Re: [Rdkit-discuss] RDKit Descriptors

[Greg L. <gre...@gm...>]

Dear Kirk,

On Thu, Sep 18, 2008 at 12:58 AM, Robert DeLisle <rkd...@gm...> wrote:
> I've finally found time to start using RDKit and started with descriptor
> calculation.  Following the examples on the wiki
> (http://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit), I get a
> KeyError any time I attempt to obtain HeavyAtomCount, RingCount,

HeavyAtomCount and RingCount were introduced after the May release, so
they're in the subversion version of the code. They will be in the Q3
release (which will happen sometime in the next couple of weeks,
hopefully).

> PEOP_VSA,
> SMR_VSA, Slogp_VSA, EState_VSA, and VSA_Estate.

The various X_VSA descriptors are vector-valued and you access them by
element, so you could ask for PEOE_VSA4 or Slogp_VSA10.

> (BTW, what is the
> difference between the two last VSA descriptors?)

The "standard" VSA descriptors provide map summed VSA values into bins
determined by the other descriptor. So, for example, SMR_VSA uses
atomic contributions to the VSA and uses bins determined by atomic
contributions to the SMR. EState_VSA is the same, it just uses atomic
EState values. VSA_EState is reversed: atomic EState values are put
into bins determined by the VSA contributions.

Best Regards,
-greg