Tobias Girschick wrote:
> 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...
Right, but the engine needs to be redesign to work under JWS and its
classloader behaviour - which is not trivial.
Regards,
Nina
>
> 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] <mailto:[email protected]>
>>> Web: http://wwwkramer.in.tum.de/people/girschic
>>>
>>>
>>>
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>>>
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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] <mailto:[email protected]>
> Web: http://wwwkramer.in.tum.de/people/girschic
>
>
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