Hmm – good question … I don't have that as lumped hydrohphobe. When you look at
experimental values then you get e.g.:
Exp predACD predChemAxon
Benzene: 2.13 2.22 1.97
Nitrobenzene 1.85 1.95 1.91
So I would agree on the argument. My experience from X-rays is that the major
interaction I have seen so far was H-acceptor with water or backbone.
For the more complete fdef file – yes that's still on.
Ciao
Nik
From: JP <jeanpaul.ebe...@inhibox.com<mailto:jeanpaul.ebe...@inhibox.com>>
Date: Monday, October 21, 2013 11:17 AM
To:
"rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Discuss"
<rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>>
Subject: [Rdkit-discuss] Chemistry 101 question...
yo RDKitters,
A quick question about some chemistry found in the RDKit from a computer
scientist.
Why is the nitro ("Nitro2") group in DATA/BaseFeatures.fdef and
Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef specified as
LumpedHydrophobe?
# nitro groups in the RD code are always: *-[N+](=O)[O-]
DefineFeature Nitro2 [N;D3;+](=O)[O-]
Family LumpedHydrophobe
Weights 1.0,1.0,1.0
EndFeature
Why is this a hydrophobe (it looks polar to me)? Or is this one of the too
many corner cases?
Also a related question, I seem to recall that at the UGM (over a delicious
sandwich) there was talk of having a more complete fdef file out-of-the-box -
is this still on?
Many Thanks Folks,
JP
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