Good Morning Tim, The RDKit EnumerateStereoisomers function accomplishes this through the ‘tryEmbedding’ flag: https://github.com/rdkit/rdkit/blob/d20e5cadc81bf6c7b4e590124866f178f2f2fe28/rdkit/Chem/EnumerateStereoisomers.py#L8
It attempts to generate a 3D conformer for the given stereo configuration and fails the configuration if the conformer isn’t reasonable. Not fast, but it is reliable. -Brian > > On Sep 27, 2021, at 8:06 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > > > I have Python code to enumerate undefined chiral centres in a molecule. > Mostly this works fine, but for some constrained structures this can generate > stereochemistry that makes no sense. For instance consider NC1CC2CCC1C2: > <#1 (2).png> > > > These two make sense: > <#2.png> > > <#3.png> > > > But these two don't: > <#5.png> > > <#4.png> > > > Is there a way to filter out the invalid ones? > > Thanks > Tim > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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