Yeah, this is definitely a bug. @Ling: thanks for raising it. @Ivan: thanks for simplifying the example!
I created a github issue here: https://github.com/rdkit/rdkit/issues/4674 -greg On Thu, Nov 4, 2021 at 11:33 PM Ivan Tubert-Brohman < ivan.tubert-broh...@schrodinger.com> wrote: > That does seem like a bug. You can also see it without involving > DeleteSubstructs, by starting from different SMILES representations of the > same molecule: > > >>> m1 = Chem.MolFromSmiles('FC12C3CCCC1C32F') > > > >>> m2 = Chem.MolFromSmiles('C12C3CCCC1C32') > > > >>> m3 = Chem.MolFromSmiles('C1CC2C3C(C1)C23') > > >>> Chem.MolToSmiles(m2) == Chem.MolToSmiles(m3) > > True > > >>> m1.GetSubstructMatch(m2) > > (1, 2, 3, 4, 5, 6, 7) > > >>> m1.GetSubstructMatch(m3) > > () > > Note that if you parse the problem SMILES as a SMARTS, you do get a match: > > >>> m4 = Chem.MolFromSmarts('C1CC2C3C(C1)C23') > > > >>> m1.GetSubstructMatch(m4) > > (4, 3, 2, 1, 6, 5, 7) > > Another interesting bit is that while the Inchis of m2 and m3 are also the > same, the conversion produces a warning about stereochemistry: > > >>> Chem.MolToInchi(m2) == Chem.MolToInchi(m3) > > [18:26:48] WARNING: Omitted undefined stereo > [18:26:48] WARNING: Omitted undefined stereo > True > > Ivan > > On Wed, Nov 3, 2021 at 3:59 PM Ling Chan <lingtrek...@gmail.com> wrote: > >> Dear colleagues, >> >> I have a molecule "FC12C3CCCC1C32F". I stripped it of the F's, and tried >> to do a GetSubstructMatch. It worked. But if I reconstruct the stripped >> molecule from a smiles string, it does not. Please see attached. >> >> I suppose some info is lost when you reconstruct the stripped core from a >> smiles string. But still, I would think it should match anyway. >> >> Another issue is that the 2D depiction has the left most carbons lying >> exactly on top of each other, creating a false impression. A better >> depiction would be like the second attached image. (Not sure if this is >> easy to fix though.) >> >> Thank you for you attention. >> >> Ling >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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