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The protein structure modules of BioJava.
package org.biojava.nbio.structure.align;
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Feb 11, 2013
* Author: Andreas Prlic
*
*/
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.ce.*;
import org.biojava.nbio.structure.align.client.FarmJobParameters;
import org.biojava.nbio.structure.align.client.JFatCatClient;
import org.biojava.nbio.structure.align.client.PdbPair;
import org.biojava.nbio.structure.align.client.StructureName;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.util.SynchronizedOutFile;
import org.biojava.nbio.structure.domain.DomainProvider;
import org.biojava.nbio.structure.domain.DomainProviderFactory;
import org.biojava.nbio.structure.domain.RemoteDomainProvider;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
import org.biojava.nbio.structure.io.PDBFileReader;
import org.biojava.nbio.core.util.ConcurrencyTools;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
import java.util.SortedSet;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.atomic.AtomicBoolean;
/** Performs a multi threaded database search for an input protein structure
*
* @author Andreas Prlic
*
*/
public class MultiThreadedDBSearch {
private final static Logger logger = LoggerFactory.getLogger(MultiThreadedDBSearch.class);
AtomicBoolean interrupted ;
StructureAlignment algorithm;
String outFile;
String name1;
int nrCPUs;
AtomCache cache;
File resultList;
SortedSet representatives;
boolean domainSplit;
Structure structure1;
String customFile1;
String customChain1;
public MultiThreadedDBSearch(String name, Structure structure,
String outFile,
StructureAlignment algorithm,
int nrCPUs, boolean domainSplit){
interrupted = new AtomicBoolean(false);
this.name1= name;
this.structure1 = structure;
this.outFile = outFile;
this.algorithm = algorithm;
this.nrCPUs = nrCPUs;
this.domainSplit = domainSplit;
cache = new AtomCache();
String serverLocation = FarmJobParameters.DEFAULT_SERVER_URL;
if ( representatives == null){
SortedSet repre = JFatCatClient.getRepresentatives(serverLocation,40);
logger.info("got {} representatives for comparison", repre.size());
representatives = repre;
}
}
public String getCustomFile1() {
return customFile1;
}
/** set the file path for a custom, user provided file, not a standard PDB file.
*
* @param customFile1
*/
public void setCustomFile1(String customFile1) {
this.customFile1 = customFile1;
}
public String getCustomChain1() {
return customChain1;
}
/** sets a chain in a custom, user provided file
*
* @param customChain1
*/
public void setCustomChain1(String customChain1) {
this.customChain1 = customChain1;
}
public AtomCache getAtomCache() {
return cache;
}
public void setAtomCache(AtomCache cache) {
this.cache = cache;
}
public StructureAlignment getAlgorithm() {
return algorithm;
}
public void setAlgorithm(StructureAlignment algo) {
this.algorithm = algo;
}
public String getOutFile() {
return outFile;
}
public void setOutFile(String outFile) {
this.outFile = outFile;
}
public static String getLegend(String algorithmName){
if ( algorithmName.equalsIgnoreCase(CeMain.algorithmName) ||
algorithmName.equalsIgnoreCase(CeSideChainMain.algorithmName) ||
algorithmName.equalsIgnoreCase(CeCPMain.algorithmName)) {
return "# name1\tname2\tscore\tz-score\trmsd\tlen1\tlen2\tcov1\tcov2\t%ID\tDescription\t " ;
}
// looks like a FATCAT alignment
return "# name1\tname2\tscore\tprobability\trmsd\tlen1\tlen2\tcov1\tcov2\t%ID\tDescription\t " ;
}
public File getResultFile() {
return resultList;
}
public void setResultFile(File resultList) {
this.resultList = resultList;
}
public void run(){
File outFileF = null;
SynchronizedOutFile out ;
try {
checkLocalFiles();
if ( interrupted.get())
return;
String header = "# algorithm:" + algorithm.getAlgorithmName();
String legend = getLegend(algorithm.getAlgorithmName());
outFileF = new File(outFile);
if ( ! outFileF.isDirectory()){
logger.error("{} is not a directory, can't create result files in there...", outFileF.getAbsolutePath());
interrupt();
cleanup();
}
if ( name1 == null)
name1 = "CUSTOM";
resultList = new File(outFileF,"results_" + name1 + ".out");
logger.info("writing results to {}", resultList.getAbsolutePath());
out = new SynchronizedOutFile(resultList);
out.write(header);
out.write(AFPChain.newline);
out.write(legend);
out.write(AFPChain.newline);
if ( name1.equals("CUSTOM")) {
String config1 = "#param:file1=" + customFile1;
out.write(config1);
out.write(AFPChain.newline);
if ( customChain1 != null) {
String config2 = "#param:chain1=" + customChain1;
out.write(config2);
out.write(AFPChain.newline);
}
}
if ( algorithm.getAlgorithmName().startsWith("jCE")){
ConfigStrucAligParams params = algorithm.getParameters();
if ( params instanceof CeParameters){
CeParameters ceParams = (CeParameters) params;
if ( ceParams.getScoringStrategy() != CeParameters.ScoringStrategy.DEFAULT_SCORING_STRATEGY) {
String scoring = "#param:scoring=" + ceParams.getScoringStrategy();
out.write(scoring);
out.write(AFPChain.newline);
}
}
}
out.flush();
} catch (IOException e){
logger.error("Error while loading representative structure {}", name1, e);
interrupt();
cleanup();
return;
} catch (StructureException e) {
logger.error("Error while loading representative structure {}", name1, e);
interrupt();
cleanup();
return;
}
int nrJobs = 0;
DomainProvider domainProvider;
try {
domainProvider = DomainProviderFactory.getDomainProvider();
ConcurrencyTools.setThreadPoolSize(nrCPUs);
Atom[] ca1 = StructureTools.getRepresentativeAtomArray(structure1);
for (String repre : representatives){
if( domainSplit ) {
SortedSet domainNames = domainProvider.getDomainNames(repre);
//logger.debug(repre +" got domains: " +domainNames);
if( domainNames == null || domainNames.size()==0){
// no domains found, use whole chain.
