Upgrading Jchem table from 2.4.3 to

User 95285039c0

28-03-2009 15:14:31


I have just upgraded to IJC and after restart the application IJC started to regenerate the previous Jchem table.

It takes too long time. I have ~1500 rows, and the process is still running for 2 days and the regeneration process ratio is 65%.

Is it normal?


ChemAxon fa971619eb

28-03-2009 15:18:32

No this is not normal.

Regenarion of that number of structures would usually only take a minute of so.

The usual reason for slow regeneration is when you have added lots of chemical terms columns that involve complex (slow) calculations. Could this be the reason?


User 95285039c0

28-03-2009 15:33:20


Not really, there are just a few chemical terms such as iupac name.

Have you any other idea?

ChemAxon fa971619eb

28-03-2009 15:40:45

Well, any one of the calculations could be causing the problem, but the majority are typically very fast.

Another cause could be if you have applied some standardization rules to the JChem table, but again these do not normally cause a problem.

I would check to make sure that the process is still running. Click on the small progress bar in the bottom right corner and it will pop up a window showing the exact progress. I this is still moving forward then I would leave it to complete and then investigate the cause afterwards. There is nothing that can really be done while it is running.


User 95285039c0

28-03-2009 15:45:29

This is the best what we can do, as I could realise.

I am waiting for the end of the process.

Thank you for remarks.

After the process will end i will report you the chemical terms used in the database.


User 95285039c0

01-04-2009 18:16:54


Finally, after almost 4 days the update was done successfully. 1800 records and one 2 chemical terms, Iupac name and bioavailability.

And, so far now there is licence conflict. The chemical terms fileds say unlicensed calculator plugin.

Have you any idea why?



ChemAxon fa971619eb

01-04-2009 18:22:59

Which license is it saysing is missing?

The regenerations should certainly not take anything like that amount of time. It should be jsut a few minutes for that number of structures.

Are you abe to send us the structures so that we can examine this (they can be sent privately if this helps)?


User 95285039c0

01-04-2009 18:38:33

All kind of Chemical terms (except the basics like molecular mass, composition) I try to add to the schema seems to not licensed.

Unfortunately I'm not able to send the database.

ChemAxon fa971619eb

01-04-2009 18:56:07

Do you have licenses for the calcuator plugins you need?

You would not have been able to add the iupac name or bioavailability fields without them.

Look in Help->Licenses to see what licenses you have, and to load your license file if they are not present.


User 95285039c0

01-04-2009 19:02:08

OK, It works now.

I wondered that if i updated the license file with the license manager it is enough.

I was wrong.



ChemAxon fa971619eb

13-05-2009 08:36:30

We found a possible casue of this slow regeneration that you should investigate prior to updating again.

We found a bug in the current version that can result in chemical terms columns not being deleted from the database. This happens when you delete multiple chemical terms columns in one session. Only the first will be correctly deleted and any other ones would be left in the database, but removed from use in IJC. One consequence of this would be that the chemical terms values would be recalculated when the JChem tables are udpated, and if there were many of these it could explain why the table regeneration was so slow. This may have affected you if you had added and deleted lots of chemical terms columns.

To examine this open the schema editor and show the unused columns for each of the JChem entities. Do this by toggling the "Filter unused database artifacts" button in the schema editor toolbar (its the second last icon). If you see some columns that look like they are chemical terms columns then promote them to a field and then delete them. See the attached screenshot.  LOGP and TPSA are such columns (the columns begining with CD_ are NOT chemical terms columns and do not need attention).

Note, because of the bug you will need to delete them one at a time, disconnecting and reconnecting each time!.

If this was the case then the next time the tables need regenerating it should be much faster.

The bug is fixed in the upcomming 2.5 release.