Re: [Rdkit-discuss] RDKit Descriptors

[Robert D. <rkd...@gm...>]

Greg,

Thank you for the response.

I was able to get PEOE_VSA1 through PEOE_VSA14, SMR_VSA1 through SMR_VSA10,
and EState_VSA1 through EState_VSA11 working.  Are these the correct limits
on the vector components?

I was unable, however, to get Slogp_VSA or VSA_EState working with any
integer suffix between 1 and 10.

I've also done a correlation analysis on all the descriptors that I've
gotten working.  After computing descriptors for some 24,000 compounds I
removed those with less than 10% variance and limited correlations between
variables to a maximum of 0.85 (using KNIME).  I'm happy to send a list of
the resulting descriptors or a correlation matrix if you or anyone else is
interested.



On Wed, Sep 17, 2008 at 11:36 PM, Greg Landrum <gre...@gm...>wrote:

> 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
>