Exception in ConformerPlugin

Hi


I am trying to generate conformers for Amantadine with Jchem 3.2.1.


The methode run of ConformerPlugin is failing in the following code





try {


CPlugin.setMolecule(d2);


CPlugin.setMaxNumberOfConformers(50);


CPlugin.setPrehydrogenize(true); CPlugin.setOptimization(ConformerPlugin.OPTIMIZATION_NORMAL);


CPlugin.setLowestEnergyConformerCalculation(false);


CPlugin.setTimelimit(2400);


CPlugin.setDiversity(0.1);


System.out.println("before run");


CPlugin.run();


System.out.println("after run");


conf = CPlugin.getConformers();


} catch (PluginException e) {


System.out.println("Plugin Exception");


e.printStackTrace();


}





with





before run


Exception in thread "main" java.lang.AbstractMethodError: java.lang.Exception.getMessage()Ljava/lang/String;


at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:295)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)


at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)


at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1484)


at chemaxon.marvin.modelling.build.FragFragFuser.nextFuse(FragFragFuser.java:770)


at chemaxon.marvin.modelling.build.FragFragFuser.invokeBuild(FragFragFuser.java:410)


at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:289)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)


at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)


at chemaxon.marvin.modelling.build.FragClean$MultiFragBuildCommand.build(FragClean.java:664)


at chemaxon.marvin.modelling.build.FragClean.startClean(FragClean.java:98)


at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:1438)


at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)


at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3203)


at chemaxon.struc.Molecule.clean(Molecule.java:590)


at chemaxon.marvin.calculations.ConformerPlugin.calculateConformers(ConformerPlugin.java:418)


at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:251)








The exception isn't catch, even if a "general" Exception catch is used instead of PluginException





Any clue ?

I have also an exception on Chlorothiazide. Trapped but an error occurs














ERROR! Exception: 3 >= 3


This build will report FAIL, exception not thrown.


java.lang.ArrayIndexOutOfBoundsException: 3 >= 3


at java.util.Vector.elementAt(Vector.java:432)


at chemaxon.marvin.modelling.build.FragFragFuser.nextFuse(FragFragFuser.java:971)


at chemaxon.marvin.modelling.build.FragFragFuser.invokeBuild(FragFragFuser.java:410)


at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:289)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)


at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)


at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1484)


at chemaxon.marvin.modelling.build.FragFragFuser.nextFuse(FragFragFuser.java:770)


at chemaxon.marvin.modelling.build.FragFragFuser.invokeBuild(FragFragFuser.java:410)


at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:289)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)


at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)


at chemaxon.marvin.modelling.build.FragClean$MultiFragBuildCommand.build(FragClean.java:664)


at chemaxon.marvin.modelling.build.FragClean.startClean(FragClean.java:98)


at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:1438)


at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)


at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3203)


at chemaxon.struc.Molecule.clean(Molecule.java:590)


at chemaxon.marvin.calculations.ConformerPlugin.calculateConformers(ConformerPlugin.java:418)


at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:251)

We are examining the problem and will answer you soon in details.





Best regards,


Zsolt

Hi


Any update on this problem ?


Thanks


Fabien

Hi Fabien,





It has been fixed in the development version and will arrive in the next release.





Best wishes,





Ödön

FTillier wrote:

Hi Any update on this problem ? Thanks Fabien