Hi Markus,“c1ccc(cc1)-c1nnc(n1)-c1ccccc1” is different from
"c1ccc(cc1)-c1nncn1-c1ccccc1", so you cannot remove the parentheses.
The error "Can't kekulize mol." is caused by the triazole in your molecule.
"c1nncn1" tells that the molecule is aromatic, but it do not tell where the H
is.
For example, "C1=NN=CN1" is "4H-1,2,4-triazole" and "C1=NC=NN1" is
1H-1,2,4-triazole. They are different in Kekulize but both of them can
represented by "c1nncn1"
There's two solutions I suggest:1. use
`Chem.MolFromSmiles('c1ccc(cc1)-c1nnc(n1)-c1ccccc1',False)` (reference:
http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfiles-module.html#MolFromSmiles)
2. Manually Kekulize it:
`Chem.MolFromSmiles('c1ccc(cc1)-C1=NN=C(N1)-c1ccccc1')` . This indicate the H
is on the 4'N.
Hongbin Yang
From: Markus MetzDate: 2017-04-27 09:30To: RDKit DiscussSubject:
[Rdkit-discuss] Another Can't kekulize mol observationHello all:
I obtained this smiles string:c1ccc(cc1)-c1nnc(n1)-c1ccccc1by removing atoms
from the n1 in parentheses.
Using:mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nnc(n1)-c1ccccc1")throws an error:
Can't kekulize mol.
Using mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nncn1-c1ccccc1")
works fine.
Is there any workaround?Any input is highly appreciated.
Cheers,Markus
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