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<!DOCTYPE HTML>

<head>

<title>Source code</title>

</head>

<body>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

020<a id="line.20"> */</a>

021<a id="line.21">package demo;</a>

022<a id="line.22"></a>

023<a id="line.23"></a>

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

025<a id="line.25">import org.biojava.nbio.structure.Structure;</a>

026<a id="line.26">import org.biojava.nbio.structure.StructureException;</a>

027<a id="line.27">import org.biojava.nbio.structure.io.StructureFiletype;</a>

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

029<a id="line.29">import org.biojava.nbio.structure.align.util.AtomCache;</a>

030<a id="line.30">import org.biojava.nbio.structure.asa.AsaCalculator;</a>

031<a id="line.31">import org.biojava.nbio.structure.asa.GroupAsa;</a>

032<a id="line.32"></a>

033<a id="line.33">import java.io.IOException;</a>

034<a id="line.34"></a>

035<a id="line.35">public class DemoAsa {</a>

036<a id="line.36"></a>

037<a id="line.37"> private static final boolean hetAtoms = false;</a>

038<a id="line.38"></a>

039<a id="line.39"> public static void main(String[] args) throws IOException, StructureException {</a>

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

041<a id="line.41"> String pdbCode = args[0];</a>

042<a id="line.42"> int numThreads = Integer.parseInt(args[1]);</a>

043<a id="line.43"></a>

044<a id="line.44"> demoAsa(pdbCode, numThreads);</a>

045<a id="line.45"> }</a>

046<a id="line.46"></a>

047<a id="line.47"> private static void demoAsa(String pdbCode, int numThreads) throws IOException, StructureException {</a>

048<a id="line.48"></a>

049<a id="line.49"> AtomCache cache = new AtomCache();</a>

050<a id="line.50"> cache.setFiletype(StructureFiletype.CIF);</a>

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

052<a id="line.52"> StructureIO.setAtomCache(cache);</a>

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

054<a id="line.54"> Structure structure = StructureIO.getStructure(pdbCode);</a>

055<a id="line.55"></a>

056<a id="line.56"> long start = System.currentTimeMillis();</a>

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

058<a id="line.58"> AsaCalculator asaCalc = new AsaCalculator(structure,</a>

059<a id="line.59"> AsaCalculator.DEFAULT_PROBE_SIZE,</a>

060<a id="line.60"> 1000, numThreads, hetAtoms);</a>

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

062<a id="line.62"> GroupAsa[] groupAsas = asaCalc.getGroupAsas();</a>

063<a id="line.63"></a>

064<a id="line.64"> long end = System.currentTimeMillis();</a>

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

066<a id="line.66"></a>

067<a id="line.67"> double tot = 0;</a>

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

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

070<a id="line.70"></a>

071<a id="line.71"> for (GroupAsa groupAsa: groupAsas) {</a>

072<a id="line.72"> System.out.printf("%1s\t%5s\t%3s\t%6.2f\n",</a>

073<a id="line.73"> groupAsa.getGroup().getChainId(),</a>

074<a id="line.74"> groupAsa.getGroup().getResidueNumber(),</a>

075<a id="line.75"> groupAsa.getGroup().getPDBName(),</a>

076<a id="line.76"> groupAsa.getAsaU());</a>

077<a id="line.77"> tot+=groupAsa.getAsaU();</a>

078<a id="line.78"> }</a>

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

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

081<a id="line.81"> System.out.printf("Total area: %9.2f\n",tot);</a>

082<a id="line.82"> System.out.printf("Time: %4.1fs\n",((end-start)/1000.0));</a>

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

084<a id="line.84"></a>

085<a id="line.85"> System.out.println("Testing scaling: ");</a>

086<a id="line.86"> double[] runTimes = new double[numThreads];</a>

087<a id="line.87"> for (int nThreads=1;nThreads<=numThreads;nThreads++) {</a>

088<a id="line.88"> start = System.currentTimeMillis();</a>

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

090<a id="line.90"> asaCalc = new AsaCalculator(structure,</a>

091<a id="line.91"> AsaCalculator.DEFAULT_PROBE_SIZE,</a>

092<a id="line.92"> 1000, numThreads, hetAtoms);</a>

093<a id="line.93"></a>

094<a id="line.94"> // only calculating all atom ASAs without keeping the returned value</a>

095<a id="line.95"> asaCalc.calculateAsas();</a>

096<a id="line.96"></a>

097<a id="line.97"> end = System.currentTimeMillis();</a>

098<a id="line.98"> runTimes[nThreads-1] = (end-start)/1000.0;</a>

099<a id="line.99"></a>

100<a id="line.100"> }</a>

101<a id="line.101"> for (int nThreads=1;nThreads<=numThreads;nThreads++) {</a>

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

103<a id="line.103"> }</a>

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

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

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

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

108<a id="line.108"></a>

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

</pre>

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