but both of them can represented by
>>>> "c1nncn1"
>>>>
>>>> There's two solutions I suggest:
>>>> 1. use `Chem.MolFromSmiles('c1ccc(cc1)-c1nnc(n1)-c1c1',False)`
>>>> (reference: http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfi
&
i
>>> les-module.html#MolFromSmiles)
>>>
>>> 2. Manually Kekulize it:
>>> `Chem.MolFromSmiles('c1ccc(cc1)-C1=NN=C(N1)-c1c1')`
>>> . This indicate the H is on the 4'N.
>>>
>>>
>>> --
>>> Hon
cc1)-c1nnc(n1)-c1c1',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)-c1c1')`
>> . This indicate the H is on the 4'N.
>&g
;
>
> *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:
> c1cc
Hi Markus,“c1ccc(cc1)-c1nnc(n1)-c1c1” is different from
"c1ccc(cc1)-c1nncn1-c1c1", 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
Hello all:
I obtained this smiles string:
c1ccc(cc1)-c1nnc(n1)-c1c1
by removing atoms from the n1 in parentheses.
Using:
mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nnc(n1)-c1c1")
throws an error: Can't kekulize mol.
Using
mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nncn1-c1c1")
works fine.
6 matches
Mail list logo