Re: [Cdk-devel] Trouble using Smiles Parser / Generator

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

Hey Jay,
if you want to do this the method parseBond in SmilesGenerator, line 1224=
 ff.,=20
would be the place to append wedge information. As you said this would be=
=20
different from the chiral smiles concept from daylight, which abstracts f=
rom=20
the way things are painted.
Stefan

Am Saturday 06 September 2003 17:26 schrieben Sie:
> Hey Stefan,
> Thanks for clearing up my confusion regarding the stereochemisty.  I wa=
s
> acutally using the smiles generator and parser as part of a learning to=
ol,
> so I am wondering how the bond (wedges) information could be retained? =
 Can
> you please tell me which area of the code looks specifically at retaini=
ng
> bond information or where I can append the bond information so that it
> shows up in the smiles.  I realize that the newly generated smiles woul=
d
> not be "true" smiles anymore.
>
> Thanks,
> Jay
>
>
> ----- Original Message -----
> From: "Stefan Kuhn" <ste...@un...>
> To: "Jaya Deep Tunuguntla" <tj...@ho...>;
> <cdk...@li...>
> Sent: Saturday, September 06, 2003 4:53 AM
> Subject: Re: [Cdk-devel] Trouble using Smiles Parser / Generator
>
>
> Hey Jay,
> since I wrote the chiral smiles generator, it's probably my task to ans=
wer:
> 2) The parser does currently not understand chiralities. They will be
> ignored.
> 1) Could you send the example for me to check ? Generally speaking the
> generator works :-) Are you sure that your configuration is actually a
> valid stereochemical configuration ? Just that there are some wedge bon=
ds
> does not mean it is valid. Often the wedges are just for, well,
> illustration. Another thing: Is your molecule fully saturated ? Often
> chiralities only make sense if all Hs are given. Therefore I recommand =
to
> use fully saturated molecules for chiral smiles generation. If you send=
 me
> the example (as mdl would be best) I could check it.
> Stefan
>
> Am Friday 05 September 2003 09:14 schrieb Jaya Deep Tunuguntla:
> > Hey,
> > I am trying to generate smiles using the smiles generator and parser
> > classes, but there seem to be some problems... 1) I am not able to ge=
t
> > stereochemistry (bond into/out of the page) in the smiles. 2) I get a
> > string "SP1" in the smiles, but the parser doesn't inderstand it.
> >
> > If you have a solution or suggestion regarding the above problems, pl=
ease
> > let me know.
> >
> > Thanks,
> > Jay

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu