ArrayIndexOutOfBoundsException

We see this error in our logs a lot - I don't have an example molecule to duplicate it however.





java.lang.ArrayIndexOutOfBoundsException: 6


at chemaxon.calculations.pKa.getNitrogenBasicType(pKa.java:8356)


at chemaxon.calculations.pKa.setBasicAtoms(pKa.java:8178)


at chemaxon.calculations.pKa.getApKa(pKa.java:839)


at chemaxon.calculations.pKa.getAcidicpKa(pKa.java:138)


at chemaxon.calculations.Ionizer.initMicropk0(Ionizer.java:1175)


at chemaxon.calculations.Ionizer.calcStartValues(Ionizer.java:1134)


at chemaxon.calculations.Ionizer.initMsCalculation(Ionizer.java:1083)


at chemaxon.calculations.Ionizer.calcMicroSpecies(Ionizer.java:419)


at chemaxon.calculations.Ionizer.calculatepKa(Ionizer.java:1898)


at chemaxon.calculations.Ionizer.calculatepKa(Ionizer.java:1884)


at chemaxon.marvin.calculations.pKaPlugin.run(pKaPlugin.java:435)

Hi,





What version of Marvin/JChem are you running?





Best regards,


Zsolt

jchem 3.2.5

Thanks the info. We are checking it.

Hi,





From the exception message you have sent it seems to me you are using an older version of JChem.





Are you sure you are using JChem 3.2.5?





This bug has already been fixed, and it should work in JChem 3.2.5. We have tested the pKa module on a large data set, and we haven't got any "ArrayIndexOutOfBoundsException” messages.





Jozsi

Hi,








May be the "java.lang.ArrayIndexOutOfBoundsException: 6...." message that you obtained from a logs file was created with an older JChem.


Is it possible?





Jozsi