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averagemicrospeciescharge error
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Zoltán

Joined: 20 Jul 2012
Posts: 9

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Link to postPosted: Sat Nov 10, 2012 3:49 pmPost subject: averagemicrospeciescharge error Reply with quote

./marvinbeans/bin/cxcalc 'CC(=O)NC1=CC=C(C=C1)C1=C(C#N)C(N)=NC2=C1CC1=C2C=CC(O)=C1' averagemicrospeciescharge

 

CC(=O)NC1=CC=C(C=C1)C1=C(C#N)C(N)=NC2=C1CC1=C2C=CC(O)=C1        1

"java.lang.ArrayIndexOutOfBoundsException: 0
  at chemaxon.calculations.pka.AcidicPKa.getIonizedSideInc(AcidicPKa.java:2188)
  at chemaxon.calculations.pka.AcidicPKa.getOHAcidicpKa(AcidicPKa.java:1860)
    at chemaxon.calculations.pka.AcidicPKa.getAlcoholicAcidicpKa(AcidicPKa.java:89)
        at chemaxon.calculations.pka.AcidicPKa.calculate(AcidicPKa.java:72)
   at chemaxon.calculations.pka.IntrinsicIonization.getApKa(IntrinsicIonization.java:782)
 at chemaxon.calculations.pka.IntrinsicIonization.getAcidicpKa(IntrinsicIonization.java:246)
   at chemaxon.calculations.pka.PKaLargeModel.getProteinMicropka(PKaLargeModel.java:1863)
 at chemaxon.calculations.pka.PKaLargeModel.calcProteinMicropKa(PKaLargeModel.java:1644)
        at chemaxon.calculations.pka.PKaLargeModel.calcMicropKa(PKaLargeModel.java:888)
       at chemaxon.calculations.pka.PKaLargeModel.reCalcAtomSet(PKaLargeModel.java:606)
       at chemaxon.calculations.pka.PKaLargeModel.calcProteinIonization(PKaLargeModel.java:456)
      at chemaxon.calculations.pka.PKaLargeModel.calcMacropKa(PKaLargeModel.java:2458)
       at chemaxon.calculations.pka.PKaLargeModel.calcChargepHDist(PKaLargeModel.java:3052)
  at chemaxon.calculations.pka.PKaLargeModel.calcIsoelectricPoint(PKaLargeModel.java:3229)
       at chemaxon.marvin.calculations.IsoelectricPointPlugin.run(IsoelectricPointPlugin.java:276)
    at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
      at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
   at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:59)
   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:334)
 at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
     at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
 at java.util.concurrent.FutureTask.run(FutureTask.java:166)
   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
     at java.lang.Thread.run(Thread.java:679)
"
id      Charge
1       averagemicrospeciescharge:FAILED

 

some SMILES that also fail:

CC(=O)NC1=CC=C(C=C1)C1=C(C#N)C(N)=NC2=C1CC1=C2C=CC(O)=C1

C12C3C=CC(=CC=3CC=1C(=C(C#N)C(N)=N2)C1=CC=C(CO)O1)O

C1(=C(C#N)C(N)=NC2C3=C(C(=CC=C3)O)CC=21)C1C(C)=NNC=1C

 

cxcalc version: 5.11.3

Jozsef
ChemAxon personnel
Joined: 25 May 2004
Posts: 568

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Link to postPosted: Mon Nov 12, 2012 11:05 amPost subject: Reply with quote

Hi,

Thank you for reporting this bug. The fix  will be available in the 5.11.4 release asap.

Jozsi

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