Technical Support Forum Index
Technical Support Forum
Access ChemAxon scientists and developers here. For registration and login issues contact website support.

Support Ticket System is replacing forum

This forum was converted into a searchable archive. You cannot add posts here any more. For support please use our new Ticket System.

Create your first ticket
Stereoisomer Count problem with CXCALC
To watch this topic for replies  Register (enables digests) or give email address:
This topic is locked: you cannot edit posts or make replies.
Display posts from previous:   
    View previous topic :: View next topic    
Author Message
Stephen

Joined: 21 Nov 2011
Posts: 3

View user's profile

Back to top
Link to postPosted: Tue Mar 17, 2015 12:49 pmPost subject: Stereoisomer Count problem with CXCALC Reply with quote

I've been having some problems with the calculation of properties for a series of molecules using CXCALC.

I've tracked it down to the following molecule: CCOC(=O)C=C=C

which causes CXCALC stereoisomercount to fail.

The calculation aborts even with the -g flag set, interrupting the calculation for the rest of the file.

Error report as shown below.

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$1.call(Worker.java:45)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
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:9279)
        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)
        (...)

László
ChemAxon personnel
Joined: 14 Jan 2011
Posts: 78

View user's profile

Back to top
Link to postPosted: Wed Mar 18, 2015 3:51 pmPost subject: Reply with quote

Hi,

Which version of Marvin do you use? This bug was fixed a few months ago.

Best regards,
Laszlo 

Stephen

Joined: 21 Nov 2011
Posts: 3

View user's profile

Back to top
Link to postPosted: Thu Mar 19, 2015 9:40 amPost subject: Reply with quote

Hi Lazlo,

I'm running 6.3.2.

Best, Steve.

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

View user's profile

Back to top
Link to postPosted: Thu Mar 19, 2015 10:55 amPost subject: Reply with quote

Hi, 

As this issue was fixed a long ago, we highly suggest that you update your current version to the latest. You shouldn't encounter this issue there.

Best regards, 

Daniel

This topic is locked: you cannot edit posts or make replies.
Page 1 of 1


To watch this topic for replies   Register (enables digests) or give email address  
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You cannot download files in this forum