Hello Jan,
This has been discussed not long ago:
http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg03671.html
Your second Smarts string is the "Chemaxon Smarts" in this discussion.
There may not be an easy way out. You may need to do it in two steps and
add back the non-amide N-C bonds.
Ling
________________________________
From: Jan Domanski <jan...@gmail.com>
To: rdkit-discuss@lists.sourceforge.net
Sent: Saturday, March 8, 2014 11:55 AM
Subject: [Rdkit-discuss] Rotatable bonds, amide bonds and SMARTS
Hi guys,
Not sure if this is a bug or SMARTS mishandling on my part. I'm trying to
select all the rotatable bond in the molecule attached, the SMARTS string for
doing that is either
'[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]'
or
'[!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]'
The latter is a popular SMARTS example I found on a bunch of pages. It's a more
complex version which tries to filter-out non-rotatable amides amides but (not
esters).
I find that with the amide smarts, the bond between N and the non-amide carbon
is treated as non rotatable. For an amino acid this would correspond to the
N-C_alpha bond, and should be allowed to rotate freely.
For the attached molecule I'm having to resolve to crazy hacks to get the
proper rot bond selection. Again: what I want is a SMARTS selection that will
give me all the rotatable bonds as in "dude_dud38_ace_xtal-lig_bonds3.png".
Files attached, version used is RDKit_2013_09_1
Thanks,
- Jan
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