Hi Tobias,
Descriptor engine relies on introspection to find classes implementing
certain (descriptor) interfaces. Since Java Web Start mechanism for
loading classes is a bit different , this behaviour is not quite
unexpected.
Although I am not an author of it, I've struggled before with trying to
make Descriptor engine load classess from jars other than CDK / on the
default class path. A (rough) workaround is to explicitly define the
descriptor class names in a list, but that's far from elegant.
Regards,
Nina
Tobias Girschick wrote:
> Hello,
>
> I have come across a weird behaviour (or at least for me it seems
> weird) of the DescriptorEngine when I use it to calculate all
> available molecular descriptors for a set of Molecules.
> It normally works perfectly fine, but when I tried to use it within
> Java Webstart, it seems that it did not do anything.
>
> My code:
> DescriptorEngine engine = new
> DescriptorEngine(DescriptorEngine.MOLECULAR);
> // as long as we have molecules in the set
> while (it.hasNext()){
> IAtomContainer ac = (IAtomContainer) it.next();
> try{
> engine.process(ac);
> } catch (CDKException c)
> c.printStackTrace();
> logger.warning("problem with descriptor engine");
> }
>
> Map<Object, Object> props = ac.getProperties();
> Iterator<Object> iter = props.keySet().iterator();
>
> // for all calculated descriptors
> while (iter.hasNext()){
> Object obj_key = iter.next();
> // for debugging
> System.err.println("c"+ props.get(obj_key));
> }
> ...
> }
>
> Normally the line System.err.println() in the end of the code snippet
> gives a lot of different stuff, e.g. References ....
> But if I wrap it in Java Webstart, the only property that is there is:
>
> cCopyright Ak Gasteiger, University of Erlangen-Nuernberg, Germany
>
> Any idea what might be the problem? Shouldn't the engine tell me
> somehow if something didn't work?
>
> Thanks for your help in advance
> Regards,
> Tobias
>
>
> --
> Dipl.-Bioinf. Tobias Girschick
>
> Technische Universität München
> Institut für Informatik
> Lehrstuhl I12 - Bioinformatik
> Bolzmannstr. 3
> 85748 Garching b. München, Germany
>
> Room: MI 01.09.042
> Phone: +49 (89) 289-18002
> Email: tobias.girsch...@in.tum.de <mailto:tobias.girsch...@in.tum.de>
> Web: http://wwwkramer.in.tum.de/people/girschic
>
>
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