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Chemaxon PKA (java exception occuring) [message #2416] Wed, 28 May 2025 13:24 Go to next message
jeffchem is currently offline  jeffchem
Messages: 1
Registered: May 2025
Junior Member
Hi DataWarrior folks.

I'm having an issue with the Chemaxon PKA calculation.

I'm trying to calculate the higest basic pKa; ChemAxon method under the Ionization section.
a) I have chemaxon license.
b) I am using the capka.jar (downloaded from Chemaxon site)
c) cLogD at ph=7.4; via logP and ChemAxon pKa works fine.

When I run DataWarrior from the command line and print to a log file. DataWarior.exe > out.txt
I can see that there is an exception occuring in the java code.
Unexpected ChemAxon Exception:java.lang.NoSuchMethodError: 'void chemaxon.marvin.calculations.pKaPlugin.setMolecule(chemaxon. struc.Molecule)'

Has anyone else encountered this issue? Any work arounds?

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Re: Chemaxon PKA (java exception occuring) [message #2418 is a reply to message #2416] Fri, 30 May 2025 14:38 Go to previous message
thomas is currently offline  thomas
Messages: 731
Registered: June 2014
Senior Member
it looks like DataWarrior doesn't find the capka.jar when you start from the command line. If you launch datawarrior_xxx.jar from the command line on any platform, then you could add the capka.jar to the class path. If you just start DataWarrior.exe on Windows, you should make sure that the working directory for DataWarrior is the installation directory...

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