Hi Tim, Yes, you need to set the property manually if you would like the chiral flag to be set in the mol file.
The code behaves this way because otherwise it would need to guess what the user intended (as well as how they interpret/use the chiral flag). -greg On Mon, Jul 13, 2020 at 1:28 PM Tim Dudgeon <tdudgeon...@gmail.com> wrote: > 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 > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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