Hi Markus,
I tried to put together a comprehensible explanation in his gist:
https://gist.github.com/ptosco/1088937ce332bd66c999a2a5fbc855b3
Please also refer to the following threads on the mailing list:
https://sourceforge.net/p/rdkit/mailman/message/29679834/
https://sourceforge.net/p/rdkit/mailman/message/36696340/
and to this blog post by Roger Sayle:
https://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/
for further clarifications.
Cheers,
p.
On 05/11/2019 19:52, Markus Heller wrote:
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>
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*Markus Heller, PhD*
Senior Scientist
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