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First entry of the SubstructLibrary module (#1493)
* First entry of the SubstructLibrary module * Switch to shared_ptrs for memory safety * run clang-format and add a test * only build when threadsafe_sss is enabled, only test when test_multithreaded is enabled * Adds PRECONDITION * Adds exceptions for out of range errors * Changes getQueryBits to makeQueryBits for clarity * Adds API point to add Binary and Smiles directly * Replaces 0 with NULL for clarity. * Removes debugging code. * Makes endIdx non-inclusive * Adds substruct searching options * Adds preconditions * Small documentation cleanup and removes a line of code. * Add DataStructs library dependency * Actually uses passed in parameters * Adds TrustedSmiles/Binary inputs * Adds more api testing options/trusted smiles and binary inputs * Finalizes API adds docs and doctests * Minor copyright fixes and such
This commit is contained in:
Brian Kelley
committed by
Greg Landrum
Greg Landrum
parent
cd6d3a8f88
commit
d8722b1c64
285
Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp
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285
Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp
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// Copyright (c) 2017, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include "SubstructLibrary.h"
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#include <RDGeneral/RDThreads.h>
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#include <boost/atomic.hpp>
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#include <GraphMol/Substruct/SubstructMatch.h>
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namespace RDKit {
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struct Bits {
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const ExplicitBitVect *queryBits;
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const FPHolderBase *fps;
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bool recursionPossible;
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bool useChirality;
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bool useQueryQueryMatches;
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Bits(const FPHolderBase *fps, const ROMol &m,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches) :
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fps(fps),
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recursionPossible(recursionPossible),
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useChirality(useChirality),
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useQueryQueryMatches(useQueryQueryMatches)
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{
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if(fps) {
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queryBits = fps->makeFingerprint(m);
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} else
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queryBits = NULL;
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}
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bool check(unsigned int idx) const {
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if (fps) {
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return fps->passesFilter(idx, *queryBits);
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}
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return true;
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}
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};
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unsigned int SubstructLibrary::addMol(const ROMol &m) {
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unsigned int size = mols->addMol(m);
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if (fps) {
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unsigned int fpsize = fps->addMol(m);
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CHECK_INVARIANT(size==fpsize,
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"#mols different than #fingerprints in SubstructLibrary");
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}
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return size;
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}
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namespace {
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// end is exclusive here
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void SubSearcher(const ROMol &in_query,
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const Bits &bits,
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const MolHolderBase& mols,
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std::vector<unsigned int> &idxs,
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unsigned int start,
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unsigned int end,
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unsigned int numThreads,
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boost::atomic<int> &counter,
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const int maxResults) {
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ROMol query(in_query);
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MatchVectType matchVect;
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for(unsigned int idx=start; idx<end; idx+=numThreads) {
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if(!bits.check(idx)) continue;
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// need shared_ptr as it (may) controls the lifespan of the
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// returned molecule!
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const boost::shared_ptr<ROMol> &m = mols.getMol(idx);
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const ROMol *mol = m.get();
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if (SubstructMatch(*mol, query, matchVect,
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bits.recursionPossible, bits.useChirality, bits.useQueryQueryMatches)) {
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// this is squishy when updating the counter. While incrementing is atomic
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// several substructure runs can update the counter beyond the maxResults
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// This okay: if we get one or two extra, we can fix it on the way out
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if (maxResults != -1 && counter >= maxResults) break;
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idxs.push_back(idx);
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if (maxResults != -1) counter++;
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}
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}
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}
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// end is inclusive here
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void SubSearchMatchCounter(const ROMol &in_query, const Bits &bits,
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const MolHolderBase &mols, unsigned int start,
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unsigned int end, int numThreads,
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boost::atomic<int> &counter) {
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ROMol query(in_query);
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MatchVectType matchVect;
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for(unsigned int idx=start; idx<end; idx+=numThreads) {
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if(!bits.check(idx)) continue;
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// need shared_ptr as it (may) controls the lifespan of the
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// returned molecule!
