Ah, great thanks Paolo!
On Fri, Jul 22, 2022 at 11:44 AM Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> Hi Susan,
>
> If you use [#1] in your SMARTS query, for your molecule to match there
> should be a real hydrogen atom in your molecule graph, while in your
> molecule you only have implicit hydrogens, unless you explicitly add them
> calling Chem.AddHs():
>
> print(Chem.AddHs(m).HasSubstructMatch(q))
> True
>
> Cheers,
> p.
>
> On Fri, Jul 22, 2022 at 12:13 PM Susan Leung <susanhle...@gmail.com>
> wrote:
>
>> Hi all,
>>
>>
>>
>> I am trying to do substructure search using query atom lists, but I am
>> seeing unexpected behaviour when I have hydrogen in my query atom list…
>>
>>
>>
>> import rdkit
>>
>> print(rdkit.__version__)
>>
>> from rdkit import Chem
>>
>>
>>
>> >>2022.03.2
>>
>>
>>
>> ## having carbon in the query atom list seems to work as expected
>>
>> q = Chem.MolFromSmarts('[#17,#6]-[#6]-[#17]')
>>
>> m = Chem.MolFromSmiles('ClCCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>> m = Chem.MolFromSmiles('CCCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>>
>>
>> >>True
>>
>> >>True
>>
>>
>>
>> ## having hydrogen in the query atom list doesn't work as expected
>>
>> q = Chem.MolFromSmarts('[#17,#1]-[#6]-[#17]')
>>
>> m = Chem.MolFromSmiles('ClCCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>> m = Chem.MolFromSmiles('CCl')
>>
>> print(m.HasSubstructMatch(q))
>>
>>
>>
>> >>True
>> >>False
>>
>>
>>
>> Best wishes,
>>
>>
>>
>> Susan
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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