void testIssue294() {
BOOST_LOG(rdInfoLog) << "---- Test Issue294\n Watch memory usage."
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi";
std::string fgrpFile =
rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt";
SmilesMolSupplier suppl(fname, " ", 0, 1, false);
auto *fparams = new FragCatParams(1, 6, fgrpFile, 1.0e-8);
FragCatalog fcat(fparams);
FragCatGenerator catGen;
std::vector<ROMol *> mols;
ROMol *m = suppl.next();
while (m) {
mols.push_back(m);
catGen.addFragsFromMol(*m, &fcat);
try {
m = suppl.next();
} catch (FileParseException &) {
m = nullptr;
}
}
int nents = fcat.getNumEntries();
TEST_ASSERT(nents == 21);
FragFPGenerator fpGen;
m = mols[0];
for (unsigned int i = 0; i < 200; i++) {
for (std::vector<ROMol *>::const_iterator mi = mols.begin();
mi != mols.end(); mi++) {
ExplicitBitVect *fp = fpGen.getFPForMol(*(*mi), fcat);
delete fp;
}
}
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
}
void test1() {
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi";
std::string fgrpFile =
rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt";
SmilesMolSupplier suppl(fname, " ", 0, 1, false);
auto *fparams = new FragCatParams(1, 6, fgrpFile, 1.0e-8);
TEST_ASSERT(fparams->getNumFuncGroups() == 15);
FragCatalog fcat(fparams);
FragCatGenerator catGen;
std::vector<std::unique_ptr<ROMol>> mols;
unsigned int nDone = 0;
ROMol *m = suppl.next();
while (m) {
mols.push_back(std::unique_ptr<ROMol>(m));
nDone += 1;
catGen.addFragsFromMol(*m, &fcat);
try {
m = suppl.next();
} catch (FileParseException &) {
m = nullptr;
}
}
TEST_ASSERT(mols.size() == 16);
TEST_ASSERT(nDone == 16);
int nents = fcat.getNumEntries();
std::cerr << " " << nents << std::endl;
TEST_ASSERT(nents == 21);
FragFPGenerator fpGen;
BOOST_LOG(rdInfoLog) << "----- Test 1" << std::endl;
testMols(mols, fpGen, fcat);
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
//----------------------------------------------------------
// SERIALIZATION TESTS
//----------------------------------------------------------
// make sure we can pickle and unpickle parameter objects:
FragCatParams newParams;
std::string pickle = fparams->Serialize();
newParams.initFromString(pickle);
TEST_ASSERT(newParams.getLowerFragLength() == fparams->getLowerFragLength());
TEST_ASSERT(newParams.getUpperFragLength() == fparams->getUpperFragLength());
TEST_ASSERT(newParams.getTolerance() == fparams->getTolerance());
TEST_ASSERT(newParams.getNumFuncGroups() == fparams->getNumFuncGroups());
// make sure we can pickle and unpickle catalog entries:
const FragCatalogEntry *fpEntry = fcat.getEntryWithIdx(0);
auto *fpEntry2 = new FragCatalogEntry();
fpEntry2->initFromString(fpEntry->Serialize());
TEST_ASSERT(fpEntry->getDescription() == fpEntry2->getDescription());
TEST_ASSERT(fpEntry->getOrder() == fpEntry2->getOrder());
TEST_ASSERT(fpEntry->getBitId() == fpEntry2->getBitId());
TEST_ASSERT(fpEntry2->match(fpEntry, 1e-8));
TEST_ASSERT(fpEntry->match(fpEntry2, 1e-8));
delete fpEntry2;
// test catalogs' initFromString:
FragCatalog fcat2;
fcat2.initFromString(fcat.Serialize());
TEST_ASSERT(fcat2.getNumEntries() == fcat.getNumEntries());
BOOST_LOG(rdInfoLog) << "----- Test 2" << std::endl;
testMols(mols, fpGen, fcat2);
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
// and the pickle ctor:
FragCatalog *fcat3 = new FragCatalog(fcat.Serialize());
TEST_ASSERT(fcat3->getNumEntries() == fcat.getNumEntries());
BOOST_LOG(rdInfoLog) << "----- Test 3" << std::endl;
testMols(mols, fpGen, *fcat3);
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
//----------------------------------------------------------
// test issue 115
//----------------------------------------------------------
BOOST_LOG(rdInfoLog) << "----- Test Issue 115" << std::endl;
delete fparams;
fparams = new FragCatParams(3, 3, fgrpFile, 1.0e-8);
TEST_ASSERT(fparams->getNumFuncGroups() == 15);
delete fcat3;
fcat3 = new FragCatalog(fparams);
suppl.reset();
nDone = 0;
while (!suppl.atEnd()) {
nDone++;
ROMol *m = suppl.next();
catGen.addFragsFromMol(*m, fcat3);
delete m;
}
TEST_ASSERT(nDone == suppl.length());
TEST_ASSERT(fcat3->getNumEntries() == 21);
TEST_ASSERT(fcat3->getFPLength() == 10);
for (unsigned int i = 0; i < fcat3->getFPLength(); i++) {
TEST_ASSERT(fcat3->getEntryWithBitId(i)->getOrder() == 3);
}
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
//----------------------------------------------------------
// test issue 117
//----------------------------------------------------------
BOOST_LOG(rdInfoLog) << "----- Test Issue 117" << std::endl;
delete fparams;
fparams = new FragCatParams(1, 2, fgrpFile, 1.0e-8);
delete fcat3;
fcat3 = new FragCatalog(fparams);
ROMol *tmpMol = SmilesToMol("OC(N)CO");
TEST_ASSERT(tmpMol);
catGen.addFragsFromMol(*tmpMol, fcat3);
TEST_ASSERT(fcat3->getNumEntries() == 1);
// std::cout << fcat3->getEntryWithBitId(0)->getDescription() << std::endl;
TEST_ASSERT(fcat3->getEntryWithBitId(0)->getDescription() ==
"C(<-O>)<-N>C<-O>");
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
delete tmpMol;
delete fparams;
delete fcat3;
}
