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Open Source Chemistry Library
/*
* 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.
*
* @author Thomas Sander
*/
package com.actelion.research.chem.reaction;
import com.actelion.research.calc.ProgressController;
import com.actelion.research.chem.*;
import com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512;
import com.actelion.research.chem.descriptor.DescriptorHandlerReactionFP;
import com.actelion.research.util.IntArrayComparator;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.TreeSet;
import java.util.concurrent.ConcurrentLinkedQueue;
import java.util.concurrent.atomic.AtomicInteger;
public class ReactionSearch {
private static final boolean MULTITHREADED_SEARCH = true;
private volatile ReactionSearchSpecification mSpecification;
private volatile ReactionSearchDataSource mDataSource;
private volatile StructureSearchController mSearchController;
private volatile ProgressController mProgressController;
private volatile Reaction[] mQueryReaction;
private volatile StereoMolecule[] mQueryReactant,mQueryProduct,mQueryRetron;
private volatile long[] mQueryHash;
private volatile DescriptorHandlerLongFFP512 mDescriptorHandlerFFP512;
private volatile DescriptorHandlerReactionFP mDescriptorHandlerRxnFP;
private volatile long[][] mQueryReactionDescriptor,mQueryReactantDescriptor,mQueryProductDescriptor,mQueryRetronDescriptor;
private volatile int mMaxSSSMatches,mMaxNonSSSMatches,mStatus;
private volatile long mStopTime,mMaxMillis;
private ConcurrentLinkedQueue mResultQueue;
private AtomicInteger mSMPIndex,mMatchCount;
/**
* This contructs a new structure search, which upon calling start()
* runs a multithreaded structure search on the structure rows provided by dataSource.
* If a searchController is given, this is asked for every row, whether the row
* meets all preconditions and qualifies for the search.
* @param specification
* @param dataSource
* @param searchController may be null, if all rows need to be searched
* @param progressController may be null
*/
public ReactionSearch(ReactionSearchSpecification specification,
ReactionSearchDataSource dataSource,
StructureSearchController searchController,
ProgressController progressController) {
mSpecification = specification;
mDataSource = dataSource;
mSearchController = searchController;
mProgressController = progressController;
mStatus = StructureSearch.SEARCH_PENDING;
if (mSpecification != null) {
// define needed descriptor handlers
if (mSpecification.isSimilaritySearch()) {
mDescriptorHandlerRxnFP = DescriptorHandlerReactionFP.getDefaultInstance();
}
else if (mSpecification.isSubreactionSearch()
|| mSpecification.isRetronSearch()) {
mDescriptorHandlerFFP512 = DescriptorHandlerLongFFP512.getDefaultInstance();
}
}
}
/**
* If the search shall be aborted once it exceeds a given number of matches,
* then define the maximum number of matches with this method before starting the search.
* In case a search would return more than the defined maximum of allowed matches,
* then the search would stop at the allowed maximum and return those matches.
* @param maxSSSMatches maximum number of allowed sub-reaction/retron search matches (0: no limit)
* @param maxNonSSSMatches maximum number of allowed matches for other search types (0: no limit)
*/
public void setMatchLimit(int maxSSSMatches, int maxNonSSSMatches) {
mMaxSSSMatches = maxSSSMatches;
mMaxNonSSSMatches = maxNonSSSMatches;
}
/**
* If the search shall be aborted once it exceeds a given elapsed time limit,
* then define the maximum allowed search time in milliseconds.
* If a search time limit is reached, then the search would return all matches found.
