Hi,
I'm trying to understand how to properly use explicit hydrogens in substructure
searches. Below is an example. I would like to find all molecules that
contain my query with hydrogens at the nitrogens, and I thought I was on the
right track ... Why does the first query with the explicit H not match m1?
Thanks
Markus
<code>
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
IPythonConsole.ipython_useSVG = True
m1 = Chem.MolFromSmiles('c1cn[nH]c1N')
m2 = Chem.MolFromSmiles('CNc1ccn[nH]1')
m3 = Chem.MolFromSmiles('Nc1ccnn(C)1')
# do not remove explicit H
params = Chem.SmilesParserParams()
params.removeHs=False
query = Chem.MolFromSmiles('c1cn[nH]c(N([H])([H]))1', params)
# first should be True, but all are False
m1.HasSubstructMatch(query)
m2.HasSubstructMatch(query)
m3.HasSubstructMatch(query)
# rebuild query with explicit H removed, not what I want
query = Chem.MolFromSmiles('c1cn[nH]c(N([H])([H]))1')
m1.HasSubstructMatch(query)
m2.HasSubstructMatch(query)
m3.HasSubstructMatch(query)
</code>
--
Markus Heller, PhD
Senior Scientist
Direct: 604.827.1122 Main: 604.827.1147
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