021package demo;

022

023

024

025import org.biojava.nbio.structure.Structure;

026import org.biojava.nbio.structure.StructureException;

027import org.biojava.nbio.structure.io.StructureFiletype;

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

029import org.biojava.nbio.structure.align.util.AtomCache;

030import org.biojava.nbio.structure.asa.AsaCalculator;

031import org.biojava.nbio.structure.asa.GroupAsa;

032

033import java.io.IOException;

034

035public class DemoAsa {

036

037 private static final boolean hetAtoms = false;

038

039 public static void main(String[] args) throws IOException, StructureException {

040

041 String pdbCode = args[0];

042 int numThreads = Integer.parseInt(args[1]);

043

044 demoAsa(pdbCode, numThreads);

045 }

046

047 private static void demoAsa(String pdbCode, int numThreads) throws IOException, StructureException {

048

049 AtomCache cache = new AtomCache();

050 cache.setFiletype(StructureFiletype.CIF);

051

052 StructureIO.setAtomCache(cache);

053

054 Structure structure = StructureIO.getStructure(pdbCode);

055

056 long start = System.currentTimeMillis();

057

058 AsaCalculator asaCalc = new AsaCalculator(structure,

059 AsaCalculator.DEFAULT_PROBE_SIZE,

060 1000, numThreads, hetAtoms);

061

062 GroupAsa[] groupAsas = asaCalc.getGroupAsas();

063

064 long end = System.currentTimeMillis();

065

066

067 double tot = 0;

068

069

070

071 for (GroupAsa groupAsa: groupAsas) {

072 System.out.printf("%1s\t%5s\t%3s\t%6.2f\n",

073 groupAsa.getGroup().getChainId(),

074 groupAsa.getGroup().getResidueNumber(),

075 groupAsa.getGroup().getPDBName(),

076 groupAsa.getAsaU());

077 tot+=groupAsa.getAsaU();

078 }

079

080

081 System.out.printf("Total area: %9.2f\n",tot);

082 System.out.printf("Time: %4.1fs\n",((end-start)/1000.0));

083

084

085 System.out.println("Testing scaling: ");

086 double[] runTimes = new double[numThreads];

087 for (int nThreads=1;nThreads<=numThreads;nThreads++) {

088 start = System.currentTimeMillis();

089

090 asaCalc = new AsaCalculator(structure,

091 AsaCalculator.DEFAULT_PROBE_SIZE,

092 1000, numThreads, hetAtoms);

093

094 // only calculating all atom ASAs without keeping the returned value

095 asaCalc.calculateAsas();

096

097 end = System.currentTimeMillis();

098 runTimes[nThreads-1] = (end-start)/1000.0;

099

100 }

101 for (int nThreads=1;nThreads<=numThreads;nThreads++) {

102 System.out.printf(nThreads+" threads, time: %4.1fs -- x%2.1f\n",runTimes[nThreads-1],runTimes[0]/runTimes[nThreads-1]);

103 }

104

105

106 }

107

108

109}

</pre>

</div>

</main>

</body>

</html>

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

FilesExpand file tree

DemoAsa.html

Latest commit

History

DemoAsa.html

File metadata and controls