Hi,
Sorry for the extremely slow reply, thanks for the insights and I hope you
all had a excellent Christmas break.
I think the best thing is to roll my own definition of a bond which would
be rotatable if not for the fact that it's an amide. Something like
$([NH]!D1)-&!@C=O and then take that number of these bonds away from
RDKit's rotatable bond count. If you simply take away the number of amides
calculated by RDKit from the number of rotatable bonds you hit an error
where an amide bond was not considered rotatable in the first place (for
example because the N was terminal).
The Chemaxon definition of rotatable bonds troubles me somewhat. Given the
following molecule:
CC(=O)NCC
it claims there are no rotatable bonds at all. The non-amide N-C bond is
discounted because one of the atoms fulfils the pattern ([NH]!@C(=O)), that
is it is a N connected to a C=O group, even though this connection is not
made by the N-C bond in question.
Thanks again,
Yours,
Toby Wright
--
InhibOx Ltd
Oxford
On 24 December 2013 15:46, Gerebtzoff, Gregori <gregori.gerebtz...@roche.com
> wrote:
> Hi Toby,
>
> One additional note on what Greg wrote:
> you can define another smarts pattern for the identification of rotatable
> bonds:
> Lipinski.RotatableBondSmarts = Chem.MolFromSmarts("...")
>
> Some smarts from the literature:
> Daylight:
> [!$(*#*)&!D1&$(*(-[!#1])~[!#1])]-&!@[!$(*#*)&!D1&$(*(-[!#1])~[!#1])]
> Chemaxon: [!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]
>
> Best,
>
> Grégori
>
>
>
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