On Friday 12 November 2004 17:24, Ola Spjuth wrote: > Maybe I have messed something up... I get > > java.lang.NoSuchMethodError: org.openscience.cdk.Atom.getX3d()D > at > org.jmol.adapter.cdk.CdkModelAdapter$AtomIterator.getX(CdkModelAdapter.java >:243) at > org.openscience.jmol.viewer.datamodel.FrameBuilder.buildFrame(FrameBuilder. >java:68) at > org.openscience.jmol.viewer.managers.ModelManager.setClientFile(ModelManage >r.java:81) at > org.openscience.jmol.viewer.JmolViewer.openClientFile(JmolViewer.java:1001) > > > I have included the following jars in my runtime config: > > <library name="jars/CDK/cdk-render.jar"> > <library name="jars/CDK/cdk-apps.jar"> > <library name="jars/CDK/cdk-core.jar"> > <library name="jars/CDK/cdk-experimental.jar"> > <library name="jars/CDK/cdk-extra.jar"> > <library name="jars/CDK/cdk-io.jar"> > <library name="jars/CDK/cdk-standard.jar"> > <library name="jars/CDK/cdk-test.jar"> > <library name="jars/CDK/cdk-libio.jar"> > <library name="jars/Jmol.jar"> > > I thought there was some kind of conflict since Jmol.jar includes a lot > of CDK-packages. Anyway, when I replace Jmol.jar with JmolApplet.jar, > all works fine when I do a viewer.openStringInline with a > SmarterModelAdapter. Can you make any sense of this? > > Well, looking at the classes I see the following inconsistencies (if > that is what they are): > > in my cdk-core.jar: > org.openscience.cdk.Atom: getX2D() > > in Jmol.jar > org.openscience.cdk.Atom: getX2d()
That changed some time ago. See the CDK News 1.2 due tomorrow :) It should be in the ChangeLog article... Jmol.jar is uptodate... but you need to upgrade your CDK libs... the october release of CDK should be fine. > Could this be the answer to this? Yes, I think so. > How should I resolve this? Update your CDK installation. > I might be > using outdate cdk-core.jar but the Jmol.jar is taken from v10beta16... Indeed. > What I would like is to have a Jmol and CDK in separate jars, maybe I > should take the time to build my own Jmol as well... It's CDK that you need to recompile... > Thanks for the help! Ok, please try to update your CDK installation and try again with the same Jmol.jar... and let me know if that improves things. Egon -- [EMAIL PROTECTED] PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 ------------------------------------------------------- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_id=5588&alloc_id=12065&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