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const boost::shared_ptr<ROMol> &m = mols.getMol(idx);
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const ROMol *mol = m.get();
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if (SubstructMatch(*mol, query, matchVect,
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bits.recursionPossible, bits.useChirality,
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bits.useQueryQueryMatches)) {
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counter++;
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}
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}
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}
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std::vector<unsigned int> internalGetMatches(const ROMol &query,
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MolHolderBase &mols,
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const FPHolderBase *fps,
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unsigned int startIdx, unsigned int endIdx,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches,
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int numThreads=-1,
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int maxResults=1000)
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{
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PRECONDITION(startIdx < mols.size(), "startIdx out of bounds");
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PRECONDITION(endIdx > startIdx, "endIdx > startIdx");
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if (numThreads == -1)
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numThreads = (int)getNumThreadsToUse(numThreads);
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else
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numThreads = std::min(numThreads, (int)getNumThreadsToUse(numThreads));
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endIdx = std::min(mols.size(), endIdx);
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if (endIdx < numThreads) numThreads = endIdx;
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boost::thread_group thread_group;
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boost::atomic<int> counter(0);
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std::vector<std::vector<unsigned int> > internal_results(numThreads);
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// needed because boost::thread can only handle 10 arguments
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Bits bits(fps, query, recursionPossible, useChirality, useQueryQueryMatches);
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for(int thread_group_idx=0; thread_group_idx < numThreads; ++thread_group_idx) {
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// need to use boost::ref otherwise things are passed by value
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thread_group.add_thread(new boost::thread(
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SubSearcher, boost::ref(query), bits, boost::ref(mols),
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boost::ref(internal_results[thread_group_idx]),
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startIdx + thread_group_idx, endIdx, numThreads, boost::ref(counter),
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maxResults));
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}
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thread_group.join_all();
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delete bits.queryBits;
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std::vector<unsigned int> results;
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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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results.insert(results.end(), internal_results[thread_group_idx].begin(),
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internal_results[thread_group_idx].end());
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}
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// this is so we don't really have to do locking on the atomic counter...
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if (maxResults != -1 && rdcast<int>(results.size()) > maxResults)
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results.resize(maxResults);
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return results;
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}
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int internalMatchCounter(const ROMol &query,
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MolHolderBase &mols,
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const FPHolderBase *fps,
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unsigned int startIdx, unsigned int endIdx,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches,
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int numThreads=-1)
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{
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PRECONDITION(startIdx < mols.size(), "startIdx out of bounds");
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PRECONDITION(endIdx > startIdx, "endIdx > startIdx");
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endIdx = std::min(mols.size(), endIdx);
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if(numThreads == -1)
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numThreads = (int)getNumThreadsToUse(numThreads);
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else
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numThreads = std::min(numThreads, (int)getNumThreadsToUse(numThreads));
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if (endIdx < numThreads) numThreads = endIdx;
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boost::thread_group thread_group;
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boost::atomic<int> counter(0);
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Bits bits(fps, query, recursionPossible, useChirality, useQueryQueryMatches);
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for(int thread_group_idx=0; thread_group_idx < numThreads; ++thread_group_idx) {
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// need to use boost::ref otherwise things are passed by value
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thread_group.add_thread(new boost::thread(
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SubSearchMatchCounter, boost::ref(query), bits, boost::ref(mols),
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startIdx + thread_group_idx, endIdx, numThreads, boost::ref(counter)));
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}
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thread_group.join_all();
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delete bits.queryBits;
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return (int)counter;
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}
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}
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std::vector<unsigned int> SubstructLibrary::getMatches(const ROMol &query,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches,
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int numThreads,
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int maxResults) {
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return getMatches(query, 0, mols->size(), recursionPossible, useChirality, useQueryQueryMatches,
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numThreads, maxResults);
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}
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std::vector<unsigned int> SubstructLibrary::getMatches(const ROMol &query,
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unsigned int startIdx, unsigned int endIdx,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches,
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int numThreads, int maxResults) {
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return internalGetMatches(query, *mols, fps, startIdx, endIdx,
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recursionPossible, useChirality, useQueryQueryMatches,
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numThreads, maxResults);
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}
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unsigned int SubstructLibrary::countMatches(const ROMol &query,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches,
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int numThreads)
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{
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return countMatches(query, 0, mols->size(),
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recursionPossible, useChirality, useQueryQueryMatches,
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numThreads);
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}
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unsigned int SubstructLibrary::countMatches(const ROMol &query,
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unsigned int startIdx,
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unsigned int endIdx,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches,
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int numThreads) {
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return internalMatchCounter(query, *mols, fps, startIdx, endIdx,
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recursionPossible, useChirality, useQueryQueryMatches,
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numThreads);
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}
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bool SubstructLibrary::hasMatch(const ROMol &query,
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bool recursionPossible,
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bool useChirality,
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bool useQueryQueryMatches,
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int numThreads) {
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const int maxResults = 1;
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return getMatches(query,
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recursionPossible, useChirality, useQueryQueryMatches,
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numThreads, maxResults).size() > 0;
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}
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bool SubstructLibrary::hasMatch(const ROMol &query, unsigned int startIdx,
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unsigned int endIdx, bool recursionPossible,
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bool useChirality, bool useQueryQueryMatches,
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int numThreads) {
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const int maxResults = 1;
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return getMatches(query, startIdx, endIdx,
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recursionPossible, useChirality, useQueryQueryMatches,
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numThreads, maxResults).size() > 0;
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}
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}
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