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https://github.com/rdkit/rdkit.git
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c5dc6cc258
* - enable SubstructLibrary to build without threading support - enforce consistency across single- and multi-threaded runs - improve performance on single-threaded runs avoiding overhead of spawning threads - consolidate internalCountMatches and internalGetMatches into one function to reduce code duplication - fix a bug in Python CountMatches whjich would run on 1000 threads * reverted Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp as it is now in its own PR (#3558) * - added missing cast - removed unnecessary std::make_move_iterator - added Brian's test Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
66 lines
2.0 KiB
C++
66 lines
2.0 KiB
C++
//
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// Copyright (C) 2020 Brian P. Kelley
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "SubstructLibrary.h"
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#include "PatternFactory.h"
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#include <RDGeneral/RDThreads.h>
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#ifdef RDK_THREADSAFE_SSS
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#include <thread>
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#include <future>
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#endif
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namespace RDKit {
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namespace {
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void fillPatterns(const SubstructLibrary &slib,
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const PatternHolder &fph,
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std::vector<ExplicitBitVect*> &fps,
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unsigned int start, unsigned int end, unsigned int numThreads) {
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for (unsigned int idx = start;
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idx < end;
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idx += numThreads) {
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fps[idx] = fph.makeFingerprint( *slib.getMol(idx).get() );
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}
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}
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}
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void addPatterns(SubstructLibrary &sslib, int numThreads) {
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PRECONDITION(sslib.getFpHolder().get() == nullptr, "Substruct library already has fingerprints");
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numThreads = (int)getNumThreadsToUse(numThreads);
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boost::shared_ptr<PatternHolder> ptr(new PatternHolder);
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std::vector<ExplicitBitVect *> & fps = ptr->getFingerprints();
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unsigned int startIdx = 0;
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unsigned int endIdx = sslib.getMolecules().size();
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fps.resize(endIdx);
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#ifdef RDK_THREADSAFE_SSS
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std::vector<std::future<void>> thread_group;
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for (int thread_group_idx = 0; thread_group_idx < numThreads;
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++thread_group_idx) {
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// need to use std::ref otherwise things are passed by value
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thread_group.emplace_back(std::async(
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std::launch::async, fillPatterns, std::ref(sslib), std::ref(*ptr),
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std::ref(fps), startIdx + thread_group_idx, endIdx, numThreads));
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}
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for (auto &fut : thread_group) {
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fut.get();
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}
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#else
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fillPatterns(sslib, *ptr, fps, 0, sslib.size(), 1);
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#endif
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if (ptr->size() != sslib.size()) {
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throw ValueErrorException("Number of fingerprints generated not equal to current number of molecules");
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}
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sslib.getFpHolder() = ptr;
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sslib.resetHolders();
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}
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}
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