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/
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