error logD

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

-1

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.calculations.pka.IntrinsicIonization.setCarboAmidHBond(IntrinsicIonization.java:8068)

at chemaxon.calculations.pka.IntrinsicIonization.setHBondTable(IntrinsicIonization.java:5585)

at chemaxon.calculations.pka.Ionizer.calcStartValues(Ionizer.java:2114)

at chemaxon.calculations.pka.Ionizer.initMsCalculation(Ionizer.java:1956)

at chemaxon.calculations.pka.Ionizer.calcMicroSpecies(Ionizer.java:1012)

at chemaxon.calculations.training.logp.LogDPredictor.calclogD(LogDPredictor.java:281)

at chemaxon.calculations.training.logp.LogDPredictor.predict(LogDPredictor.java:334)

at chemaxon.marvin.calculations.logDPlugin.run(logDPlugin.java:575)

at chemaxon.marvin.plugin.DemoCalculatorPluginRunner.runPlugin(DemoCalculatorPluginRunner.java:187)

at chemaxon.marvin.plugin.DemoCalculatorPluginRunner.runPlugin(DemoCalculatorPluginRunner.java:171)

at chemaxon.marvin.plugin.DemoCalculatorPluginRunner.runPlugin(DemoCalculatorPluginRunner.java:92)

at chemaxon.marvin.plugin.DemoCalculatorPluginRunner.run(DemoCalculatorPluginRunner.java:58)

at chemaxon.marvin.plugin.CalculatorPluginRunnerImpl.run(CalculatorPluginRunnerImpl.java:62)

at chemaxon.marvin.plugin.CalculatorPluginManager.callback(CalculatorPluginManager.java:73)

at chemaxon.marvin.plugin.PluginManager.callback(PluginManager.java:95)

at chemaxon.marvin.common.swing.MolPanel$4.run(MolPanel.java:3881)

Oracle Corporation Java 1.8.0-ea

please help me,

Best Regards,

Hi, 

I can't see the attached SD file you mentioned. Can you attach it?

Thanks, 

Daniel

dszisz wrote:

Hi,  I can't see the attached SD file you mentioned. Can you attach it? Thanks,  Daniel

I can't attach it.

can you help me without this especially file?

I'm so sorry. 

Hi, 

No, because we can't reproduce and investigate the error without knowing what caused it. Are your molecules confidential?

Daniel

Hi, 

Thank you for this bug report. We managed to reproduce it, and will fix it soon.

Daniel

Thank you so much.

Regards,

Vahideh

Hi, 

I have taken a look at your molecule, and the error is because your molecule contains incorrect functional groups with aromatic bonds, e.g. an ester group with an aromatic bond (that causes a valence error), or a amide group (plane) with an aromatic bond. This causes the logD plugin to crash. 

I suggest that you correct your structure and try the calculation again. However, we will improve the plugin's ability to handle this type of error. 

I hope this helps, 

Daniel

Hi, 

We have fixed this issue. The fix is already available in Marvin version 16.10.10.

Daniel

Thanks for your supporting.

Regards,

Vahideh