submit(name1, repre, ca1, algorithm, outFileF, out, cache);
nrJobs++;
continue;
}
//logger.debug("got " + domainNames.size() + " for " + repre);
for( String domain : domainNames){
submit(name1, domain, ca1, algorithm, outFileF, out, cache);
nrJobs++;
}
} else {
submit(name1, repre, ca1, algorithm, outFileF, out, cache);
nrJobs++;
}
}
} catch(IOException e) {
logger.error("Error while fetching representative domains", e);
interrupt();
cleanup();
return;
} catch (StructureException e) {
logger.error("Error while fetching representative domains", e);
interrupt();
cleanup();
return;
}
ThreadPoolExecutor pool = ConcurrencyTools.getThreadPool();
logger.info("{}", pool.getPoolSize());
long startTime = System.currentTimeMillis();
try {
while ( pool.getCompletedTaskCount() < nrJobs-1 ) {
//long now = System.currentTimeMillis();
//logger.debug( pool.getCompletedTaskCount() + " " + (now-startTime)/1000 + " " + pool.getPoolSize() + " " + pool.getActiveCount() + " " + pool.getTaskCount() );
// if ((now-startTime)/1000 > 60) {
//
// interrupt();
// logger.debug("completed: " + pool.getCompletedTaskCount());
// }
if ( interrupted.get())
break;
Thread.sleep(2000);
}
out.close();
}
catch (Exception e){
logger.error("Exception: ", e);
interrupt();
cleanup();
}
if (domainProvider instanceof RemoteDomainProvider){
RemoteDomainProvider remote = (RemoteDomainProvider) domainProvider;
remote.flushCache();
}
long now = System.currentTimeMillis();
logger.info("Calculation took : {} sec.", (now-startTime)/1000);
logger.info("{} {} {} {}", pool.getCompletedTaskCount(), pool.getPoolSize(), pool.getActiveCount(), pool.getTaskCount());
}
private void checkLocalFiles() throws IOException, StructureException {
logger.info("Checking local PDB installation in directory: {}", cache.getPath());
File f = new File(cache.getPath());
if ( ! f.isDirectory()) {
logger.error("The path {} should point to a directory!", f.getAbsolutePath());
}
if ( ! f.canWrite()) {
logger.error("You do not have permission to write to {}. There could be a problem if the PDB installation is not up-to-date with fetching missing PDB files.", f.getAbsolutePath());
}
DomainProvider domainProvider = DomainProviderFactory.getDomainProvider();
for (String repre : representatives){
if ( interrupted.get())
return;
if( domainSplit ) {
SortedSet domainNames = domainProvider.getDomainNames(repre);
//logger.debug(repre +" got domains: " +domainNames);
if( domainNames == null || domainNames.size()==0){
// no domains found, use whole chain.
//submit(name1, repre, ca1, algorithm, outFileF, out, cache);
checkFile(repre);
continue;
}
//logger.debug("got " + domainNames.size() + " for " + repre);
for( String domain : domainNames){
//submit(name1, domain, ca1, algorithm, outFileF, out, cache);
checkFile(domain);
}
} else {
//submit(name1, repre, ca1, algorithm, outFileF, out, cache);
checkFile(repre);
}
}
if ( domainProvider instanceof RemoteDomainProvider ) {
RemoteDomainProvider remoteP = (RemoteDomainProvider) domainProvider;
remoteP.flushCache();
}
logger.info("done checking local files...");
}
private void checkFile(String repre) throws IOException, StructureException {
StructureName name = new StructureName(repre);
PDBFileReader reader = new PDBFileReader();
reader.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);
reader.setPath(cache.getPath());
reader.setFileParsingParameters(cache.getFileParsingParams());
reader.prefetchStructure(name.getPdbId());
}
private void submit(String name12, String repre, Atom[] ca1, StructureAlignment algorithm , File outFileF , SynchronizedOutFile out , AtomCache cache ) {
CallableStructureAlignment ali = new CallableStructureAlignment();
PdbPair pair = new PdbPair(name1, repre);
try {
ali.setCa1(ca1);
} catch (Exception e){
logger.error("Exception: ", e);
ConcurrencyTools.shutdown();
return;
}
ali.setAlgorithmName(algorithm.getAlgorithmName());
ali.setParameters(algorithm.getParameters());
ali.setPair(pair);
ali.setOutFile(out);
ali.setOutputDir(outFileF);
ali.setCache(cache);
ConcurrencyTools.submit(ali);
}
/** stops what is currently happening and does not continue
*
*
*/
public void interrupt() {
interrupted.set(true);
ExecutorService pool = ConcurrencyTools.getThreadPool();
pool.shutdownNow();
try {
DomainProvider domainProvider = DomainProviderFactory.getDomainProvider();
if (domainProvider instanceof RemoteDomainProvider){
RemoteDomainProvider remote = (RemoteDomainProvider) domainProvider;
remote.flushCache();
}
} catch (IOException e) {
// If errors occur, the cache should be empty anyways
}
}
public void cleanup()
{
structure1 = null;
}
}
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