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ReactionMechanismGenerator / RMG-Java

The Java version of RMG: Reaction Mechanism Generator
http://rmg.sourceforge.net/
MIT License
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ArrayIndexOutOfBoundsException in jing.chem.Species.generateMolFileString(Species.java:1370) #138

Closed rwest closed 13 years ago

rwest commented 13 years ago

This occurred when trying to make the InChI in order to look up a quantum chemistry result. I don't know what the chemgraph in question is because the exception was not caught in such a way as to display it. (error handling could be improved around here; maybe around ChemGraph.getThermoData?)
Anyway, here's the tail of my log:


Created new reaction: C2O4JJ(2596) + CH3O2J(137) --> C3H3O6JJJ(10624)
Pre-existing successful quantum result for ILBZONYSPFNORS-UHFFFAOYAT (InChI=1/C3H6O6/c4-1(5)7-3-8-2(6)9-3/h1-6H) has been found. This log file will be used.
Point group: C1
Thermo for ILBZONYSPFNORS-UHFFFAOYAT: -263.97   101.57  35.86   43.39   49.81   54.96   62.4    67.44   74.85   
java.lang.ArrayIndexOutOfBoundsException: 4
    at jing.chem.Species.generateMolFileString(Species.java:1370)
    at jing.chem.Species.generateInChI(Species.java:1152)
    at jing.chem.ChemGraph.generateInChI(ChemGraph.java:1274)
    at jing.chem.ChemGraph.getModifiedInChIKeyAnew(ChemGraph.java:1574)
    at jing.chem.QMTP.getQMFileName(QMTP.java:2030)
    at jing.chem.QMTP.generateThermoData(QMTP.java:216)
    at jing.chem.ChemGraph.generateThermoData(ChemGraph.java:1300)
    at jing.chem.ChemGraph.getThermoData(ChemGraph.java:1821)
    at jing.chem.Species.findStablestThermoData(Species.java:338)
    at jing.chem.Species.(Species.java:118)
    at jing.chem.Species.make(Species.java:878)
    at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1196)
    at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:232)
    at jing.rxnSys.RateBasedPDepRME.addSpeciesToCore(RateBasedPDepRME.java:317)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:235)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3963)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1452)
    at RMG.main(RMG.java:57)
Exception in thread "main" jing.chem.FailGenerateThermoDataException
    at jing.chem.ChemGraph.generateThermoData(ChemGraph.java:1310)
    at jing.chem.ChemGraph.getThermoData(ChemGraph.java:1821)
    at jing.chem.Species.findStablestThermoData(Species.java:338)
    at jing.chem.Species.(Species.java:118)
    at jing.chem.Species.make(Species.java:878)
    at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1196)
    at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:232)
    at jing.rxnSys.RateBasedPDepRME.addSpeciesToCore(RateBasedPDepRME.java:317)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:235)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3963)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1452)
    at RMG.main(RMG.java:57)
gmagoon commented 13 years ago

fixed bug limiting molFile generation to 4 or fewer radicals

closed by 43e4f35c21efa3d53ca8c6af9172df545f52120f