Re: [Rdkit-discuss] Explicit H in substructure searches

[Paolo T. <pao...@gm...>]

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>
>
> -- 
>
> *Markus Heller, PhD*
>
> Senior Scientist
>
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