Hi there,
Thanks for the quick answer! And apologies for the ultra-slow reply... Yes,
I bumped into that thread shortly after posting (sorry). I agree that the
default behavior in rdkit is not ideal but most sane in this case.
The least hacky why around the problem I found was to "swap" the amide
smarts around, to get the 'other' side of the bond. Such that
([NH]!@C(=O))
(C(=O)!@[NH])
Then the two patterns are
patt1 =
Chem.MolFromSmarts("[!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]")
patt1 =
Chem.MolFromSmarts("[!$(C(=O)!@[NH])&!D1&!$(*#*)]-&!@[!$(C(=O)!@[NH])&!D1&!$(*#*)]")
Each pattern represents a set of bonds, the symmetric difference between
the two sets gives "missing" rotatable bonds neighboring the amide; the
amide bond is not selected in both cases.
Still this is not satisfactory. I'm a novice to SMARTS-land but it just
blew my mind that there isn't a pattern to do this selection, and that the
examples on the web are 'wrong' ("don't trust all you find on the
internet", greetings to capt Obvious)
Thanks,
- Jan
On 8 March 2014 17:38, S.L. Chan <slch...@yahoo.com> wrote:
> 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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