Error with cxcalc and stereoisomers plugin

User 5d66f4118f

28-10-2014 15:39:33

Dear ChemAxon communauty,


I am a new to both ChemAxon and java. I looked in the forum but could not find any answer to my problem.


I am facing two distinct issues when trying to use the plugin stereoisomers of cxcalc.

Here a simple  example to illustrate the problem :
cxcalc -g stereoisomers "C(C)C=C=CO" "O=C([O-])CC1NC(=S)N(c2ccccc2)C1=O"


The expected behavior would be that the stereoisomers from both molecules are sent to the stantdard output, and if something happens for the first molecule, then it gets skipped, but this is not what happens.

First, the plugin fails on the first molecule, which throws the error displayed beneath.
Secondly, even though I specified the "-g" option, the second molecule is not computed by cxcalc.


What I am doing wrong?


Thank you for your help!


Jose Manuel
OS : Centos 6.5
Version of the calculator plugin : 6.3.1


java.util.concurrent.ExecutionException:
chemaxon.util.concurrent.processors.WorkUnitException:
java.lang.StackOverflowError

    at
chemaxon.util.concurrent.processors.WorkUnitData.getResult(WorkUnitData.java:79)

    at
chemaxon.util.concurrent.processors.ScheduledWorkUnitData.getResult(ScheduledWorkUnitData.java:60)

    at
chemaxon.util.concurrent.processors.WorkUnitDataIterator.getNext(WorkUnitDataIterator.java:74)

    at chemaxon.marvin.Calculator.run(Calculator.java:1499)

    at chemaxon.marvin.Calculator.run(Calculator.java:1400)

    at chemaxon.marvin.Calculator.main(Calculator.java:2078)

Caused by:
chemaxon.util.concurrent.processors.WorkUnitException:
java.lang.StackOverflowError

    at
chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:70)

    at
chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:51)

    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.StackOverflowError

    at
chemaxon.calculations.clean.Clean2D.getDesiredBondLength(Clean2D.java:15212)

    at
chemaxon.calculations.clean.Clean2D.getDesiredBondLength(Clean2D.java:15196)

    at
chemaxon.calculations.clean.Clean2D.setXY(Clean2D.java:6666)

    at
chemaxon.calculations.clean.Clean2D.setCoordsForLigands(Clean2D.java:10039)

    at
chemaxon.calculations.clean.Clean2D.setCoordinatesForLigands(Clean2D.java:10095)

    at
chemaxon.calculations.clean.Clean2D.generateCoordinatesBackTrack(Clean2D.java:9214)

    at
chemaxon.calculations.clean.Clean2D.generateCoordinatesBackTrack(Clean2D.java:9301)

    at
chemaxon.calculations.clean.Clean2D.generateCoordinatesBackTrack(Clean2D.java:9279)

    at
chemaxon.calculations.clean.Clean2D.generateCoordinatesBackTrack(Clean2D.java:9279)

    at
chemaxon.calculations.clean.Clean2D.generateCoordinatesBackTrack(Clean2D.java:9279)

    at
chemaxon.calculations.clean.Clean2D.generateCoordinates(Clean2D.java:8755)

    at
chemaxon.calculations.clean.Clean2D.calcInitialGeometry(Clean2D.java:1761)

    at
chemaxon.calculations.clean.Clean2D.cleanFragment(Clean2D.java:1332)

    at
chemaxon.calculations.clean.Clean2D.cleanMoleculeStructure(Clean2D.java:1127)

    at
chemaxon.calculations.clean.Clean2D.clean(Clean2D.java:652)

    at
chemaxon.calculations.clean.Clean2D.clean(Clean2D.java:633)

    at
chemaxon.calculations.clean.Cleaner.cleanMolGraph(Cleaner.java:241)

    at
chemaxon.calculations.clean.Cleaner.cleanMol(Cleaner.java:331)

    at
chemaxon.calculations.clean.Cleaner.clean(Cleaner.java:53)

    at
chemaxon.calculations.clean.CleanerUtil.clean(CleanerUtil.java:28)

    at
chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:5592)

    at
chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:5453)

    at chemaxon.marvin.calculations.StereoisomerPlugin.calculateTetrahedralStereoisomers(StereoisomerPlugin.java:363)

    at
chemaxon.marvin.calculations.StereoisomerPlugin.calculateTetrahedralStereoisomers(StereoisomerPlugin.java:406)

    at
chemaxon.marvin.calculations.StereoisomerPlugin.calculateTetrahedralStereoisomers(StereoisomerPlugin.java:406)
(and so on)

ChemAxon 5fc3e8d7d0

04-11-2014 10:42:31

Dear Jose,


This is a bug in Stereoisomer Plugin. We are planning the complete re-implementation of the plugin.
We will notify you, if the new version is available on the ChemAxon website.


Best regards,
Laszlo