void testSDMemoryCorruption() {
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Data/NCI/first_200.props.sdf";
SDMolSupplier sdsup(fname,true);
std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf";
std::ostream *os=new std::ofstream(ofile.c_str());
//std::ostream *os=new std::stringstream();
SDWriter *writer = new SDWriter(os,false);
STR_VECT names;
#if 1
ROMol *m1=sdsup.next();
MolOps::sanitizeMol(*(RWMol *)m1);
#else
ROMol *m1=SmilesToMol("C1CC1");
TEST_ASSERT(m1);
#endif
sdsup.reset();
int nDone=0;
while (!sdsup.atEnd()) {
//std::cerr<<nDone<<std::endl;
ROMol *mol = sdsup.next();
//std::cerr<<"m:"<<mol<<std::endl;
TEST_ASSERT(mol);
std::string mname;
mol->getProp("_Name", mname);
names.push_back(mname);
//std::cerr<<" w"<<std::endl;
writer->write(*mol);
//std::cerr<<" ok"<<std::endl;
delete mol;
nDone++;
}
CHECK_INVARIANT(nDone == 200, "");
writer->flush();
CHECK_INVARIANT(writer->numMols() == 200, "");
delete writer;
#if 1
// now read in the file we just finished writing
SDMolSupplier reader(ofile);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
std::string mname;
mol->getProp("_Name", mname);
CHECK_INVARIANT(mname == names[i], "");
delete mol;
i++;
}
#endif
}
void testSDWriter() {
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
SDMolSupplier sdsup(fname);
std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.sdf";
SDWriter *writer = new SDWriter(ofile);
STR_VECT names;
while (!sdsup.atEnd()) {
ROMol *mol = sdsup.next();
std::string mname;
mol->getProp("_Name", mname);
names.push_back(mname);
writer->write(*mol);
delete mol;
}
writer->flush();
CHECK_INVARIANT(writer->numMols() == 16, "");
// make sure we can close() the writer and delete it:
writer->close();
delete writer;
// now read in the file we just finished writing
SDMolSupplier reader(ofile);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
std::string mname;
mol->getProp("_Name", mname);
CHECK_INVARIANT(mname == names[i], "");
delete mol;
i++;
}
// now read in a file with aromatic information on the bonds
std::string infile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_arom.sdf";
SDMolSupplier nreader(infile);
i = 0;
while (!nreader.atEnd()) {
ROMol *mol = nreader.next();
std::string mname;
mol->getProp("_Name", mname);
CHECK_INVARIANT(mname == names[i], "");
i++;
delete mol;
}
}
void testSDWriterStrm() {
std::string rdbase = getenv("RDBASE");
{
std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
SDMolSupplier sdsup(fname);
std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_few.sdf";
std::ofstream *oStream=new std::ofstream(ofile.c_str());
SDWriter *writer = new SDWriter(oStream);
STR_VECT names;
while (!sdsup.atEnd()) {
ROMol *mol = sdsup.next();
std::string mname;
mol->getProp("_Name", mname);
names.push_back(mname);
writer->write(*mol);
delete mol;
}
writer->flush();
CHECK_INVARIANT(writer->numMols() == 16, "");
delete writer;
// now read in the file we just finished writing
SDMolSupplier reader(ofile);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
std::string mname;
mol->getProp("_Name", mname);
CHECK_INVARIANT(mname == names[i], "");
delete mol;
i++;
}
}
{
// now read in a file with aromatic information on the bonds
std::string infile = rdbase + "/Code/GraphMol/FileParsers/test_data/outNCI_arom.sdf";
SDMolSupplier nreader(infile);
unsigned int i = 0;
while (!nreader.atEnd()) {
ROMol *mol = nreader.next();
TEST_ASSERT(mol);
++i;
delete mol;
}
TEST_ASSERT(i==16);
}
}
void SetSDWriterProps(SDWriter &writer, python::object props) {
// convert the python list to a STR_VECT
STR_VECT propNames;
PySequenceHolder<std::string> seq(props);
for (unsigned int i = 0; i < seq.size(); i++) {
propNames.push_back(seq[i]);
}
writer.setProps(propNames);
}
void testGitHubIssue62() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing GitHubIssue62." << std::endl;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
double energyValues[] =
{ 38.687, 174.698, 337.986, 115.248,
2.482, 1.918, 10.165, 98.469, 39.078,
267.236, 15.747, 202.121, 205.539,
20.044, 218.986, 79.627 };
SmilesMolSupplier smiSupplier(pathName + "/Issue62.smi");
SDWriter *sdfWriter = new SDWriter(pathName + "/Issue62.sdf");
for (unsigned int i = 0; i < smiSupplier.length(); ++i) {
ROMol *mol = MolOps::addHs(*(smiSupplier[i]));
TEST_ASSERT(mol);
std::string molName = "";
if (mol->hasProp(common_properties::_Name)) {
mol->getProp(common_properties::_Name, molName);
}
DGeomHelpers::EmbedMolecule(*mol);
ForceFields::ForceField *field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize(200, 1.e-6, 1.e-3);
TEST_ASSERT(!needMore);
sdfWriter->write(*mol);
double e = field->calcEnergy();
BOOST_LOG(rdErrorLog) << molName << " " << e << std::endl;
TEST_ASSERT(fabs(e - energyValues[i]) < 1.);
}
sdfWriter->close();
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
}
void WriteMolToSD(SDWriter &writer, ROMol &mol, int confId) {
writer.write(mol, confId);
}
