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;
}
void test1Canonicalization() {
ROMol *mol = SmilesToMol("C", 0, 1);
Conformer *conf = new Conformer(1);
conf->setAtomPos(0, RDGeom::Point3D(4.0, 5.0, 6.0));
int cid = mol->addConformer(conf, true);
RDGeom::Point3D pt = computeCentroid(*conf);
CHECK_INVARIANT(comparePts(pt, RDGeom::Point3D(4.0, 5.0, 6.0)), "");
RDGeom::Transform3D *trans = computeCanonicalTransform(*conf);
transformConformer(*conf, *trans);
CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(0.0, 0.0, 0.0)), "");
conf->setAtomPos(0, RDGeom::Point3D(4.0, 5.0, 6.0));
canonicalizeConformer(*conf);
CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(0.0, 0.0, 0.0)), "");
delete mol;
//delete conf;
delete trans;
// lets try two points now
mol = SmilesToMol("CC", 0, 1);
conf = new Conformer(2);
conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.5, 0.0, 0.0));
cid = mol->addConformer(conf, true);
trans = computeCanonicalTransform(*conf);
canonicalizeConformer(*conf);
CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(0.0, 1.5, 0.0));
trans = computeCanonicalTransform(*conf);
canonicalizeConformer(*conf);
CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
delete mol;
delete trans;
mol = SmilesToMol("CC", 0, 1);
conf = new Conformer(2);
conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.5, 0.0, 0.0));
cid = mol->addConformer(conf, true);
trans = computeCanonicalTransform(*conf);
transformConformer(*conf, *trans);
canonicalizeConformer(*conf);
CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
delete mol;
delete trans;
mol = SmilesToMol("C1CC1", 0, 1);
conf = new Conformer(3);
conf->setAtomPos(0, RDGeom::Point3D(0.58, -0.66, -0.08));
conf->setAtomPos(1, RDGeom::Point3D(-0.88, -0.18, -0.04));
conf->setAtomPos(2, RDGeom::Point3D(.26, 0.82, 0.14));
cid = mol->addConformer(conf, true);
//trans = computeCanonicalTransform(*conf);
//transformConformer(*conf, *trans);
canonicalizeConformer(*conf);
CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.6418, 0.6158, 0.0)), "");
CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(-0.2029, -0.8602, 0.0)), "");
CHECK_INVARIANT(comparePts(conf->getAtomPos(2), RDGeom::Point3D(0.8447, 0.2445, 0.0)), "");
MolToMolFile(*mol, "junk.mol", 0);
//CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
//CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
delete mol;
std::string rdbase = getenv("RDBASE");
std::string fname1 = rdbase + "/Code/GraphMol/MolTransforms/test_data/1oir.mol";
mol = MolFileToMol(fname1);
std::string fname2 = rdbase + "/Code/GraphMol/MolTransforms/test_data/1oir_canon.mol";
ROMol *mol2 = MolFileToMol(fname2);
Conformer &conf1 = mol->getConformer(0);
canonicalizeConformer(conf1);
Conformer &conf2 = mol2->getConformer();
unsigned int i, nats = mol->getNumAtoms();
for (i = 0; i < nats; ++i) {
CHECK_INVARIANT(comparePts(conf1.getAtomPos(i), conf2.getAtomPos(i)), "");
}
delete mol;
delete mol2;
}
ROMol *TDTMolSupplier::parseMol(std::string inLine) {
PRECONDITION(dp_inStream, "no stream");
Utils::LocaleSwitcher ls;
std::size_t startP = inLine.find("<");
std::size_t endP = inLine.find_last_of(">");
std::string smiles = inLine.substr(startP + 1, endP - startP - 1);
ROMol *res = SmilesToMol(smiles, 0, df_sanitize);
if (res && res->getNumAtoms() > 0) {
// -----------
// Process the properties:
d_line++;
std::getline(*dp_inStream, inLine);
while (!dp_inStream->eof() && inLine.find("|") != 0) {
endP = inLine.find("<");
std::string propName = inLine.substr(0, endP);
boost::trim_if(propName, boost::is_any_of(" \t"));
startP = endP + 1;
if (propName == common_properties::TWOD && d_confId2D >= 0) {
std::string rest = inLine.substr(startP, inLine.size() - startP);
std::vector<double> coords;
TDTParseUtils::ParseNumberList(rest, coords, dp_inStream);
Conformer *conf = new Conformer(res->getNumAtoms());
conf->setId(d_confId2D);
conf->set3D(false);
for (unsigned int atIdx = 0; atIdx < res->getNumAtoms(); atIdx++) {
if (2 * atIdx + 1 < coords.size()) {
conf->setAtomPos(
atIdx,
RDGeom::Point3D(coords[2 * atIdx], coords[2 * atIdx + 1], 0.0));
} else {
// we're going to let this slide... but maybe we should do something
// else?
}
}
res->addConformer(conf, false);
} else if (propName == "3D" && d_confId3D >= 0) {
std::string rest = inLine.substr(startP, inLine.size() - startP);
std::vector<double> coords;
TDTParseUtils::ParseNumberList(rest, coords, dp_inStream);
Conformer *conf = new Conformer(res->getNumAtoms());
conf->setId(d_confId3D);
conf->set3D(true);
for (unsigned int atIdx = 0; atIdx < res->getNumAtoms(); atIdx++) {
if (3 * atIdx + 2 < coords.size()) {
conf->setAtomPos(
atIdx, RDGeom::Point3D(coords[3 * atIdx], coords[3 * atIdx + 1],
coords[3 * atIdx + 2]));
} else {
// we're going to let this slide... but maybe we should do something
// else?
}
}
res->addConformer(conf, false);
} else {
endP = inLine.find_last_of(">");
if (endP == std::string::npos) {
std::ostringstream errout;
errout << "no end tag found for property" << propName;
throw FileParseException(errout.str());
} else {
std::string propVal = inLine.substr(startP, endP - startP);
res->setProp(propName, propVal);
if (propName == d_nameProp)
res->setProp(common_properties::_Name, propVal);
}
}
std::getline(*dp_inStream, inLine);
}
}
return res;
}
