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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