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."