(Now with link - you can tell it's Friday night) Hi Mark, Alexis,
Yes, I was too fast in composing my previous reply and I did not pay enough attention to the molecules. After reading Alexis' reply, I looked more carefully at his original question and at that point I remembered having seen a similar behaviour before from RDKit on condensed ring systems featuring exocyclic bonds and relative mailing list discussions. So I did a bit of searching and I fished out the (long) thread that deals with exactly this behaviour. https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAAsqebGxOwJtH32T5jC%3DoBZN6G1JE_NwsEqKUO8%2BmUCqmABCzQ%40mail.gmail.com/#msg36448625 I hope that helps, cheers p. On Fri, Nov 27, 2020 at 7:31 PM Mark Mackey <m...@cresset-group.com> wrote: > Hi Paolo, > > > > Hmmm, I think this is displaying a bug (or at the very least unexpected > behaviour) in the aromaticity code. The issue isn’t the aromaticity of the > imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’ > second molecule is identical to the first except that one bond in the > 5-membered ring was broken, and that (to my eyes at least) should not > affect whether the 6-membered ring is seen as aromatic. > > > > Regards, > > Mark. > > > > *From:* Paolo Tosco <paolo.tosco.m...@gmail.com> > *Sent:* 27 November 2020 17:04 > *To:* Alexis Parenty <alexis.parenty.h...@gmail.com> > *Cc:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net> > *Subject:* Re: [Rdkit-discuss] canonicalization of two aromatic molecules > returning two different forms (kekule and aromatic) > > > > Hi Alexis, > > > > The second molecule (smiles2) is indeed aromatic, but the first (smiles1) > is not, as the imidazole ring condensed to the pyridine is partially > saturated. > > The smiles1a analogue where I have added a double bond is aromatic, and > upon canonicalization it yields an aromatic SMILES as expected. > > > > Cheers, > > p. > > > > *from* rdkit *import* Chem > > In [2]: > > mol1 *=* Chem*.*MolFromSmiles("N12C=CC=CC1=NCC2") > > In [3]: > > mol1 > > Out[3]: > > In [4]: > > smiles1 *=* Chem*.*MolToSmiles(mol1) > > In [5]: > > smiles1 > > Out[5]: > > 'C1=CC2=NCCN2C=C1' > > In [6]: > > mol2 *=* Chem*.*MolFromSmiles("CN=C1C=CC=CN1C") > > In [7]: > > mol2 > > Out[7]: > > In [8]: > > smiles2 *=* Chem*.*MolToSmiles(mol2) > > In [9]: > > smiles2 > > Out[9]: > > 'CN=c1ccccn1C' > > > > > > > > > > > > > > > > > > In [10]: > > mol1a *=* Chem*.*MolFromSmiles("N12C=CC=CC1=NC=C2") > > In [11]: > > mol1a > > Out[11]: > > In [12]: > > smiles1a *=* Chem*.*MolToSmiles(mol1a) > > In [13]: > > smiles1a > > Out[13]: > > 'c1ccn2ccnc2c1' > > > > On Fri, Nov 27, 2020 at 5:09 PM Alexis Parenty < > alexis.parenty.h...@gmail.com> wrote: > > Hi everyone, > > > > Why is it that when I canonicalize the following smiles_1 I get its > unexpected kekule form, whereas when I canonicalize a similar smiles_2, I > get its expected aromatic form? > > > > From rdkit import Chem > > smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2") > smiles > > ==> 'C1=CC2=NCCN2C=C1' > > > > smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C") > smiles2 > > ==> 'CN=c1ccccn1C' > > > > I would like to get the aromatic form in both cases... Is there a way to > force the aromatic form? > > > > Best, > > Alexis > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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