Dear Jennifer, Many thanks for your response. Very useful tutorial on Inchi. I did not know about the FixedH option:
inchi = Chem.MolToInchi(mol, options='/FixedH') Best, Alexis On Tue, 18 Jun 2019 at 13:20, Jennifer Hemmerich <jennyhemmeric...@gmail.com> wrote: > Dear Alexis, > > if you calculate the Standard Inchi it is invariant to tautomers (see > here: https://www.inchi-trust.org/technical-faq-2/#6.1). Therefore the > information which tautomer was converted is lost due to the Inchi > conversion. If you want to keep the tautomer information you need to use > the fixedH attribute for the inchi. But beware this makes it a non standard > Inchi, and thus might not be comparable to other Inchis. > > Hope this helps, > > Jennifer > On 18.06.19 12:59, Alexis Parenty wrote: > > Dear RdKiters, > > Why is it that the stable tautomer of the following structure is lost > during inchi/smiles conversion? > > > [image: image.png] > > mol = Chem.MolFromSmiles(*"Cc1ccc([nH]nc2)c2c1"*) > inchi = Chem.MolToInchi(mol) > mol = Chem.MolFromInchi(inchi) > smiles = Chem.MolToSmiles(mol) > print(smiles) > > *==> Cc1ccc2n[nH]cc2c1* > > > > The H has shifted on the wrong Nitrogen… > > Interestingly, if you remove the methyl, the shift no longer happens: > > mol = Chem.MolFromSmiles(*"c1([nH]nc2)c2cccc1"*) > inchi = Chem.MolToInchi(mol) > mol = Chem.MolFromInchi(inchi) > smiles = Chem.MolToSmiles(mol)print(smiles)==> *c1([nH]nc2)c2cccc1* > > > > Same issue for any secondary amides: if you pass the smiles of a secondary > amide, you end-up with the following unstable tautomer: > > > [image: image.png] > > Thanks, > > > > Alexis > > > _______________________________________________ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://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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