Re: [Cdk-jchempaint] double bond stereo info smiles

[Stefan K. <ste...@eb...>]

> Now I see that with "Tools/Create SMILES" I can get both forms. Do you plan
> to include both possibilities in the saving menu?
Ah ok, I think nobody thought about that. I think this should become a setting 
and should be easy to do.
>
> Another thing: Do you plan to allow drawing and saving SMARTS too in
> future? I think it would be very useful for generating inputs for
> representing combinatorial libraries, substructure searches, etc.
This is heavily worked on by Mark in our group right now. I think he likes 
input on that.
Stefan
>
> Thanks!!
>
> Robert
>
> Stefan Kuhn <ste...@eb...> írta:
> >Sorry, I should have had a look at JCP before answering. JCP actually does
> > the >
>
> E/Z stuff, I get F/C(=C\(Br)I)Cl for your example. If you use JavaScript, >
> notice there is a getSmiles and getSmilesChiral method.>
> Another problem is that the SmilesReader ignores chiralities right now. So
> if > you read in the smiles, the arrangment is arbitrarry, even if /\ are
> in the > smiles.>
> Stefan>
>
> On Tuesday 16 February 2010 09:55:32 Kiss Robert wrote:>
>
> > Dear JChemPaint Developers,>
> >
> > First of all I would like to say that JChemPaint is a very nice
> > structure> drawer especially the latest version, so thanks to all the
> > people> participated in its development!>
> >
> > I had a small problem though. I drew a simple molecule with a double
> > bond.> In the first case the double bond had a defined stereo, while in
> > the second> case it was undefined. If I exported these molecules into MDL
> > mol files the> corresponding value in the bond block was "0" for the
> > defined and "3" for> the undefined cases, which is correct. I also tried
> > to export these> structures as SMILES strings, but unfortunately I got
> > the same SMILES for> both molecules:>
> >
> > FC(=C(Cl)Br)I>
> >
> > In SMILES, trans/cis double bonds can be described with slashes,
> > therefore> I think the molecule with defined parities should have slashes
> > in the> exported SMILES, but unfortunately it does not. Could you please
> > confirm> this is a bug or I do something wrong? Thanks!!>
> >
> > I attach the two molecules as png.>
> >
> > Cheers,>
> > Robert Kiss>
> > Research Associate>
> > Heriot-Watt University>
>
> -- >
> Stefan Kuhn B. Sc. M. A.>
> Software Engineer in the Chemoinformatics and Metabolism Team>
> European Bioinformatics Institute (EBI)>
> Wellcome Trust Genome Campus>
> Hinxton, Cambridge CB10 1SD UK>
> Phone +44 1223 49 2657>
> Fax +44 (0)1223 494 468>
>
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-- 
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468