[Rdkit-discuss] HasSubstructureMatch using query atom list with hydrogen

[Susan Leung]

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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