Hello all: Thank you very much for your messages.
As I would like to process many molecules manually editing smiles is
unfortunately not an option.
Therefore I tried to automatize this step using the method ReplaceAtom of
the class EditableMol.
I defined an Hatom and tried to use it. Upon executing attached notebook
the input molecule is unchanged.
Do you have another suggestions which might help answer my question?
Best,
Markus
On Wed, Apr 26, 2017 at 11:46 PM, Peter S. Shenkin <shen...@gmail.com>
wrote:
> 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.rdmolfi
>> les-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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>>
>
Cannot_Kekulize.ipynb
Description: Binary data
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