LogP calculation :: ArrayIndexOutOfBoundsException - Bug?

Dear support,

I have an issue with calculating the logP of a molecule using the Java API. The molecule in question is the following: SMILES: Nc1nc2n(Cc3ccccc3F)nnc2c2nc(nn12)-c1ccco1

The process stops with an ArrayIndexOutOfBoundsException. I attached a test class to this post. is this a bug?

Thank you very much!

Matthias

 

--------------------------------

Error code:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 6
    at chemaxon.calculations.pka.IntrinsicIonization.getHeteroAraNCount(IntrinsicIonization.java:2009)
    at chemaxon.calculations.pka.IntrinsicIonization.isCrossArom(IntrinsicIonization.java:11124)
    at chemaxon.calculations.pka.IntrinsicIonization.getNitrogenBasicType(IntrinsicIonization.java:10120)
    at chemaxon.calculations.pka.IntrinsicIonization.setBasicAtoms(IntrinsicIonization.java:9960)
    at chemaxon.calculations.pka.IntrinsicIonization.getApKa(IntrinsicIonization.java:828)
    at chemaxon.calculations.pka.IntrinsicIonization.getAcidicpKa(IntrinsicIonization.java:261)
    at chemaxon.calculations.pka.Ionizer.initializepKaType(Ionizer.java:2473)
    at chemaxon.calculations.pka.Ionizer.calcStartValues(Ionizer.java:2013)
    at chemaxon.calculations.pka.Ionizer.initMsCalculation(Ionizer.java:1930)
    at chemaxon.calculations.training.logp.LogPPredictorImpl.isMacropKaCalcRequiredBylogP(LogPPredictorImpl.java:288)
    at chemaxon.calculations.training.logp.LogPPredictorImpl.createIonizer(LogPPredictorImpl.java:579)
    at chemaxon.calculations.training.logp.LogPPredictorImpl.predict(LogPPredictorImpl.java:263)
    at chemaxon.calculations.training.AtomicContributionBasedPredictor.predictWithError(AtomicContributionBasedPredictor.java:180)
    at chemaxon.calculations.training.logp.LogPPredictorImpl.predictWithError(LogPPredictorImpl.java:743)
    at chemaxon.marvin.calculations.logPPlugin.run(logPPlugin.java:547)
    at databasepreparation.LogPTest.<init>(LogPTest.java:46)
    at databasepreparation.LogPTest.main(LogPTest.java:52)

Hi,

 

Yes, this was a bug.Thanks for reporting.

The fixed version is available in the  6.1.1 bug fix release. 

Jozsi

Thanks for the prompt answer, Jozsi!

Is this version already released?

 

Best,

Matthias

Hi,

Yes.

There was a bug fix release.

 

Jozsi

Could you provide me with a download link, please. I am somehow unable to find it on the webpage.

Cheers,

Matthias

Hi,

 

Here is the  "download" site:

http://www.chemaxon.com/download/

 

A short info about the latest release: 

http://www.chemaxon.com/marvin/help/developer/changes.html

 

Jozsi

That`s where I went looking for version 6.1.1, yes. :) But I could only find a download for the 6.1.0 release...

Hi,

 

Oh,I am sorry.   Yes, a funny thing happened. The 6.1.1 release have been rolled back and will not be released. I have been informed by the release coordinator stuff.

The 6.1.2 fix will be released asap instead of the 6.1.1.!

 

Jozsi