Technical Support Forum Index
Technical Support Forum
Access ChemAxon scientists and developers here. For registration and login issues contact website support.
FAQFAQ   SearchSearch   DigestsDigests

Support Ticket System is replacing forum

This forum was converted into a searchable archive. You cannot add posts here any more. For support please use our new Ticket System.

Create your first ticket
exception generated when predicting pKa with user trained -
To watch this topic for replies  Register (enables digests) or give email address:
This topic is locked: you cannot edit posts or make replies.
Display posts from previous:   		     View previous topic :: View next topic    
Author Message
Jun

Joined: 01 Dec 2005
Posts: 56

View user's profile
Back to top
Link to postPosted: Fri Mar 18, 2016 1:57 pmPost subject: exception generated when predicting pKa with user trained - Reply with quote

Hi, I got this exception when predicting pKa trained with our own data. If I don't use the trained model, the prediction is fine.

 

"java.lang.ArrayIndexOutOfBoundsException: -1\n    at chemaxon.calculations.pka.IntrinsicIonization.setSemiAraInc(IntrinsicIonization.java:9386)\n    at chemaxon.calculations.pka.IntrinsicIonization.setHBondTable(IntrinsicIonization.java:5428)\n    at chemaxon.calculations.pka.Ionizer.getMicropKa(Ionizer.java:1217)\n    at chemaxon.calculations.pka.Ionizer.calcSpeciesRatio(Ionizer.java:3245)\n    at chemaxon.calculations.pka.Ionizer.calcSpeciesOrder(Ionizer.java:3417)\n    at chemaxon.calculations.pka.Ionizer.calcMsDistribution(Ionizer.java:3651)\n    at chemaxon.calculations.pka.Ionizer.calculatepKa(Ionizer.java:3975)\n    at chemaxon.calculations.pka.Ionizer.calculatepKa(Ionizer.java:3894)\nat chemaxon.marvin.calculations.pKaPlugin.run(pKaPlugin.java:767)\n

 

any idea?

 
Jun

Joined: 01 Dec 2005
Posts: 56

View user's profile
Back to top
Link to postPosted: Fri Mar 18, 2016 2:00 pmPost subject: Re: exception generated when predicting pKa with user trained - Reply with quote
fengjun wrote:

Hi, I got this exception when predicting pKa trained with our own data. If I don't use the trained model, the prediction is fine.

 

"java.lang.ArrayIndexOutOfBoundsException: -1\n    at chemaxon.calculations.pka.IntrinsicIonization.setSemiAraInc(IntrinsicIonization.java:9386)\n    at chemaxon.calculations.pka.IntrinsicIonization.setHBondTable(IntrinsicIonization.java:5428)\n    at chemaxon.calculations.pka.Ionizer.getMicropKa(Ionizer.java:1217)\n    at chemaxon.calculations.pka.Ionizer.calcSpeciesRatio(Ionizer.java:3245)\n    at chemaxon.calculations.pka.Ionizer.calcSpeciesOrder(Ionizer.java:3417)\n    at chemaxon.calculations.pka.Ionizer.calcMsDistribution(Ionizer.java:3651)\n    at chemaxon.calculations.pka.Ionizer.calculatepKa(Ionizer.java:3975)\n    at chemaxon.calculations.pka.Ionizer.calculatepKa(Ionizer.java:3894)\nat chemaxon.marvin.calculations.pKaPlugin.run(pKaPlugin.java:767)\n

 

any idea?

 

Also, this only happens in API call or use cxcalc command line version. If I just paste the molecule within marvin sketch, and do calculation within it, it works fine.

 
Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

View user's profile
Back to top
Link to postPosted: Fri Mar 18, 2016 4:14 pmPost subject: Reply with quote

Hi, 

We would need some molecules that failed to reproduce the error message. Can you send us any? 

We also need to know which version of cxcalc you use.

Thank you very much, 

Daniel
Jun

Joined: 01 Dec 2005
Posts: 56

View user's profile
Back to top
Link to postPosted: Fri Mar 18, 2016 4:39 pmPost subject: Reply with quote
dszisz wrote:

Hi, 

We would need some molecules that failed to reproduce the error message. Can you send us any? 

We also need to know which version of cxcalc you use.

Thank you very much, 

Daniel

Attached a fake molecule, and the trained model. the version is 15.12.14.0
Jun

Joined: 01 Dec 2005
Posts: 56

View user's profile
Back to top
Link to postPosted: Tue Mar 22, 2016 1:35 pmPost subject: Reply with quote
dszisz wrote:

Hi, 

We would need some molecules that failed to reproduce the error message. Can you send us any? 

We also need to know which version of cxcalc you use.

Thank you very much, 

Daniel

Any update? is the problem reproducible on your end? Is the problem already fixed in the newest version? thanks.

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

View user's profile
Back to top
Link to postPosted: Tue Mar 22, 2016 4:32 pmPost subject: Reply with quote

Hi, 

We have managed to reproduce the problem, but we need time to provide fix for that. The problem seems to exist in the newer versions as well. We will fix it ASAP. 

Daniel
Jun

Joined: 01 Dec 2005
Posts: 56

View user's profile
Back to top
Link to postPosted: Tue Jul 19, 2016 2:51 pmPost subject: Reply with quote
dszisz wrote:

Hi, 

We have managed to reproduce the problem, but we need time to provide fix for that. The problem seems to exist in the newer versions as well. We will fix it ASAP. 

Daniel

Hi, any update on this? thanks,

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

View user's profile
Back to top
Link to postPosted: Wed Jul 20, 2016 2:51 pmPost subject: Reply with quote

Hi, 

Our colleague who deals with this issue is on holiday now. We will need some time to sort it out. 

Thank you for your patience. 

Daniel
ChemAxon.com
Forums
Support
Structure based predictions: Calculator Plugins & Chemical Terms
exception generated when predicting pKa with user trained -
This topic is locked: you cannot edit posts or make replies.
Page 1 of 1

To watch this topic for replies   Register (enables digests) or give email address  
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You cannot download files in this forum