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https://github.com/rdkit/rdkit.git
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c8aa10c80f
* Fixes #3797 * [WIP] Add tautomer queries to the substruct library * Add TautomerQuery to CMake * Add missing TautomerQuery functions, python wrapper and tests * Add python wrappers for Substruct Library Tautomer Queries * Explictly label non-const pattern function now that we have both * Use boost::shared_ptr not std::shared_ptr * Fix java builds * One more try to fix java builds * Fix Java Tests * Run clang format * Reenable tests * Fix annoyingly stupid bug and annoying commit of debug code * Fix documentation * reenable ifdef threadsafe check * Throw warning and perform tautomer search instead of bailing with incorrect fingerprints * Simplfy api with templates * Fix SubstructLibrary java issues * minor API cleanup * simplify the SWIG wrappers Co-authored-by: Brian Kelley <bkelley@relaytx.com> Co-authored-by: greg landrum <greg.landrum@gmail.com>
92 lines
2.7 KiB
C++
92 lines
2.7 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, const FPHolderBase &fph,
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std::vector<ExplicitBitVect *> &fps, unsigned int start,
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unsigned int end, unsigned int numThreads) {
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for (unsigned int idx = start; idx < end; idx += numThreads) {
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auto mol = slib.getMol(idx);
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if (mol.get()) {
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fps[idx] = fph.makeFingerprint(*mol.get());
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} else {
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// Make an empty FP
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fps[idx] = fph.makeFingerprint(ROMol());
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}
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}
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}
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} // namespace
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namespace {
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void internalAddPatterns(SubstructLibrary &sslib, int numThreads,
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boost::shared_ptr<FPHolderBase> *patterns) {
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PRECONDITION(sslib.getFpHolder().get() == nullptr,
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"Substruct library already has fingerprints");
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numThreads = (int)getNumThreadsToUse(numThreads);
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boost::shared_ptr<FPHolderBase> ptr;
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if (patterns) {
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ptr = *patterns;
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} else {
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ptr = boost::shared_ptr<FPHolderBase>(new PatternHolder);
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}
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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(
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"Number of fingerprints generated not equal to current number of "
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"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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} // namespace
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void addPatterns(SubstructLibrary &sslib, int numThreads) {
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internalAddPatterns(sslib, numThreads, nullptr);
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}
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void addPatterns(SubstructLibrary &sslib,
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boost::shared_ptr<FPHolderBase> patterns, int numThreads) {
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PRECONDITION(patterns.get() != nullptr, "Null PatternHolder");
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internalAddPatterns(sslib, numThreads, &patterns);
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}
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} // namespace RDKit
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