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vahideh

Joined: 08 Nov 2015
Posts: 6

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Link to postPosted: Fri Sep 30, 2016 9:48 amPost subject: error logD Reply with quote

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,

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Fri Sep 30, 2016 12:50 pmPost subject: Reply with quote

Hi, 

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

Thanks, 

Daniel

vahideh

Joined: 08 Nov 2015
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Link to postPosted: Fri Sep 30, 2016 1:29 pmPost subject: Reply with quote

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. 

Daniel
ChemAxon personnel
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Link to postPosted: Fri Sep 30, 2016 1:55 pmPost subject: Reply with quote

Hi, 

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

Daniel

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Mon Oct 03, 2016 10:04 amPost subject: Reply with quote

Hi, 

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

Daniel

vahideh

Joined: 08 Nov 2015
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Link to postPosted: Mon Oct 03, 2016 3:22 pmPost subject: Reply with quote

Thank you so much.

Regards,

Vahideh

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Tue Oct 04, 2016 2:48 pmPost subject: Reply with quote

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

Daniel
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Joined: 22 Jan 2012
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Link to postPosted: Tue Oct 11, 2016 1:58 pmPost subject: Reply with quote

Hi, 

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

Daniel

vahideh

Joined: 08 Nov 2015
Posts: 6

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Link to postPosted: Wed Nov 02, 2016 5:19 pmPost subject: Reply with quote

Thanks for your supporting.

Regards,

Vahideh

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