void testSmilesWriterStrm() {
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
std::string oname = rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
std::ofstream *oStream=new std::ofstream(oname.c_str());
STR_VECT propNames;
propNames.push_back(std::string("Column_2"));
SmilesWriter *writer = new SmilesWriter(oStream, " ");
writer->setProps(propNames);
STR_VECT names;
STR_VECT props;
ROMol *mol = nSup->next();
while (mol) {
std::string mname, pval;
mol->getProp("_Name", mname);
mol->getProp("Column_2", pval);
names.push_back(mname);
props.push_back(pval);
writer->write(*mol);
delete mol;
try {
mol = nSup->next();
} catch (FileParseException &) {
break;
}
}
writer->flush();
delete writer;
delete nSup;
// now read the molecules back in a check if we have the same properties etc
nSup = new SmilesMolSupplier(oname);
int i = 0;
mol = nSup->next();
while (mol){
std::string mname, pval;
mol->getProp("_Name", mname);
mol->getProp("Column_2", pval);
CHECK_INVARIANT(mname == names[i], "");
CHECK_INVARIANT(pval == props[i], "");
i++;
delete mol;
try {
mol = nSup->next();
} catch (FileParseException &) {
break;
}
}
}
void testSmilesWriterClose() {
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
std::string oname = rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles.csv";
STR_VECT propNames;
propNames.push_back(std::string("Column_2"));
SmilesWriter *writer = new SmilesWriter(oname," ","");
writer->setProps(propNames);
STR_VECT props;
ROMol *mol = nSup->next();
while (mol) {
std::string mname, pval;
mol->getProp("Column_2", pval);
mol->setProp("_Name","bogus");
props.push_back(pval);
writer->write(*mol);
delete mol;
try {
mol = nSup->next();
} catch (FileParseException &) {
break;
}
}
writer->close();
delete nSup;
// now read the molecules back in a check if we have the same properties etc
nSup = new SmilesMolSupplier(oname,",",0,-1);
int i = 0;
mol = nSup->next();
while (mol){
std::string mname, pval;
mol->getProp("_Name", mname);
TEST_ASSERT(mname!="bogus");
mol->getProp("Column_2", pval);
TEST_ASSERT(pval == props[i]);
i++;
delete mol;
try {
mol = nSup->next();
} catch (FileParseException &) {
break;
}
}
}
void SetSmiWriterProps(SmilesWriter &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 testSmilesWriter2() {
{
std::stringstream ss;
SmilesWriter *writer = new SmilesWriter(&ss, " ","Name",false);
RWMol *mol;
mol = SmilesToMol("c1ccccc1");
//MolOps::Kekulize(*mol);
writer->write(*mol);
delete mol;
mol = SmilesToMol("F[C@H](Cl)Br");
writer->write(*mol);
delete mol;
writer->flush();
TEST_ASSERT(ss.str()=="c1ccccc1 0\nFC(Cl)Br 1\n");
delete writer;
}
{
std::stringstream ss;
SmilesWriter *writer = new SmilesWriter(&ss, " ","Name",false,false,true);
RWMol *mol;
mol = SmilesToMol("c1ccccc1");
MolOps::Kekulize(*mol);
writer->write(*mol);
delete mol;
mol = SmilesToMol("F[C@H](Cl)Br");
writer->write(*mol);
delete mol;
writer->flush();
TEST_ASSERT(ss.str()=="C1=CC=CC=C1 0\nF[C@H](Cl)Br 1\n");
delete writer;
}
}
