Exception in Clean3D. Failed structure [leconformer]

User 317f3868f4

30-10-2015 09:56:59

Hello,

I have been experiencing some errors in Clean3D invoking Cxcalc (
leconformer).  Please see below.


Also, perhaps some spell checks of your error messages are in order:

"Consystency error in FragmentStore: conformer count mismatch"  # <-- [Consistency] 


Please advise. Thanks!


Enrique

====================== 


Exception in Clean3D. Failed structure:BrC1=CC2=CN=COC3=CN=CC3=NC(O1)=N2


java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: java.lang.ArrayIndexOutOfBoundsException: 12


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:241)


at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:367)


at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)


at chemaxon.marvin.modelling.build.FragClean.startCleanOnSingleFragment(FragClean.java:194)


at chemaxon.marvin.modelling.interfacing.InvokeFFFBuildCalculation.invoke(InvokeFFFBuildCalculation.java:40)


at chemaxon.marvin.modelling.interfacing.MultifragMoleculeAdapter.invoke(MultifragMoleculeAdapter.java:49)


at chemaxon.marvin.modelling.interfacing.CxnMoleculeAdapter.invoke(CxnMoleculeAdapter.java:53)


at chemaxon.marvin.modelling.interfacing.InvokeCalculation.invoke(InvokeCalculation.java:28)


at chemaxon.calculations.clean.Clean3D.modfunc_0(Clean3D.java:859)


at chemaxon.calculations.clean.Clean3D.optimization3D(Clean3D.java:362)


at chemaxon.calculations.clean.Cleaner.cleanMolGraph(Cleaner.java:265)


at chemaxon.calculations.clean.Cleaner.cleanMol(Cleaner.java:329)


at chemaxon.calculations.clean.Cleaner.clean(Cleaner.java:63)


at chemaxon.marvin.calculations.ConformerPlugin.calculateLowestEnergyConformer(ConformerPlugin.java:586)


at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:388)


at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:91)


at chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit.call(ReusablePluginWorkUnit.java:65)


at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:73)


at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:58)


at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:50)


at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(WorkUnitWorker.java:51)


at chemaxon.util.concurrent.processors.WorkUnitWorker.work(WorkUnitWorker.java:36)


at chemaxon.util.concurrent.worker.Worker$1.call(Worker.java:45)


at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)


at java.util.concurrent.FutureTask.run(FutureTask.java:138)


at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)


at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)


at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)


at java.util.concurrent.FutureTask.run(FutureTask.java:138)


at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)


at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)


at java.lang.Thread.run(Thread.java:662)


Caused by: java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: java.lang.ArrayIndexOutOfBoundsException: 12


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:241)


at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:306)


at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)


at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:757)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.nextConformer(FragFragFuseBuildCommand.java:470)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeFuse(FragFragFuseBuildCommand.java:3840)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:228)


... 32 more


Caused by: java.lang.UnsupportedOperationException: java.lang.ArrayIndexOutOfBoundsException: 12


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:241)


at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:306)


at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)


at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:757)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.nextConformer(FragFragFuseBuildCommand.java:470)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeFuse(FragFragFuseBuildCommand.java:3840)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:228)


... 39 more


Caused by: java.lang.ArrayIndexOutOfBoundsException: 12


at chemaxon.marvin.modelling.build.fafuse.FragmentAtomFuseItem.doRICT(FragmentAtomFuseItem.java:1723)


at chemaxon.marvin.modelling.build.fafuse.FuseBuilder.makeCoords2_0(FuseBuilder.java:765)


at chemaxon.marvin.modelling.build.fafuse.FuseBuilder.makeCoords2(FuseBuilder.java:284)


at chemaxon.marvin.modelling.build.DirectFragmentBuildCommand.invokeClean(DirectFragmentBuildCommand.java:150)


at chemaxon.marvin.modelling.build.DirectFragmentBuildCommand.invokeBuild_0(DirectFragmentBuildCommand.java:287)


at chemaxon.marvin.modelling.build.DirectFragmentBuildCommand.invokeBuild(DirectFragmentBuildCommand.java:236)


at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)


at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:306)


at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)


at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:757)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.nextConformer(FragFragFuseBuildCommand.java:




Exception in Clean3D. Failed structure:BrC1=CC2=CN=COC3=CN=CC3=NC(O1)=N2




java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: java.lang.ArrayIndexOutOfBoundsException: 12




