I've noticed that when writing a 3D molfile that has been generated by RDKit (in my case using AllChem.EmbedMolecule) and has chirality present that the chiral flag is not set. At least it is not always set, I can't be exactly sure. My exact scenario is to read a chiral SMILES, convert to 3D using EmbedMolecule and then write to SDF.
I also note that there is a magical '_MolFileChiralFlag' property that it seems if set to 1 results in the chiral flag being set. So the question here is is it the responsibility of the developer to set this '_MolFileChiralFlag' property when the molecule is known to be chiral (e.g. using the Chem.FindMolChiralCenters() method) or am I missing something here? Thanks Tim
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