Hi Adelene, this gist
https://gist.github.com/ptosco/1e1c23ad24c90444993fa1db21ccb48b shows how to add stereo annotations to RDKit 2D depictions, and also how to access the double bond stereochemistry programmatically. Cheers, p. On Tue, Oct 20, 2020 at 12:24 PM Adelene LAI <adelene....@uni.lu> wrote: > Hi RDKit Community, > > > Is there a way to preserve undefined stereochemistry aka unspecified > stereochemistry when doing MolFromSmiles? > > I'm working with a bunch of molecules, some with stereochemistry defined, > some without. > > > If stereochemistry is undefined in the SMILES, I would like it to stay > that way when converted to a Mol, but this doesn't seem to be the case: > > > > mol = > Chem.MolFromSmiles('CC(C)(C1=CC(=C(C(=C1)Br)O)Br)C(=CC(C(=O)O)Br)CC(=O)O') > > mol > > One would expect that C=C to either be crossed, as in PubChem's depiction: > > https://pubchem.ncbi.nlm.nih.gov/compound/139598257#section=2D-Structure > > <https://pubchem.ncbi.nlm.nih.gov/compound/139598257#section=2D-Structure> > > > or that single bond to be squiggly, as in CDK's depiction: > > But it's not just a matter of depiction, as it seems internally, mol is > equivalent to its stereochem-specific sibling (Entgegen form) > > > CC(C)(C1=CC(=C(C(=C1)Br)O)Br)/C(=C/C(C(=O)O)Br)/CC(=O)O > > > > I've tried sanitize=False, but it doesn't seem to have any effect. I > would prefer not having to manually SetStereo(Chem.BondStereo.STEREOANY) > for every molecule with undefined stereochem (not sure how I would even go > about that...). > > > Possibly related to: > > > https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570 > > > > <https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570> > > https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAHOi4k3revAu-9qhFt0MpUpr0aADQ9d8bV2XT6FurTEKimCQng%40mail.gmail.com/#msg36365128 > o = Chem.MolFromSmiles('C/C=C/C') > > > <https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/C00BE94F-6F6F-466A-83D4-3045C9006026%40gmail.com/#msg34929570> > https://www.rdkit.org/docs/source/rdkit.Chem.EnumerateStereoisomers.html > > https://github.com/openforcefield/openforcefield/issues/146 > > > > > Any help would be much appreciated. > > > Thanks, > > Adelene > > > > > > > > > Doctoral Researcher > > Environmental Cheminformatics > > UNIVERSITÉ DU LUXEMBOURG > > > LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE > > 6, avenue du Swing, L-4367 Belvaux > > T +356 46 66 44 67 18 > > [image: github.png] adelenelai > > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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