* @param maxMillis maximum allowed elapsed search milliseconds (0: no limit)
*/
public void setTimeLimit(long maxMillis) {
mMaxMillis = maxMillis;
}
public String getCompletionStatus() {
return StructureSearch.COMPLETION_TEXT[mStatus];
}
public int[] start() {
if (!mDataSource.isSupportedSearchType(mSpecification)) {
mStatus = StructureSearch.SEARCH_TYPE_NOT_SUPPORTED;
return null;
}
mMatchCount = new AtomicInteger(0);
if (!mSpecification.isNoReactionSearch()) {
final int queryReactionCount = mSpecification.getReactionCount();
if (queryReactionCount == 0) {
mStatus = StructureSearch.QUERY_MISSING;
return null;
}
if (mSpecification.isSubreactionSearch()
|| mSpecification.isSimilaritySearch()) {
mQueryReaction = new Reaction[queryReactionCount];
mQueryReactant = new StereoMolecule[queryReactionCount];
mQueryProduct = new StereoMolecule[queryReactionCount];
for (int i=0; i 0) {
String[] idcodes = mSpecification.getEncodedQuery(i).substring(0, index).split(ReactionEncoder.MOLECULE_DELIMITER_STRING);
for (String idcode:idcodes)
mQueryHash[i] += CanonizerUtil.StrongHasher.hash(idcode);
}
}
}
else if (mSpecification.isNoStereoSearch()) {
mQueryHash = new long[queryReactionCount];
for (int i=0; i 0) {
String[] idcodes = mSpecification.getEncodedQuery(i).substring(0, index).split(ReactionEncoder.MOLECULE_DELIMITER_STRING);
for (String idcode:idcodes)
mQueryHash[i] += CanonizerUtil.getNoStereoHash(
new IDCodeParser(false).getCompactMolecule(idcode), false);
}
}
}
}
mSMPIndex = new AtomicInteger(mDataSource.getRowCount());
mResultQueue = new ConcurrentLinkedQueue<>();
if (mProgressController != null && mSpecification.getReactionCount() > 1023)
mProgressController.startProgress("Searching reactions", 0, mSpecification.getReactionCount());
mStopTime = (mMaxMillis == 0) ? Long.MAX_VALUE : System.currentTimeMillis() + mMaxMillis;
mStatus = StructureSearch.SEARCH_RUNNING;
if (MULTITHREADED_SEARCH) {
int threadCount = Runtime.getRuntime().availableProcessors();
SearchThread[] t = new SearchThread[threadCount];
for (int i = 0; i 1) {
mSMPIndex = new AtomicInteger(mQueryReactionDescriptor.length);
int threadCount = Math.min(queryReactionCount, Runtime.getRuntime().availableProcessors());
Thread[] t = new Thread[threadCount];
for (int i=0; i 1) { // gather all products within product[0]
mol[0] = new StereoMolecule(mol[0]);
for (int i=1; i= 0) {
if ((mProgressController != null && mProgressController.threadMustDie())) {
mStatus = StructureSearch.SEARCH_STOPPED;
break;
}
if (System.currentTimeMillis() > mStopTime) {
mStatus = StructureSearch.TIME_LIMIT_EXCEEDED;
break;
}
if (mProgressController != null && row%1024==1023)
mProgressController.updateProgress(mSpecification.getReactionCount()-row);
if (mSearchController == null || mSearchController.rowQualifies(row)) {
boolean isMatch = false;
if (mSpecification.isSubreactionSearch()
|| mSpecification.isRetronSearch()) {
if (mMaxSSSMatches != 0 && mMatchCount.get() > mMaxSSSMatches) {
mStatus = StructureSearch.COUNT_LIMIT_EXCEEDED;
break;
}
if (mSpecification.isSubreactionSearch()) {
long[] reactantFFP = mDataSource.getMergedReactantDescriptor(row);
long[] productFFP = mDataSource.getMergedProductDescriptor(row);
mSRSearcher.setReaction(mDataSource.getReactionCode(row), mDataSource.getMapping(row), mDataSource.getCoordinates(row), reactantFFP, productFFP);
for (int i = 0; i inReactantCount) {
isMatch = true;
break;
}
}
}
}
}
}
}
else {
if (mMaxNonSSSMatches != 0 && mMatchCount.get() > mMaxNonSSSMatches) {
mStatus = StructureSearch.COUNT_LIMIT_EXCEEDED;
break;
}
if (mSpecification.isNoReactionSearch()) {
isMatch = true;
}
else if (mSpecification.isSimilaritySearch()) {
for (int i=0; i= mSpecification.getReactionCenterSimilarity()
&& mDescriptorHandlerRxnFP.getPeripherySimilarity(mQueryReactionDescriptor[i], mDataSource.getReactionDescriptor(row))
>= mSpecification.getPeripherySimilarity()) {
isMatch = true;
break;
}
}
}
else if (mSpecification.isExactSearch()) {
for (int i=0; i matchList) {
int equivalentCount = 0;
TreeSet uniqueSet = new TreeSet<>(new IntArrayComparator());
for (int[] match:matchList) {
int[] mappingNo = new int[match.length];
boolean foundZero = false;
for (int i=0; i