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3e00673a28
* fixes #1636 a bit of refactoring of the tests * Fixes #2077 Add better confId handling to the chemical feature machinery
123 lines
3.8 KiB
C++
123 lines
3.8 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "MolChemicalFeature.h"
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#include "MolChemicalFeatureDef.h"
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#include "MolChemicalFeatureFactory.h"
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#include "FeatureParser.h"
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <vector>
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#include <sstream>
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#include <set>
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#include <algorithm>
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namespace RDKit {
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FeatSPtrList MolChemicalFeatureFactory::getFeaturesForMol(
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const ROMol &mol, const char *includeOnly, int confId) const {
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PRECONDITION(includeOnly, "bad limits");
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std::string limits(includeOnly);
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#ifdef USE_VFLIB
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AR_MOLGRAPH *molG = getMolGraph(mol);
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#endif
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FeatSPtrList res;
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int idx = 1;
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typedef std::vector<std::pair<std::string, std::set<int>>> MatchSetCollection;
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MatchSetCollection matchSets;
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for (auto featDefIt = beginFeatureDefs(); featDefIt != endFeatureDefs();
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featDefIt++) {
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MolChemicalFeatureDef::CollectionType::value_type featDef = *featDefIt;
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if (limits == "" || limits == featDef->getFamily()) {
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std::vector<MatchVectType> matches;
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#ifdef USE_VFLIB
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unsigned int numMatches =
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SubstructMatch(molG, *featDef->getPattern(), matches);
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#else
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unsigned int numMatches =
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SubstructMatch(mol, *featDef->getPattern(), matches);
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#endif
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for (unsigned int i = 0; i < numMatches; i++) {
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const MatchVectType &match = matches[i];
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std::set<int> matchSet;
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for (const auto &mIt : match) {
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matchSet.insert(mIt.second);
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}
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// loop over the matches we've already found and see if this one
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// is unique:
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bool unique = true;
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for (MatchSetCollection::const_iterator vsiCI = matchSets.begin();
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vsiCI != matchSets.end(); ++vsiCI) {
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if (vsiCI->first == featDef->getFamily() &&
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std::includes(vsiCI->second.begin(), vsiCI->second.end(),
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matchSet.begin(), matchSet.end())) {
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unique = false;
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break;
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}
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}
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if (unique) {
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matchSets.push_back(std::make_pair(featDef->getFamily(), matchSet));
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// Set up the feature:
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auto *newFeat =
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new MolChemicalFeature(&mol, this, featDef.get(), idx++);
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newFeat->setActiveConformer(confId);
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MolChemicalFeature::AtomPtrContainer &atoms = newFeat->d_atoms;
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atoms.resize(match.size());
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// set up the atoms:
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for (const auto &matchIt : match) {
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int atomIdx = matchIt.second;
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int queryIdx = matchIt.first;
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atoms[queryIdx] = mol.getAtomWithIdx(atomIdx);
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}
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// finally, add this to our result:
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res.push_back(FeatSPtrList::value_type(newFeat));
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}
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}
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}
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}
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#ifdef USE_VFLIB
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#ifndef CACHE_ARMOLGRAPHS
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delete molG;
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#endif
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#endif
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return res;
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}
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MolChemicalFeatureFactory *buildFeatureFactory(const std::string &featureData) {
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std::stringstream ss(featureData);
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return buildFeatureFactory(ss);
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}
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MolChemicalFeatureFactory *buildFeatureFactory(std::istream &inStream) {
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MolChemicalFeatureFactory *res = nullptr;
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MolChemicalFeatureDef::CollectionType featDefs;
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if (parseFeatureData(inStream, featDefs) == 0) {
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// everything parsed ok
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res = new MolChemicalFeatureFactory();
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// std::copy(featDefs.begin(),featDefs.end(),res->beginFeatureDefs());
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for (MolChemicalFeatureDef::CollectionType::const_iterator ci =
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featDefs.begin();
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ci != featDefs.end(); ci++) {
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res->addFeatureDef(*ci);
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}
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}
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return res;
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}
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} // namespace RDKit
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