Hi Greg:
Your suggestions pointed me into the right direction. Thank you very much.
I tried your example but it seems (?) that the method GetAtomWithIdx() is
not available for edit_mol.
So I stored a neighbor atom which is a N atom, is aromatic and does not
belong to the same ring. I then applied the setnumexplicitHs method on the
mol.
Cheers,
Markus
On Thu, Apr 27, 2017 at 8:07 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> 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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>
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