Hi Markus,
The general rule of thumb is that if you remove an exocyclic neighbor from
an aromatic heteroatom you need to add an "explicit H" to the heteroatom.
Here's a modification of one of your pieces of code that adds that H as an
atom that's actually in the graph:
# use ReplaceAtom:
Hatom = Chem.MolFromSmiles('[H]').GetAtomWithIdx(0)
atidx = 8
edit_mol = Chem.EditableMol(mol)
edit_mol.ReplaceAtom(atidx,Hatom)
scaffold = edit_mol.GetMol()
scaffold_smiles = Chem.MolToSmiles(scaffold)
print(scaffold_smiles)
The change relative to what you were doing is the use of MolFromSmiles() to
get the H.
A more efficient approach that has the advantage of not leaving extra H
atoms in the molecule that then need to be removed is to add the "explicit
H" to the atom:
atidx = 8
nbrIdx = 7
edit_mol = Chem.RWMol(mol)
edit_mol.RemoveAtom(atidx)
edit_mol.GetAtomWithIdx(nbrIdx).SetNumExplicitHs(1)
scaffold = edit_mol.GetMol()
scaffold_smiles = Chem.MolToSmiles(scaffold)
print(scaffold_smiles)
This produces:
c1ccc(cc1)-c1n[nH]c(n1)-c1ccccc1
I hope that helps
-greg
On Thu, Apr 27, 2017 at 4:53 PM, Markus Metz <metm...@gmail.com> wrote:
> 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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>>>
>>
>
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