FragCatParams::FragCatParams(const FragCatParams &other) {
d_funcGroups.clear();
// copy consttructor
d_typeStr = other.getTypeStr();
d_lowerFragLen = other.getLowerFragLength();
d_upperFragLen = other.getUpperFragLength();
d_tolerance = other.getTolerance();
// std::cout << "In param copier\n";
const MOL_SPTR_VECT &ofgrps = other.getFuncGroups();
// const MOL_PTR_VECT &ofgrps = other.getFuncGroups();
MOL_SPTR_VECT::const_iterator fgi;
// MOL_PTR_VECT_CI fgi;
for (fgi = ofgrps.begin(); fgi != ofgrps.end(); fgi++) {
ROMol *nmol = new ROMol(*(fgi->get()));
// ROMol *nmol = new ROMol(*(*fgi));
d_funcGroups.push_back(ROMOL_SPTR(nmol));
// d_funcGroups.push_back(nmol);
}
}
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;
}