Hi Mark, Alexis,
I was too fast in composing my previous reply and I did not pay enough
attention to the molecules.
After reading Alexis' reply, I went back to 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.
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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