Chris, Thanks for the answer. Thus, the bottomline is that those missing source files are just bugs, and not deliberately left out.
Nick VANDEWIELE -----Original Message----- From: Christoph Steinbeck [mailto:[email protected]] Sent: Thursday, August 05, 2010 12:25 PM To: [email protected] Subject: Re: [Cdk-user] StructureDiagramGenerator error? 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:[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(TemplateHand >> ler.jav >> a:98) >>> at >>> org.openscience.cdk.layout.TemplateHandler.<init>(TemplateHandler.java:83) >>> at >>> >> org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(Stru >> ctureDi >> agramGenerator.java:131) >>> >>> at >>> >> org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(Stru >> ctureDi >> 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 ------------------------------------------------------------------------------ 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
