psa calculation error (for multi component molecules?)

User d664bc87ea

09-11-2012 17:14:35

./marvinbeans/bin/cxcalc 'C1(C2C=CC=CN=2)=C(CCN)C2C(=C(C=CC=2)Br)N1.Cl[H]' psa -H 7.4



Cl[H].NCCC1=C(NC2=C(Br)C=CC=C12)C1=NC=CC=C1    1            "java.lang.ArrayIndexOutOfBoundsException: -1\n    at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)\n    at chemaxon.marvin.plugin.CalculatorPlugin.restoreExplicitHydrogens(CalculatorPlugin.java:1741)\n    at chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin.getMajorMicroSpecies(MajorMicrospeciesAccessorPlugin.java:147)\n    at chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin.createModifiedInputMolecule(MajorMicrospeciesAccessorPlugin.java:127)\n    at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:852)\n    at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:799)\n    at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:777)\n    at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:760)\n    at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.setInput(PluginWorkUnit.java:72)\n    at chemaxon.marvin.Calculator$CalculatorWorkUnit.setInput(Calculator.java:341)\n    at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:58)\n    at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:51)\n    at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(WorkUnitWorker.java:51)\n    at chemaxon.util.concurrent.processors.WorkUnitWorker.work(WorkUnitWorker.java:36)\n    at chemaxon.util.concurrent.worker.Worker$1.call(Worker.java:45)\n    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)\n    at java.util.concurrent.FutureTask.run(FutureTask.java:166)\n    at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)\n    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)\n    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)\n    at java.util.concurrent.FutureTask.run(FutureTask.java:166)\n    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)\n    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)\n    at java.lang.Thread.run(Thread.java:679)\n"


 


marvin version: 5.11.3


it's weird that MarvinView doesn't throw the exception.


also, if you don't specify the pH parameter it works correctly.

User d664bc87ea

09-11-2012 17:17:15

also worth to mention that the same thing worked with version 5.10.2

User 851ac690a0

09-11-2012 20:12:35

Hi,


 


Thank you for reporting this bug.


The fix can be expected in Marvin 5.11.5.


Jozsi

User d664bc87ea

25-11-2012 22:08:04

it seems 5.11.4 fixed this as well. thx!