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Exception in Clean3D. Failed structure [leconformer]
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Enrique

Joined: 16 Sep 2014
Posts: 6

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Link to postPosted: Fri Oct 30, 2015 10:56 amPost subject: Exception in Clean3D. Failed structure [leconformer] Reply with quote

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."

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

View user's profile

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Link to postPosted: Fri Oct 30, 2015 1:02 pmPost subject: Reply with quote

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

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