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
> _______________________________________________
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> Rdkit-discuss@lists.sourceforge.net
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>
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