[Rdkit-discuss] Explicit H in substructure searches

[Markus H. <mh...@ad...>]

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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