Hi Nina,

Is there a mechanism yet of entering a smiles/(other formats)  in a form
field (or through RDF call) and putting it into a location on a server
(ambit ?) - so that hence forward the compound service can be used to
deliver the compound to other components/algorithms/models ?

Cheers
Surajit

On 13 July 2010 15:00, Nina Jeliazkova <jeliazkova.nina at gmail.com> wrote:

> Hi Surajit,
>
> One approach is to consider using representations with lower inherent
> ambiguity (InChI, MOL, CML, etc.) - needless to say all of these are
> available via OpenTox dataset services.
>
> Best regards,
> Nina
>
> On Tue, Jul 13, 2010 at 12:21 PM, surajit ray <mr.surajit.ray at gmail.com
> >wrote:
>
> > Hi Egon,
> >
> > Our workflow uses the CDK Smilesparser object to read in the smiles. In
> the
> > light of these bugs - should we be wary of certain smiles OR look at some
> > other means of reading in the smiles ?
> >
> > If so what would you advise as the best alternative to the smiles parser
> ?
> >
> > Cheers
> > Surajit
> >
> > On 13 July 2010 11:37, Egon Willighagen <egon.willighagen at gmail.com>
> > wrote:
> >
> > > Dear Dmitry,
> > >
> > > On Mon, Jul 12, 2010 at 9:42 AM, Druzhilovsky
> > > <dmitry.druzhilovsky at ibmc.msk.ru> wrote:
> > > > In my opinion, CDK is the most correct for sensing. On the other
> hand,
> > > CDK
> > > > has some bugs with SMILES periodically . So, I daresay CACTVS do for
> > > SMILES
> > > > in complex apps.
> > >
> > > I'd very much look forward to an OpenSMILES (re-)implementation. A lot
> > > of bugs have been resolved, and most reside in the aromaticity concept
> > > of SMILES, which is needlessly complex, partly because the whole
> > > aromaticity concept is ill-defined...
> > >
> > > There are some unit tests indeed still failing for the SMILES parser,
> > > but we welcome more bug reports on the SMILES parser if you find
> > > them... this is a very easy way to contribute to the CDK project...
> > >
> > > Egon
> > >
> > >
> > > --
> > > Post-doc @ Uppsala University
> > > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
> > > Homepage: http://egonw.github.com/
> > > Blog: http://chem-bla-ics.blogspot.com/
> > > PubList: http://www.citeulike.org/user/egonw/tag/papers
> > > _______________________________________________
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> > > Development at opentox.org
> > > http://www.opentox.org/mailman/listinfo/development
> > >
> >
> >
> >
> > --
> > Surajit Ray
> > Partner
> > www.rareindianart.com
> > _______________________________________________
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> >
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