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run clang-tidy with readability-braces-around-statements (#2899)

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* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke

* fix problem on windows
This commit is contained in:
Greg Landrum
2020-01-25 14:19:32 +01:00
committed by GitHub
parent fb3cad523e
commit d41752d558
261 changed files with 7449 additions and 3545 deletions
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40
Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp
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@@ -65,8 +65,9 @@ struct Bits {
useQueryQueryMatches(useQueryQueryMatches) {
if (fps) {
queryBits = fps->makeFingerprint(m);
} else
} else {
queryBits = nullptr;
}
}
bool check(unsigned int idx) const {
@@ -117,7 +118,9 @@ void SubSearcher(const ROMol &in_query, const Bits &bits,
for (unsigned int idx = start;
idx < end && (maxResults == -1 || counter < maxResults);
idx += numThreads) {
if (!bits.check(idx)) continue;
if (!bits.check(idx)) {
continue;
}
// need shared_ptr as it (may) control the lifespan of the
// returned molecule!
const boost::shared_ptr<ROMol> &m = mols.getMol(idx);
@@ -136,9 +139,13 @@ void SubSearcher(const ROMol &in_query, const Bits &bits,
// atomic
// several substructure runs can update the counter beyond the maxResults
// This okay: if we get one or two extra, we can fix it on the way out
if (maxResults != -1 && counter >= maxResults) break;
if (maxResults != -1 && counter >= maxResults) {
break;
}
idxs.push_back(idx);
if (maxResults != -1) counter++;
if (maxResults != -1) {
counter++;
}
}
}
}
@@ -151,7 +158,9 @@ void SubSearchMatchCounter(const ROMol &in_query, const Bits &bits,
ROMol query(in_query);
MatchVectType matchVect;
for (unsigned int idx = start; idx < end; idx += numThreads) {
if (!bits.check(idx)) continue;
if (!bits.check(idx)) {
continue;
}
// need shared_ptr as it (may) controls the lifespan of the
// returned molecule!
const boost::shared_ptr<ROMol> &m = mols.getMol(idx);
@@ -177,13 +186,16 @@ std::vector<unsigned int> internalGetMatches(
int maxResults = 1000) {
PRECONDITION(startIdx < mols.size(), "startIdx out of bounds");
PRECONDITION(endIdx > startIdx, "endIdx > startIdx");
if (numThreads == -1)
if (numThreads == -1) {
numThreads = (int)getNumThreadsToUse(numThreads);
else
} else {
numThreads = std::min(numThreads, (int)getNumThreadsToUse(numThreads));
}
endIdx = std::min(mols.size(), endIdx);
if (endIdx < static_cast<unsigned int>(numThreads)) numThreads = endIdx;
if (endIdx < static_cast<unsigned int>(numThreads)) {
numThreads = endIdx;
}
std::vector<std::future<void>> thread_group;
std::atomic<int> counter(0);
@@ -214,8 +226,9 @@ std::vector<unsigned int> internalGetMatches(
}
// this is so we don't really have to do locking on the atomic counter...
if (maxResults != -1 && rdcast<int>(results.size()) > maxResults)
if (maxResults != -1 && rdcast<int>(results.size()) > maxResults) {
results.resize(maxResults);
}
return results;
}
@@ -230,12 +243,15 @@ int internalMatchCounter(const ROMol &query, MolHolderBase &mols,
endIdx = std::min(mols.size(), endIdx);
if (numThreads == -1)
if (numThreads == -1) {
numThreads = (int)getNumThreadsToUse(numThreads);
else
} else {
numThreads = std::min(numThreads, (int)getNumThreadsToUse(numThreads));
}
if (endIdx < static_cast<unsigned int>(numThreads)) numThreads = endIdx;
if (endIdx < static_cast<unsigned int>(numThreads)) {
numThreads = endIdx;
}
std::vector<std::future<void>> thread_group;
std::atomic<int> counter(0);