Hi Nina,
On Wed, 2009-09-02 at 12:26 +0300, Nina Jeliazkova wrote:
> 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.
I've been thinking of that workaround, too. And I tried it yesterday
with a single descriptor. It seems calculating a single descriptor with
descriptor.calculate(ac) inside the Java Webstart seems to work. The
following example printed out the values fine:
BCUTDescriptor descriptor = new BCUTDescriptor();
Object[] par = { new Integer(3), new Integer(3) , true};
descriptor.setParameters(par);
DescriptorValue retval = descriptor.calculate(ac);
IDescriptorResult val = (IDescriptorResult) retval.getValue();
String[] names = retval.getNames();
if (val instanceof DoubleArrayResult){
DoubleArrayResult ret = (DoubleArrayResult) val;
for (int i = 0; i < ret.length(); i++){
System.out.println(ret.get(0));
}
}
But the engine approach is a much more elegant one...
Regards,
Tobias
> 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: [email protected]
> > Web: http://wwwkramer.in.tum.de/people/girschic
> >
> >
> >
> > ____________________________________________________________________
> >
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> >
>
>
--
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: [email protected]
Web: http://wwwkramer.in.tum.de/people/girschic
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