ChemicalTermsUpdateHandlerException when importing

Hello, I work at the University of Pretoria, and am trying to import the Drugbank SDF file with JChemManager.

I've added a few columns to the table that I've created, namely "donor_count", "acceptor_count", "ring_count", "rotatable_bond_count", "rule_of_five", "lead_likeness" and "bioavailability" that are linked to the functions that their names imply.

When I try to import the SDF file (that worked fine before I added the columns), it stops at molecule number 3, and throws this error:

java.util.concurrent.ExecutionException: chemaxon.util.concurrent.processors.WorkUnitException: chemaxon.jchem.db.ChemicalTermsUpdateHandlerException: Error for column RING_COUNT with structure structure = 136...

Does anyone have any advise?

Thank you

Jeanré Smit

 

Could you share the structure 136 with us?

Zsolt

Okay so the error doesn't occur on that molecule anymore, but on the first molecule it encounters. But the molecule it has problems with shouldn't matter, because it throws this exception with any SDF file I've tried (e.g. Chembl). I have attached the error window.

Please post here the Chemical Terms expression used in LOG_D column definition. Please post also the sdf source of at list one failing molecule (screenshot is not enough, we cannot use it for reproducing the error).

Zsolt

The expression is simply the built-in logD() function. The SDF's can be obtained from Chembl or Drugbank, e.g. http://www.drugbank.ca/system/downloads/current/structures/all.sdf.zip

"logD()" function does ot work without pH, see the documentation. Use "logD('7.4')", where '7.4' is the pH, or "logP()" instead.

Zsolt

Granted, that was stupid, but I think that exception could've been a bit clearer...

In any case, now that logD doesn't throw an exception, ringCount() does (around molecule 800 of Drugbank) and as far as I can tell, ringCount() doesn't take parameters.

Yes, ringCount() works without parameters. Please attach the molecule.

Zsolt

Like I've said before, I'm importing all of Drugbank's molecules and the address of the file I'm trying to import I already gave...

Jeanré,

Thanks for you information you provided so far.  It would help us to quickly isolate the issue if you already have the problem structure in hand and give it to us.  This would also help us get a solution or workaround to you faster. 

 

Thanks,

Jonathan Lee

As far as I can tell it's this molecule giving problems:

The issue is not related to Chemical Terms, the molecule cannot be imported. We will examine the error.

Zsolt

The molecule is a polimer (it contans SRU sgroup), that's why ring count cannot be calculated. It contains n*4 rings, n cannot be determined.

Zsolt