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
> > _______________________________________________
> > Development mailing list
> > Development at opentox.org
> > http://www.opentox.org/mailman/listinfo/development
> >
>
>
>
> --
> Surajit Ray
> Partner
> www.rareindianart.com
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development
>