logd errors

User d664bc87ea

23-08-2012 18:05:54

Hi,


 


Molecules in the attached sdf all fail when it comes to logd calculation with mview or cxcalc.


 


MarvinView produces the same Stack Trace for all of them:


ERROR:
Cannot run plugin: logD
4

STACK TRACE:
java.lang.ArrayIndexOutOfBoundsException: 4
    at chemaxon.calculations.pka.BasicPKa.getAvarageAliphaticRingCharge(BasicPKa.java:1212)
    at chemaxon.calculations.pka.BasicPKa.getAliphaticBasicpKa(BasicPKa.java:1543)
    at chemaxon.calculations.pka.BasicPKa.getNitrogenBPKa(BasicPKa.java:176)
    at chemaxon.calculations.pka.BasicPKa.calculate(BasicPKa.java:74)
    at chemaxon.calculations.pka.IntrinsicIonization.getBpKa(IntrinsicIonization.java:1275)
    at chemaxon.calculations.pka.IntrinsicIonization.getBasicpKa(IntrinsicIonization.java:260)
    at chemaxon.calculations.pka.Ionizer.getMicropKa(Ionizer.java:1174)
    at chemaxon.calculations.pka.Ionizer.calcSpeciesRatio(Ionizer.java:3195)
    at chemaxon.calculations.pka.Ionizer.calcSpeciesOrder(Ionizer.java:3378)
    at chemaxon.calculations.pka.Ionizer.calcMsDistribution(Ionizer.java:3541)
    at chemaxon.calculations.training.logp.LogDPredictor.calclogD(LogDPredictor.java:285)
    at chemaxon.calculations.training.logp.LogDPredictor.predict(LogDPredictor.java:325)
    at chemaxon.marvin.calculations.logDPlugin.run(logDPlugin.java:512)
    at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:200)
    at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:184)
    at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:107)
    at chemaxon.marvin.plugin.CalculatorPluginManager.callback(CalculatorPluginManager.java:77)
    at chemaxon.marvin.plugin.PluginManager.callback(PluginManager.java:92)
    at chemaxon.marvin.common.swing.MolPanel$6.run(MolPanel.java:3828)


 


Product Version: MarvinView 5.10.3
Build Date: 2012-08-13
Internal build id: 5.10.3_b102
Operating System: amd64 Linux 3.0.0-19-generic
Java: Sun Microsystems Inc. Java 1.6.0_23

ChemAxon e08c317633

30-08-2012 09:59:23

Hi,


This error will be fixed in Marvin 5.11 version.
Thanks for the report.


Zsolt