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Open Source Chemistry Library
package com.actelion.research.chem.mcs;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.atomic.AtomicBoolean;
import java.util.concurrent.atomic.AtomicLong;
import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.IDCodeParser;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.util.ErrorHashMap;
import com.actelion.research.util.Pipeline;
import com.actelion.research.util.datamodel.ByteVec;
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
public class ExhaustiveMCSGeneratorParallel {
private static final int MIN_ATOMS_MCS = 4;
private static final int MAX_THREADS = 20;
private static final long SLEEP = 100;
private Pipeline pipeFragByteVec;
private ConcurrentHashMap hmMCS_MCS;
private ArrayList liMolByteVec;
private AtomicLong ccMCSCalculations;
private int maxThreads;
private int ringStatus;
public ExhaustiveMCSGeneratorParallel(int ringStatus) {
this.ringStatus = ringStatus;
maxThreads = MAX_THREADS;
pipeFragByteVec = new Pipeline();
hmMCS_MCS = new ConcurrentHashMap();
liMolByteVec = new ArrayList();
ccMCSCalculations = new AtomicLong();
}
public List process(List liMol, File workdir) throws Exception {
System.out.println("MCS process.");
// LogHandler log = LogHandler.getLog("maximumCommonSubstructure.log");
int nProcessors = Runtime.getRuntime().availableProcessors();
int threads = Math.min(nProcessors, maxThreads);
System.out.println("MCS calculations on " + threads + " processors.");
liMolByteVec.clear();
int cc=0;
for (StereoMolecule mol : liMol) {
try {
Canonizer can = new Canonizer(mol);
String idcode = can.getIDCode();
ByteVec bv = new ByteVec(idcode);
liMolByteVec.add(bv);
pipeFragByteVec.addData(bv);
cc++;
} catch (Exception e) {
System.err.println("Molecule list size " + liMol.size() + ".");
System.err.println("Index molecule " + cc + ".");
e.printStackTrace();
}
}
List liMCSRunnable = new ArrayList();
List liMCSThread = new ArrayList();
for (int i = 0; i < nProcessors; i++) {
MCSThread mcsThread = new MCSThread(i, ringStatus);
liMCSRunnable.add(mcsThread);
Thread th = new Thread(mcsThread);
liMCSThread.add(th);
th.start();
}
System.out.println("Calculate MCS from " + liMol.size() + " molecules.");
int ccCycles=0;
while(!hasMCSCalculationFinished(liMCSThread,liMCSRunnable)) {
try {Thread.sleep(SLEEP);} catch (InterruptedException e) {e.printStackTrace();};
ccCycles++;
if(ccCycles%10==0)
System.out.println("Unique mcs " + hmMCS_MCS.size() + ", queue " + pipeFragByteVec.sizePipe() + ".");
}
List liMolMCS = new ArrayList();
IDCodeParser parser = new IDCodeParser(false);
List liIdCodeMCS = Collections.list(hmMCS_MCS.keys());
for (ByteVec bvIdCodeMCS : liIdCodeMCS) {
liMolMCS.add(parser.getCompactMolecule(bvIdCodeMCS.toStringString()));
}
return liMolMCS;
}
private boolean hasMCSCalculationFinished(List liThread, List liMCSRunnable) {
if(!pipeFragByteVec.isEmpty()){
return false;
}
boolean calculating = false;
for (MCSThread mcsThread : liMCSRunnable) {
if(mcsThread.isCalculating()){
calculating=true;
break;
}
}
if(calculating){
return false;
}
long calculated1 = ccMCSCalculations.get();
try {Thread.sleep(10000);} catch (InterruptedException e) {e.printStackTrace();}
long calculated2 = ccMCSCalculations.get();
if(calculated1 != calculated2) {
return false;
}
pipeFragByteVec.setAllDataIn(true);
boolean finished = true;
for (Thread th : liThread) {
if(th.isAlive()){
finished = false;
break;
}
}
return finished;
}
static class MCSTask {
ByteVec bcIdCode1;
ByteVec bcIdCode2;
public MCSTask(ByteVec bcIdCode1, ByteVec bcIdCode2) {
this.bcIdCode1 = bcIdCode1;
this.bcIdCode2 = bcIdCode2;
}
public MCSTask(MCSTask mcsTask) {
this.bcIdCode1 = mcsTask.bcIdCode1;
this.bcIdCode2 = mcsTask.bcIdCode2;
}
}
static class MCSResult extends MCSTask {
StereoMolecule molMCS;
public MCSResult(MCSTask mcsTask, StereoMolecule molMCS) {
super(mcsTask);
this.molMCS = molMCS;
}
}
class MCSThread implements Runnable {
int indexThread;
private MCS mcs;
private IDCodeParser idCodeParser;
private AtomicBoolean calculating;
private ErrorHashMap ehm;
private int nFailedSimilarityCalculations;
private int added;
public MCSThread(int indexThread, int ringStatus) {
this.indexThread = indexThread;
ehm = new ErrorHashMap();
idCodeParser = new IDCodeParser(false);
mcs = new MCS(ringStatus);
calculating = new AtomicBoolean();
}
public void run() {
while(!pipeFragByteVec.wereAllDataFetched()){
ByteVec bvFrag = pipeFragByteVec.pollData();
if(bvFrag==null){
calculating.set(false);
try {Thread.sleep(SLEEP);} catch (InterruptedException e) {e.printStackTrace();}
continue;
}
calculating.set(true);
for (int i = 0; i < liMolByteVec.size(); i++) {
MCSTask mcsTask = new MCSTask(liMolByteVec.get(i), bvFrag);
List liResult = processMCS(mcsTask);
for (MCSResult mcsResult : liResult) {
Canonizer can = new Canonizer(mcsResult.molMCS);
ByteVec bvMCS = new ByteVec(can.getIDCode());
if(!hmMCS_MCS.containsKey(bvMCS)){
hmMCS_MCS.put(bvMCS, bvMCS);
pipeFragByteVec.addData(bvMCS);
}
}
}
}
}
private List processMCS(MCSTask mcsTask){
List liResult=null;
try {
StereoMolecule mol1 = idCodeParser.getCompactMolecule(mcsTask.bcIdCode1.toStringString());
StereoMolecule mol2 = idCodeParser.getCompactMolecule(mcsTask.bcIdCode2.toStringString());
if(mol1.getAtoms()>mol2.getAtoms()) {
mcs.set(mol1, mol2);
} else {
mcs.set(mol2, mol1);
}
List liMolMCS = mcs.getAllCommonSubstructures();
ccMCSCalculations.incrementAndGet();
if(liMolMCS==null){
liResult=new ArrayList();
} else if(!liMolMCS.isEmpty()){
liResult=new ArrayList();
for (StereoMolecule molMCS : liMolMCS) {
liResult.add(new MCSResult(mcsTask, molMCS));
}
}
} catch (Exception e) {
e.printStackTrace();
nFailedSimilarityCalculations++;
}
return liResult;
}
public boolean isCalculating(){
return calculating.get();
}
public ErrorHashMap getEhm() {
return ehm;
}
public long getAdded() {
return added;
}
public long getComparisons() {
return ccMCSCalculations.get();
}
public int getArrFailedSimilarityCalculations() {
return nFailedSimilarityCalculations;
}
}
}