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Cleanup some problems found during an ASAN build (#4054)

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* MolFragmenter: fix a leak when exceptions are thrown

* DistGeomHelpers: fix leaks when exceptions are thrown

* SubstructLibrary: fix usage of invalid memory

* clear up leaks found during ASAN testing
This commit is contained in:
Greg Landrum
2021-04-21 16:22:04 +02:00
committed by GitHub
parent df54f9420f
commit 3a82159b57
10 changed files with 110 additions and 96 deletions
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35
Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp
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@@ -67,8 +67,8 @@ struct Bits {
}
}
Bits(const FPHolderBase *fingerprints, const TautomerQuery &m, bool recursionPossible,
bool useChirality, bool useQueryQueryMatches)
Bits(const FPHolderBase *fingerprints, const TautomerQuery &m,
bool recursionPossible, bool useChirality, bool useQueryQueryMatches)
: fps(nullptr),
recursionPossible(recursionPossible),
useChirality(useChirality),
@@ -76,15 +76,16 @@ struct Bits {
if (fingerprints) {
const TautomerPatternHolder *tp =
dynamic_cast<const TautomerPatternHolder *>(fingerprints);
if(!tp) {
BOOST_LOG(rdWarningLog) << "Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring..." << std::endl;
queryBits = nullptr;
fps = nullptr;
}
else {
fps = fingerprints;
queryBits = m.patternFingerprintTemplate(tp->getNumBits());
}
if (!tp) {
BOOST_LOG(rdWarningLog) << "Pattern fingerprints for tautomersearch "
"aren't tautomer fingerprints, ignoring..."
<< std::endl;
queryBits = nullptr;
fps = nullptr;
} else {
fps = fingerprints;
queryBits = m.patternFingerprintTemplate(tp->getNumBits());
}
} else {
queryBits = nullptr;
}
@@ -116,10 +117,10 @@ bool query_needs_rings(const ROMol &in_query) {
if (describeQuery(atom).find("Ring") != std::string::npos) {
return true;
} else if (atom->getQuery()->getDescription() == "RecursiveStructure") {
auto *rsq = (RecursiveStructureQuery *)atom->getQuery();
if (query_needs_rings(*rsq->getQueryMol())) {
return true;
}
auto *rsq = (RecursiveStructureQuery *)atom->getQuery();
if (query_needs_rings(*rsq->getQueryMol())) {
return true;
}
}
}
}
@@ -233,6 +234,7 @@ int internalGetMatches(const Query &query, MolHolderBase &mols,
maxResultsVect[thread_group_idx],
idxs ? &internal_results[thread_group_idx] : nullptr));
}
unsigned int maxEndIdx;
if (maxResults > 0) {
// If we are running with maxResults in a multi-threaded settings,
// some threads may have screened more molecules than others.
@@ -251,8 +253,7 @@ int internalGetMatches(const Query &query, MolHolderBase &mols,
// Find out out the max number of molecules that was screened by the most
// productive thread and do the same in all other threads, unless the
// max number of molecules was reached
unsigned int maxEndIdx =
*std::max_element(endIdxVect.begin(), endIdxVect.end());
maxEndIdx = *std::max_element(endIdxVect.begin(), endIdxVect.end());
for (thread_group_idx = 0; thread_group_idx < numThreads;
++thread_group_idx) {
if (endIdxVect[thread_group_idx] >= maxEndIdx) {