Great. Thanks. I suspected that would be the case, but just wanted to be sure I wasn't missing anything.
On Tue, Jul 14, 2020 at 9:42 AM Greg Landrum <greg.land...@gmail.com> wrote: > 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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