Hmm, this is an open problem I think and I don't know of an obviously good
one. You could certainly take an average (mean/median), say weighted by
stochiometry. Whether this is valid/useful/predictive will need to be
tested by some validation experiments.
I know of some groups working on it (eg Oleg Ursu at UNM) and there is some
published literature
http://onlinelibrary.wiley.com/doi/10.1002/minf.201100129/abstract
http://dx.doi.org/10.1080/10659360600562202
On Thu, Aug 22, 2013 at 4:55 PM, Martin Guetlein <
[email protected]> wrote:
> On Thu, Aug 22, 2013 at 6:28 PM, Rajarshi Guha <[email protected]>
> wrote:
> > Do you mean dot connected compounds? In that sense, most (if not all)
> QSAR
> > descriptors should be evaluating descriptors for individual components
> > separately. After that what they do depends on the application - if we're
> > talking about salt forms, probably drop the salt components.
> Alternatively,
> > if we're talking about mixtures (which is not really the case for a dot
> > connected representation), there could be various ways to generate a
> mixture
> > descriptor
>
> Hi Rajarshi,
>
> Yep, in smiles representation its dot connected compounds.
> In our data these compounds are mostly salts/ions, some mixtures and
> some isomeres.
> So in more detail, how would you compute the the descriptor values for
> the mixtures?
> For isomeres, using the mean value should be fine, what do you think?
>
> Kind regards,
> Martin
>
>
>
> >
> >
> > On Thu, Aug 22, 2013 at 12:14 PM, Martin Guetlein
> > <[email protected]> wrote:
> >>
> >> Hi,
> >>
> >> How do CDK descriptors handle molecules with multiple compounds in it?
> >>
> >> I experimented a bit, and found out that it depends on the descriptor:
> >> * most descriptors apparently just add up the values of the single
> >> compounds (like xlogp, that does make no sense does it?)
> >> * some fail for multi-compound molecules
> >> * some compute sth else
> >>
> >> My application is building QSAR models. I am not a chemist, but my
> >> feeling is that the clean but complicated solution would be to have
> >> 'set-valued features' (a set of values instead of a single value) for
> >> multi-compound molecules. But thats pretty complicated and most of my
> >> molecules have only one compound. But I think that the average value
> >> of the single compounds should be preferred for descriptors like
> >> molecular weight or logp.
> >>
> >> Kind regards,
> >> Martin
> >>
> >> P.S.: Sorry, If I missed existing discussions/documentation on this
> >> issue, I had some problems to denominate (and therefore google) this
> >> issue.
> >>
> >> --
> >> Dipl-Inf. Martin Gütlein
> >> Phone:
> >> +49 (0)761 203 8442 (office)
> >> +49 (0)177 623 9499 (mobile)
> >> Email:
> >> [email protected]
> >>
> >>
> >>
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> >
> >
> >
> > --
> > Rajarshi Guha | http://blog.rguha.net
> > NIH Center for Advancing Translational Science
>
>
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 8442 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> [email protected]
>
--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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