void testIssue346() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test Issue346" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/MolChemicalFeatures/test_data/featDef2.txt";
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
std::ifstream inStream(fName.c_str());
TEST_ASSERT(inStream.is_open());
std::istream &instrm = static_cast<std::istream &>(inStream);
factory = buildFeatureFactory(instrm);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
featDefIt = factory->beginFeatureDefs();
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "HBondDonor");
featDefIt++;
featDef = *featDefIt;
TEST_ASSERT(featDefIt != factory->endFeatureDefs());
TEST_ASSERT(featDef->getFamily() == "HBondAcceptor");
featDefIt++;
TEST_ASSERT(featDefIt == factory->endFeatureDefs());
delete (factory);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
python::dict getFeatureDefs(const MolChemicalFeatureFactory &factory){
python::dict res;
MolChemicalFeatureDef::CollectionType::const_iterator iter;
for(iter=factory.beginFeatureDefs();iter!=factory.endFeatureDefs();++iter){
std::string key= (*iter)->getFamily()+"."+(*iter)->getType();
res[key]=(*iter)->getSmarts();
}
return res;
}
void test6() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Feature Location testing." << std::endl;
ROMol *testMol;
Conformer *conf;
std::string inText;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature Carboxyl1 C(=O)[O;H1,-]\n"
" Family ZnBinder\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(inText);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
testMol = SmilesToMol("C(=O)O");
TEST_ASSERT(testMol);
conf = new Conformer(3);
testMol->addConformer(conf);
conf->setAtomPos(0, RDGeom::Point3D(0, 0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.2, 0, 0.0));
conf->setAtomPos(2, RDGeom::Point3D(0, 1.5, 0.0));
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 2);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
TEST_ASSERT(feq(featSPtr->getPos().x, 0.0));
TEST_ASSERT(feq(featSPtr->getPos().y, 1.5));
TEST_ASSERT(feq(featSPtr->getPos().z, 0.0));
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "ZnBinder");
TEST_ASSERT(featSPtr->getType() == "Carboxyl1");
TEST_ASSERT(feq(featSPtr->getPos().x, 0.4));
TEST_ASSERT(feq(featSPtr->getPos().y, 0.5));
TEST_ASSERT(feq(featSPtr->getPos().z, 0.0));
delete testMol;
delete factory;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
python::tuple getFeatureFamilies(const MolChemicalFeatureFactory &factory){
python::list res;
MolChemicalFeatureDef::CollectionType::const_iterator iter;
for(iter=factory.beginFeatureDefs();iter!=factory.endFeatureDefs();++iter){
std::string fam= (*iter)->getFamily();
if(res.count(fam)==0) res.append(fam);
}
return python::tuple(res);
}
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;
}
void testGithub252() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Github Issue #252: crash when calling "
"getPos() with no conformer."
<< std::endl;
BOOST_LOG(rdErrorLog) << " expect a precondition failure message below"
<< std::endl;
ROMol *testMol;
MolChemicalFeatureFactory *factory;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
std::string fdef =
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
testMol = SmilesToMol("CCC");
TEST_ASSERT(testMol);
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 1);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
bool ok = false;
try {
featSPtr->getPos();
} catch (const Invar::Invariant &) {
ok = true;
}
delete factory;
delete testMol;
TEST_ASSERT(ok);
BOOST_LOG(rdErrorLog) << " Done" << std::endl;
}
FeatSPtr getMolFeature(const MolChemicalFeatureFactory &factory,
const ROMol &mol, int idx, std::string includeOnly = "",
bool recompute = true) {
static FeatSPtrList feats;
if (recompute) {
feats = factory.getFeaturesForMol(mol, includeOnly.c_str());
}
if (idx < 0 || idx >= static_cast<int>(feats.size())) {
throw IndexErrorException(idx);
}
FeatSPtrList_I fi = feats.begin();
for (int i = 0; i < idx; ++i) {
++fi;
}
return (*fi);
}
void testIssue347() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test Issue347" << std::endl;
ROMol *testMol;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
std::string fdef;
fdef =
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
featDefIt = factory->beginFeatureDefs();
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
TEST_ASSERT(featDefIt == factory->endFeatureDefs());
testMol = SmilesToMol("CCC");
TEST_ASSERT(testMol);
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 1);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CTriplet");
delete factory;
// now reverse the order and we should get two matches:
fdef =
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n"
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
featDefIt = factory->beginFeatureDefs();
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
TEST_ASSERT(featDefIt == factory->endFeatureDefs());
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 3);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CPair");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CPair");
featSPtr = *(++++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CTriplet");
delete factory;
delete testMol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test5() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "FeatureFactory testing." << std::endl;
ROMol *testMol;
MatchVectType mv;
std::string inText;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature HAcceptor1 [N,O]\n"
" Family HBondAcceptor\n"
" Weights 1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(inText);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
testMol = SmilesToMol("COCN");
TEST_ASSERT(testMol);
featDef = *factory->beginFeatureDefs();
TEST_ASSERT(SubstructMatch(*testMol, *featDef->getPattern(), mv));
BOOST_LOG(rdErrorLog) << "1" << std::endl;
TEST_ASSERT(mv.size() == 1);
TEST_ASSERT(mv[0].first == 0);
TEST_ASSERT(mv[0].second == 3);
featDef = *(++factory->beginFeatureDefs());
TEST_ASSERT(SubstructMatch(*testMol, *featDef->getPattern(), mv));
BOOST_LOG(rdErrorLog) << "2" << std::endl;
TEST_ASSERT(mv.size() == 1);
TEST_ASSERT(mv[0].first == 0);
TEST_ASSERT(mv[0].second == 1 || mv[0].second == 3);
// Test using the factory to find features:
featSPtrs = factory->getFeaturesForMol(*testMol);
BOOST_LOG(rdErrorLog) << "3" << std::endl;
TEST_ASSERT(featSPtrs.size() == 3);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
// Test limiting stuff with includeOnly
featSPtrs = factory->getFeaturesForMol(*testMol, "HBondAcceptor");
BOOST_LOG(rdErrorLog) << "4" << std::endl;
TEST_ASSERT(featSPtrs.size() == 2);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
featSPtrs = factory->getFeaturesForMol(*testMol, "HBondDonor");
BOOST_LOG(rdErrorLog) << "5" << std::endl;
TEST_ASSERT(featSPtrs.size() == 1);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
featSPtrs = factory->getFeaturesForMol(*testMol, "NotPresent");
BOOST_LOG(rdErrorLog) << "6" << std::endl;
TEST_ASSERT(featSPtrs.size() == 0);
delete testMol;
delete factory;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
int getNumMolFeatures(const MolChemicalFeatureFactory &factory,
const ROMol &mol, std::string includeOnly = "") {
FeatSPtrList feats = factory.getFeaturesForMol(mol, includeOnly.c_str());
return feats.size();
}