I would just replace 'n' with '[nH]' in your existing SMILES, for the N you
want the H on.
-P.
On Thu, Apr 27, 2017 at 12:32 AM, Hongbin Yang <yanyangh...@163.com> wrote:
> 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 Metz <metm...@gmail.com>
> *Date:* 2017-04-27 09:30
> *To:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> *Subject:* [Rdkit-discuss] Another Can't kekulize mol observation
> Hello all:
>
> I obtained this smiles string:
> c1ccc(cc1)-c1nnc(n1)-c1ccccc1
> by 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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