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:[email protected]] > Sent: Wednesday, August 04, 2010 10:23 AM > To: Nick Vandewiele > Cc: [email protected] > 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 <[email protected]> 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 >> >> > ---------------------------------------------------------------------------- > -- >> The Palm PDK Hot Apps Program offers developers who use the >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> of $1 Million in cash or HP Products. Visit us here for more details: >> http://p.sf.net/sfu/dev2dev-palm >> _______________________________________________ >> Cdk-user mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> >> > > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user -- 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 ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
