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.StructureIO; 028import org.biojava.nbio.structure.align.util.AtomCache; 029import org.biojava.nbio.structure.asa.AsaCalculator; 030import org.biojava.nbio.structure.asa.GroupAsa; 031 032import java.io.IOException; 033 034public class DemoAsa { 035 036 private static final boolean hetAtoms = false; 037 038 public static void main(String[] args) throws IOException, StructureException { 039 040 String pdbCode = args[0]; 041 int numThreads = Integer.parseInt(args[1]); 042 043 demoAsa(pdbCode, numThreads); 044 } 045 046 private static void demoAsa(String pdbCode, int numThreads) throws IOException, StructureException { 047 048 AtomCache cache = new AtomCache(); 049 cache.setUseMmCif(true); 050 051 StructureIO.setAtomCache(cache); 052 053 Structure structure = StructureIO.getStructure(pdbCode); 054 055 long start = System.currentTimeMillis(); 056 057 AsaCalculator asaCalc = new AsaCalculator(structure, 058 AsaCalculator.DEFAULT_PROBE_SIZE, 059 1000, numThreads, hetAtoms); 060 061 GroupAsa[] groupAsas = asaCalc.getGroupAsas(); 062 063 long end = System.currentTimeMillis(); 064 065 066 double tot = 0; 067 068 069 070 for (GroupAsa groupAsa: groupAsas) { 071 System.out.printf("%1s\t%5s\t%3s\t%6.2f\n", 072 groupAsa.getGroup().getChainId(), 073 groupAsa.getGroup().getResidueNumber(), 074 groupAsa.getGroup().getPDBName(), 075 groupAsa.getAsaU()); 076 tot+=groupAsa.getAsaU(); 077 } 078 079 080 System.out.printf("Total area: %9.2f\n",tot); 081 System.out.printf("Time: %4.1fs\n",((end-start)/1000.0)); 082 083 084 System.out.println("Testing scaling: "); 085 double[] runTimes = new double[numThreads]; 086 for (int nThreads=1;nThreads<=numThreads;nThreads++) { 087 start = System.currentTimeMillis(); 088 089 asaCalc = new AsaCalculator(structure, 090 AsaCalculator.DEFAULT_PROBE_SIZE, 091 1000, numThreads, hetAtoms); 092 093 // only calculating all atom ASAs without keeping the returned value 094 asaCalc.calculateAsas(); 095 096 end = System.currentTimeMillis(); 097 runTimes[nThreads-1] = (end-start)/1000.0; 098 099 } 100 for (int nThreads=1;nThreads<=numThreads;nThreads++) { 101 System.out.printf(nThreads+" threads, time: %4.1fs -- x%2.1f\n",runTimes[nThreads-1],runTimes[0]/runTimes[nThreads-1]); 102 } 103 104 105 } 106 107 108}