After compiling the latest CDK version I succeed with the CDK/Jmol integration. But when loading a molecule (small or protein) I get an annoying "Cannot return notional unit cell params: no Crystal found" error message. What's the origin of this? Can I do something about it?
Regards, .../Ola On Fri, 2004-11-12 at 21:13, Egon Willighagen wrote: > 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 ------------------------------------------------------- This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS DOWNLOAD - A multidimensional database that combines robust object and relational technologies, making it a perfect match for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8 _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