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:241)




at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)




at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:367)




at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)




at chemaxon.marvin.modelling.build.FragClean.startCleanOnSingleFragment(FragClean.java:194)




at chemaxon.marvin.modelling.interfacing.InvokeFFFBuildCalculation.invoke(InvokeFFFBuildCalculation.java:40)




at chemaxon.marvin.modelling.interfacing.MultifragMoleculeAdapter.invoke(MultifragMoleculeAdapter.java:49)




at chemaxon.marvin.modelling.interfacing.CxnMoleculeAdapter.invoke(CxnMoleculeAdapter.java:53)




at chemaxon.marvin.modelling.interfacing.InvokeCalculation.invoke(InvokeCalculation.java:28)




at chemaxon.calculations.clean.Clean3D.modfunc_0(Clean3D.java:859)




at chemaxon.calculations.clean.Clean3D.optimization3D(Clean3D.java:362)




at chemaxon.calculations.clean.Cleaner.cleanMolGraph(Cleaner.java:265)




at chemaxon.calculations.clean.Cleaner.cleanMol(Cleaner.java:329)




at chemaxon.calculations.clean.Cleaner.clean(Cleaner.java:63)




at chemaxon.marvin.calculations.ConformerPlugin.calculateLowestEnergyConformer(ConformerPlugin.java:586)




at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:388)




at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:91)




at chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit.call(ReusablePluginWorkUnit.java:65)




at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:73)




at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:58)




at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:50)




at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(WorkUnitWorker.java:51)




at chemaxon.util.concurrent.processors.WorkUnitWorker.work(WorkUnitWorker.java:36)




at chemaxon.util.concurrent.worker.Worker$1.call(Worker.java:45)




at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)




at java.util.concurrent.FutureTask.run(FutureTask.java:138)




at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)




at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)




at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)




at java.util.concurrent.FutureTask.run(FutureTask.java:138)




at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)




at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)




at java.lang.Thread.run(Thread.java:662)




Caused by: java.lang.UnsupportedOperationException: java.lang.UnsupportedOperationException: java.lang.ArrayIndexOutOfBoundsException: 12




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:241)




at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)




at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:306)




at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)




at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:757)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.nextConformer(FragFragFuseBuildCommand.java:470)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeFuse(FragFragFuseBuildCommand.java:3840)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:228)




... 32 more




Caused by: java.lang.UnsupportedOperationException: java.lang.ArrayIndexOutOfBoundsException: 12




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:241)




at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)




at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:306)




at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)




at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:757)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.nextConformer(FragFragFuseBuildCommand.java:470)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeFuse(FragFragFuseBuildCommand.java:3840)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:228)




... 39 more




Caused by: java.lang.ArrayIndexOutOfBoundsException: 12




at chemaxon.marvin.modelling.build.fafuse.FragmentAtomFuseItem.doRICT(FragmentAtomFuseItem.java:1723)




at chemaxon.marvin.modelling.build.fafuse.FuseBuilder.makeCoords2_0(FuseBuilder.java:765)




at chemaxon.marvin.modelling.build.fafuse.FuseBuilder.makeCoords2(FuseBuilder.java:284)




at chemaxon.marvin.modelling.build.DirectFragmentBuildCommand.invokeClean(DirectFragmentBuildCommand.java:150)




at chemaxon.marvin.modelling.build.DirectFragmentBuildCommand.invokeBuild_0(DirectFragmentBuildCommand.java:287)




at chemaxon.marvin.modelling.build.DirectFragmentBuildCommand.invokeBuild(DirectFragmentBuildCommand.java:236)




at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:609)




at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:306)




at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:891)




at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:757)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.nextConformer(FragFragFuseBuildCommand.java:470)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeFuse(FragFragFuseBuildCommand.java:3840)




at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:228)




... 46 more




Clean failed.




BrC1=CC2=CN=COC3=CN=CC3=NC(O1)=N2




Br[#6]-1=[#6]-[#6]-2=[#6]-[#7]=[#6]-[#8]-[#6]-3=[#6]-[#7]=[#6]-[#6]-3=[#7]-[#6](-[#8]-1)=[#7]-2 9169 "leconformer: No valid conformer or structure generation failed."




470)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeFuse(FragFragFuseBuildCommand.java:3840)


at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:228)


... 46 more


Clean failed.


BrC1=CC2=CN=COC3=CN=CC3=NC(O1)=N2


Br[#6]-1=[#6]-[#6]-2=[#6]-[#7]=[#6]-[#8]-[#6]-3=[#6]-[#7]=[#6]-[#6]-3=[#7]-[#6](-[#8]-1)=[#7]-2 9169 "leconformer: No valid conformer or structure generation failed."

ChemAxon d51151248d

30-10-2015 12:02:09

Hi, 


Thank you for reporting this issue. We managed to reproduce it and will fix it as soon as our priorities let us.


Best regards, 


Daniel