Kirk,
On Wed, Oct 15, 2008 at 7:59 PM, Robert DeLisle <[email protected]> wrote:
>
> As you know, I've been working with descriptors in RDKit, and I think I've
> found a bug in the calculation of H-bond Acceptors. Attached is an example
> structure, N-methyl-1H-indole-6-carboxamide. When I calculate NumHAcceptors
> for this structure, I get 3. I've looked at numerous other strucures and it
> seems that nitrogens are always counted. I went into the code and found the
> definitions used for HAcceptors:
>
> $([O,S;H1;v2]-[!$(*=[O,N,P,S])])
> $([O,S;H0;v2])
> $([O,S;-])
> $([N&v3;H1,H2]-[!$(*=[O,N,P,S])])
> $([N;v3;H0])
> $([n,o,s;+0])
> F
>
> Unless I'm misinterpreting the SMARTS (a very good possiblity), both NH
> groups are being counted as an acceptor due to matching
> $([N&v3;H1,H2]-[!$(*=[O,N,P,S])]), but shouldn't the amide NH be excluded
> according to this same definition?
>
>
>
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