pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-04 21:54:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Fixes #2830 (#2831)

Browse Source 
* Fixes #2830

* Reenable tests

* Response to review

* Add more tests and C++ tests
This commit is contained in:
Brian Kelley
2019-12-15 00:42:31 -05:00
committed by Greg Landrum
parent d714f5128f
commit c3db12e097
5 changed files with 103 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

50
Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp
View File

@@ -38,6 +38,7 @@
#include <atomic>
#include <GraphMol/Substruct/SubstructMatch.h>
namespace RDKit {
bool SubstructLibraryCanSerialize() {
@@ -87,12 +88,30 @@ unsigned int SubstructLibrary::addMol(const ROMol &m) {
}
namespace {
// Return true if the pattern contains a ring query
bool query_needs_rings(const ROMol &in_query) {
for (auto &atom: in_query.atoms()) {
if(atom->hasQuery()) {
if (describeQuery(atom).find("Ring") != std::string::npos) {
return true;
}
}
}
for (auto &bond: in_query.bonds()) {
if(bond->hasQuery()) {
if (describeQuery(bond).find("Ring") != std::string::npos) {
return true;
}
}
}
return false;
}
// end is exclusive here
void SubSearcher(const ROMol &in_query, const Bits &bits,
const MolHolderBase &mols, std::vector<unsigned int> &idxs,
unsigned int start, unsigned int end, unsigned int numThreads,
std::atomic<int> &counter, const int maxResults) {
std::atomic<int> &counter, const int maxResults, const bool needs_rings) {
ROMol query(in_query);
MatchVectType matchVect;
for (unsigned int idx = start;
@@ -102,7 +121,15 @@ void SubSearcher(const ROMol &in_query, const Bits &bits,
// need shared_ptr as it (may) control the lifespan of the
// returned molecule!
const boost::shared_ptr<ROMol> &m = mols.getMol(idx);
const ROMol *mol = m.get();
ROMol *mol = m.get();
if (needs_rings && (!mol->getRingInfo() || !mol->getRingInfo()->isInitialized())) {
// I have no idea what happens when symmetrizeSSSR gets called
// on the same molecule twice in two threads.
// This most likely WILL NOT HAPPEN since only one molholder
// likely needs ring info.
MolOps::symmetrizeSSSR(*mol);
}
if (SubstructMatch(*mol, query, matchVect, bits.recursionPossible,
bits.useChirality, bits.useQueryQueryMatches)) {
// this is squishy when updating the counter. While incrementing is
@@ -120,7 +147,7 @@ void SubSearcher(const ROMol &in_query, const Bits &bits,
void SubSearchMatchCounter(const ROMol &in_query, const Bits &bits,
const MolHolderBase &mols, unsigned int start,
unsigned int end, int numThreads,
std::atomic<int> &counter) {
std::atomic<int> &counter, bool needs_rings) {
ROMol query(in_query);
MatchVectType matchVect;
for (unsigned int idx = start; idx < end; idx += numThreads) {
@@ -128,7 +155,14 @@ void SubSearchMatchCounter(const ROMol &in_query, const Bits &bits,
// need shared_ptr as it (may) controls the lifespan of the
// returned molecule!
const boost::shared_ptr<ROMol> &m = mols.getMol(idx);
const ROMol *mol = m.get();
ROMol *mol = m.get();
if (needs_rings && (!mol->getRingInfo() || !mol->getRingInfo()->isInitialized())) {
// I have no idea what happens when symmetrizeSSSR gets called
// on the same molecule twice in two threads.
// This most likely WILL NOT HAPPEN since only one molholder
// likely needs ring info.
MolOps::symmetrizeSSSR(*mol);
}
if (SubstructMatch(*mol, query, matchVect, bits.recursionPossible,
bits.useChirality, bits.useQueryQueryMatches)) {
counter++;
@@ -155,6 +189,7 @@ std::vector<unsigned int> internalGetMatches(
std::atomic<int> counter(0);
std::vector<std::vector<unsigned int>> internal_results(numThreads);
bool needs_rings = query_needs_rings(query);
Bits bits(fps, query, recursionPossible, useChirality, useQueryQueryMatches);
for (int thread_group_idx = 0; thread_group_idx < numThreads;
@@ -164,7 +199,7 @@ std::vector<unsigned int> internalGetMatches(
std::async(std::launch::async, SubSearcher, std::ref(query), bits,
std::ref(mols), std::ref(internal_results[thread_group_idx]),
startIdx + thread_group_idx, endIdx, numThreads,
std::ref(counter), maxResults));
std::ref(counter), maxResults, needs_rings));
}
for (auto &fut : thread_group) {
fut.get();
@@ -204,7 +239,8 @@ int internalMatchCounter(const ROMol &query, MolHolderBase &mols,
std::vector<std::future<void>> thread_group;
std::atomic<int> counter(0);
bool needs_rings = query_needs_rings(query);
Bits bits(fps, query, recursionPossible, useChirality, useQueryQueryMatches);
for (int thread_group_idx = 0; thread_group_idx < numThreads;
++thread_group_idx) {
@@ -212,7 +248,7 @@ int internalMatchCounter(const ROMol &query, MolHolderBase &mols,
thread_group.emplace_back(
std::async(std::launch::async, SubSearchMatchCounter, std::ref(query),
bits, std::ref(mols), startIdx + thread_group_idx, endIdx,
numThreads, std::ref(counter)));
numThreads, std::ref(counter), needs_rings));
}
for (auto &thread : thread_group) {
thread.get();