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]:
[cid:image001.png@01D6C4EB.7D142840]
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]:
[cid:image002.png@01D6C4EB.7D142840]
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]:
[cid:image003.png@01D6C4EB.7D142840]
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<mailto: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
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