error logD

User db3b08bf3a

30-09-2016 08:48:58

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)


Product Version:

MarvinView 16.9.12.0

 
Build Date: 2016.09.13

 
Internal build id: 

16.9.12.0-master-5636


Operating System: 









amd64 Windows 7 6.1


 



Java: 








Oracle Corporation Java 1.8.0-ea

please help me,


Best Regards,

ChemAxon d51151248d

30-09-2016 11:50:54

Hi, 


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


Thanks, 


Daniel

User db3b08bf3a

30-09-2016 12:29:14










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. 

ChemAxon d51151248d

30-09-2016 12:55:08

Hi, 


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


Daniel

ChemAxon d51151248d

03-10-2016 09:04:40

Hi, 


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


Daniel

User db3b08bf3a

03-10-2016 14:22:30

Thank you so much.


Regards,


Vahideh

ChemAxon d51151248d

04-10-2016 13:48:25

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

ChemAxon d51151248d

11-10-2016 12:58:28

Hi, 


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


Daniel

User db3b08bf3a

02-11-2016 16:19:42

Thanks for your supporting.


Regards,


Vahideh