Hi James,
Yes – I just checked the files I generated for the ph4 definitions and they
definitely do not have the tautomer recognition (guess I am just not SMART
enough for this ;-). I will follow up with Greg and see how quickly we can get
the fdef file as a contribution so people can start to add/delete/change things
in there.
I believe someone also mentioned that there might be better / other SMARTS
definitions for ph4 properties around. A pointer to those would be appreciated
on my end so maybe I can compare a bit before release?
Cheers
Nik
From: James Davidson <[email protected]<mailto:[email protected]>>
Date: Tue, 9 Oct 2012 07:47:38 +0100
To:
<[email protected]<mailto:[email protected]>>
Subject: [Rdkit-discuss] fdef files
Dear All,
At the UGM I promised to send a reminder (mainly for Greg, but possibly also
Nik?) about the potential use of two fdef files – one with and one without
explicit hydrogens. During the demo of the PyMOL interactivity with 3D ligand
+ pharmacophoric features (showfeats.py script), it was clear that explicitly
‘protonated’ nitrogens (eg in a specific tautomer of pyrrazole) were being
flagged as possible hydrogen-bond acceptors, as well as donors, due to the fdef
being used recognising the potential for a 1,2-H shift. I made the comment at
the time that in cases where the molecule had hydrogens specifically added
(perhaps a docking result), then it would probably be best to flag ‘specific’
rather than ‘potential’ Ph4 features – hence the use of separate fdef files.
My recollection (from Nik?) was that this was perhaps already the case in NIBR
user of RDKit(?)
Kind regards
James
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