Hi Toby,

On Fri, Dec 20, 2013 at 3:29 PM, Toby Wright <toby.wri...@inhibox.com>wrote:

> Hi,
>
> I have a molecule that RDKit claims to have 9 rotatable bonds but the
> chemists in my office claim to have 6. It's smiles is
> CCCCNC(=O)C1CC[NH+](CC(=O)NC(N)=O)CC1
> and my colleagues are concerned that the amide and urea groups are being
> counted as rotatable incorrectly. Is this a bug, a design decision or a
> feature?
>
>
It's not a bug and I'd be hard pressed to call it a feature, so I'd
probably go with "design decision". ;-)

The SMARTS used to recognize rotatable bonds is extremely
simple: [!$(*#*)&!D1]-&!@[!$(*#*)&!D1]. It makes no effort to account for
single bonds where the rotation is constrained, i.e. amides, ureas, the
bonds that lead to atropisomerism, and the like. If the inclusion of amides
and esters is something that bothers your chemists, you could imagine
subtracting off the number of amide bonds (also available as a descriptor)
or using a custom definition like "C(=[O,N;!R]-&!@[O,N;!D1]".

-greg
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