Hi,
I am using the following C++ script to read a molecule from a SD file (with
defined stereochemistry), but the information about the stereochemistry gets
lost. The file I am using is from glucose (ZINC03833800;
http://zinc.docking.org/substance/3833800
<http://zinc.docking.org/substance/3833800>)
When I check the chiral information of the atoms, all of them have the chiral
tag 0.
How can I keep the stereo information?
SCRIPT:
std::fstream infilestr;
infilestr.open(in_file_name.c_str( ));
RDKit::SDMolSupplier mol_supplier( in_file_name , true );
for (unsigned i = 0; i < mol_supplier.length(); ++i) {
RDKit::ROMOL_SPTR mol(mol_supplier[i]);
if (!mol){
std::cout << "Error, molecule not found!" << std::endl;
continue;
}
for (unsigned int j = 0; j < mol->getNumAtoms(); j++){
RDKit::Atom* atom = mol->getAtomWithIdx(j);
std::cout << "Chirality atom " << j+1 << ": " <<
atom->getChiralTag() << std::endl;
}
std::string usmiles = RDKit::MolToSmiles (*mol);
std::cout << "Mol: " << usmiles << std::endl;
}
OUTPUT FOR GLUCOSE (ZINC03833800):
Chirality atom 1: 0
Chirality atom 2: 0
Chirality atom 3: 0
Chirality atom 4: 0
Chirality atom 5: 0
Chirality atom 6: 0
Chirality atom 7: 0
Chirality atom 8: 0
Chirality atom 9: 0
Chirality atom 10: 0
Chirality atom 11: 0
Chirality atom 12: 0
Mol: OCC1OC(O)C(O)C(O)C1O------------------------------------------------------------------------------
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