Re: [Cdk-user] StructureDiagramGenerator error?

[Christoph S. <ste...@eb...>]

Hi again,

sorry, I should have been more constructive: So your options are to
assist the release manager (still Egon) in fixing this, or to wait until
he does it.
In any case, please file a bug report!

Cheers,

Chris

On 04/08/2010 21:40, Christoph Steinbeck wrote:
> Sure.
> The thing is: things break (it's their nature :-)) and then get fixed
> again by volunteers, like erverything here is done by volunteers.
> That stuff all used to work and broke at some point.
> 
> Cheers,
> 
> Chris
> 
> On 04/08/2010 19:33, Nick Vandewiele wrote:
>> Jules,
>>
>> Thanks for the answer.
>> Is there a reason why the source distribution misses some files compared to
>> the compiles jar files? My ignorant thinking would argue that when you
>> compile some files and wrap them in a jar, you could also just add to the
>> source distro too, no?
>>
>> I am asking this, because that I encountered similar stuff with the
>> cdk-jchempaint renderer features that also required a cdk jar, instead of
>> just the source files.
>>
>>
>> Nick VANDEWIELE
>>
>> -----Original Message-----
>> From: Jules Kerssemakers [mailto:J.K...@cm...] 
>> Sent: Wednesday, August 04, 2010 10:23 AM
>> To: Nick Vandewiele
>> Cc: cdk...@li...
>> Subject: Re: [Cdk-user] StructureDiagramGenerator error?
>>
>> Hello Nick,
>>
>> Looks like you are using the 1.2.5. version compiled from source.
>> I encountered the same problem, it comes from the fact that a few
>> template files used by the SDG are not included in the source
>> distribution, but they are included in the ready-made jar from
>> sourceforge.
>> This is already known, and should be fixed soon.
>> The exception you see printed is not fatal, your program should
>> complete normally.
>> It just looks very bad because there's a debugging
>> "System.err.println(); ex.printStackTrace();" that was accidentally
>> left in.
>>
>> here's how to fix it:
>> A) for very lazy people:
>> - Get the full CDK jarfile from sourceforge
>> - use that instead of the manually compiled cdk-from-source jarfile
>> - fixed!
>>
>> B) if you can't use A because you've made changes to the cdk-source:
>> - Again get the full CDK jarfile from sourceforge
>> - open it and find the subfolder "/org/openscience/cdk/layout/templates/"
>> - copy that folder with contents to the same place in the jar-file you use
>> - fixed!
>>
>> The templates are used by the SDG to neatly layout some idiotic
>> substructures like adamantane and cubane, which looks ugly otherwise,
>> they are not necessary for 'normal' structures.
>>
>> Cheers!
>> Jules
>>
>>
>> On 3 August 2010 17:29, Nick Vandewiele <Nic...@ug...> wrote:
>>> Hi,
>>>
>>> When using StructureDiagramGenerator.setMolecule(IMolecule) method in the
>>> code snippet below, it produces a  NullPointerException mentioned below.
>> I’m
>>> using cdk1.2.5, although I encountered the same in the cdk1.3.5 branch.
>> What
>>> am I doing wrong here?
>>>
>>> Thanks in advance,
>>>
>>> IMolecule triazole = MoleculeFactory.make123Triazole();
>>> StructureDiagramGenerator sdg = new StructureDiagramGenerator();
>>> sdg.setMolecule(triazole);
>>>
>>> Reason: null
>>> java.lang.NullPointerException
>>>       at java.io.Reader.<init>(Reader.java:61)
>>>       at java.io.InputStreamReader.<init>(InputStreamReader.java:55)
>>>       at
>>>
>> org.openscience.cdk.layout.TemplateHandler.loadTemplates(TemplateHandler.jav
>> a:98)
>>>       at
>>> org.openscience.cdk.layout.TemplateHandler.<init>(TemplateHandler.java:83)
>>>       at
>>>
>> org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(StructureDi
>> agramGenerator.java:131)
>>>
>>>       at
>>>
>> org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(StructureDi
>> agramGenerator.java:221)
>>>
>>>       at pinanol.main(filename.java:69)
>>>
>>>
>>>
>>> Nick VANDEWIELE
>>>
>>>
>> ----------------------------------------------------------------------------
>> --
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>>>
>>
>>
>> ------------------------------------------------------------------------------
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> 

-- 
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640; Mobile +44 7826 522319

Video meliora proboque deteriora sequor.
                ... Ovid, Metamorphoses VII, 20/21