Are all these structures in the considered differently?

Hi,

I am trying to load few articles which have got some structures in the form or sdf or mol files.

I also have duplicate filtering enabled in my relational database.

When I load the article set for the first time, few structures get created in the structure table.

When I load the same set again, one new structure gets added to the table. Although I was not expecting this to happen.

I have attached the file which I exported from my databse. This contain all the structures which got re-inserted every time I reloaded the same set of articles.

Can you please have a look

Many thanks,

Isha

Hi Isha,

Could you tell us which version of JChem are you using?

Thanks,

Krisztina

Hi Kristina,

I am using version 5.10.4

Thanks,

Isha

I have attached below the sdf file which every time upon getting loaded creates a new structure in the relational database.

Not sure why??

Thank you the data. This operation is really erroneous. We start to find the reason, and will correct as soon as possible.

Best regards,

Krisztina

Hi Kriztina,

Can you please let me know if there is any update on this?

Thanks,

Isha

Hi Isha,

Unfortunately, the problem seems to be more complex than it seem'd to be at the first reproduction. We could not solve it yet, it needs to be prioritized and scheduled into our workflow.

We would appreciate your help to give us further information:

How urgent would be the solution for you? Did you find this bug in production or in evaluation environment?

Do you have any other workaround to filter out duplicate structures? If not, you can try to import in "Markush library" type table; we found that duplicate filtering of the attached EXPORTEDDATA.mrv works better in Markush table.

Best regards,

Krisztina

 

Thanks Krisztina for the update. The concerned team at our end will be looking into this to analyse the impact

of this on our seach results and will let us know if and when this needs to be prioritised. 

I have also recieved a separate explanation in www.chemaxon.com%2fforum%2fviewtopic.php%3fp%3d44582%2344582" target="_blank" style="font-family: monospace; font-size: 13px;">https://www.chemaxon.com/forum/viewtopic.php?p=44582#44582 and have forwarded this to the concerned people.

Isha

Also you suggested to use "Markush library" type table.

Presently we use ANY type table. 

Can you please explain how different are they from each other and if we replace ANY with Markush what sort of changes would we be looking at?

Hi Isha,

Please find information about Markush library type tables in the following documents:

http://www.chemaxon.com/jchem/doc/dev/dbconcepts/index.html#tabletypes

http://www.chemaxon.com/jchem/doc/user/query_markush.html

Best regards,

Krisztina

Hi Krisztina,

It looks like we will need to stick with the ANY table type and cannot go with the MARKUSH ones as we get lot of different types of structures.

Can you please give us an estimated timeline for when do you think this bug could be fixed at the earliest as it seems to be affecting our search results?

When we are running an EXACT match for such structures, it only returns the last one created and so we only get to see the content which has been mapped to it, whereas we expected all the structures to be returned while running an exact match search?

So, it appears the bug is while loading the structure? While searching it only returns the last cd_id created?

Thanks,

Isha 

Hi Isha,

We start to fix the found bugs, and hopefully build the fix in the next patch release. However, could you send us other example structures of erroneous duplicate filtering ? We would like to see preferably all the structure features that may cause the problem.

Thanks,

Krisztina

We have fixed this problem, the correction will be available in the next minor (5.11.2) and major (5.12) releases.

The problem was related to initialization of our search mechanism.

Thanks for the report.

Could you check if the other problem you have reported:

https://www.chemaxon.com/forum/ftopic9552.html

is the same as this one?

Can we close this issue?

Thanks Nora...

 

I think both of them are related. I will wait for fixed release to see if it works at my end.

 

When is it supposed to be released?

 

Thanks,

Isha

The 5.11.2 release will be out in 2 weeks time.