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// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "MolChemicalFeature.h"
#include "MolChemicalFeatureDef.h"
#include "MolChemicalFeatureFactory.h"
#include "FeatureParser.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <vector>
#include <sstream>
#include <set>
#include <algorithm>
namespace RDKit {
FeatSPtrList MolChemicalFeatureFactory::getFeaturesForMol(
const ROMol &mol, const char *includeOnly, int confId) const {
PRECONDITION(includeOnly, "bad limits");
std::string limits(includeOnly);
#ifdef USE_VFLIB
AR_MOLGRAPH *molG = getMolGraph(mol);
#endif
FeatSPtrList res;
int idx = 1;
typedef std::vector<std::pair<std::string, std::set<int>>> MatchSetCollection;
MatchSetCollection matchSets;
for (auto featDefIt = beginFeatureDefs(); featDefIt != endFeatureDefs();
featDefIt++) {
MolChemicalFeatureDef::CollectionType::value_type featDef = *featDefIt;
if (limits == "" || limits == featDef->getFamily()) {
std::vector<MatchVectType> matches;
#ifdef USE_VFLIB
unsigned int numMatches =
SubstructMatch(molG, *featDef->getPattern(), matches);
#else
unsigned int numMatches =
SubstructMatch(mol, *featDef->getPattern(), matches);
#endif
for (unsigned int i = 0; i < numMatches; i++) {
const MatchVectType &match = matches[i];
std::set<int> matchSet;
for (const auto &mIt : match) {
matchSet.insert(mIt.second);
}
// loop over the matches we've already found and see if this one
// is unique:
bool unique = true;
for (MatchSetCollection::const_iterator vsiCI = matchSets.begin();
vsiCI != matchSets.end(); ++vsiCI) {
if (vsiCI->first == featDef->getFamily() &&
std::includes(vsiCI->second.begin(), vsiCI->second.end(),
matchSet.begin(), matchSet.end())) {
unique = false;
break;
}
}
if (unique) {
matchSets.push_back(std::make_pair(featDef->getFamily(), matchSet));
// Set up the feature:
auto *newFeat =
new MolChemicalFeature(&mol, this, featDef.get(), idx++);
newFeat->setActiveConformer(confId);
MolChemicalFeature::AtomPtrContainer &atoms = newFeat->d_atoms;
atoms.resize(match.size());
// set up the atoms:
for (const auto &matchIt : match) {
int atomIdx = matchIt.second;
int queryIdx = matchIt.first;
atoms[queryIdx] = mol.getAtomWithIdx(atomIdx);
}
// finally, add this to our result:
res.push_back(FeatSPtrList::value_type(newFeat));
}
}
}
}
#ifdef USE_VFLIB
#ifndef CACHE_ARMOLGRAPHS
delete molG;
#endif
#endif
return res;
}
MolChemicalFeatureFactory *buildFeatureFactory(const std::string &featureData) {
std::stringstream ss(featureData);
return buildFeatureFactory(ss);
}
MolChemicalFeatureFactory *buildFeatureFactory(std::istream &inStream) {
MolChemicalFeatureFactory *res = nullptr;
MolChemicalFeatureDef::CollectionType featDefs;
if (parseFeatureData(inStream, featDefs) == 0) {
// everything parsed ok
res = new MolChemicalFeatureFactory();
// std::copy(featDefs.begin(),featDefs.end(),res->beginFeatureDefs());
for (MolChemicalFeatureDef::CollectionType::const_iterator ci =
featDefs.begin();
ci != featDefs.end(); ci++) {
res->addFeatureDef(*ci);
}
}
return res;
}
} // namespace RDKit
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