Bond block sections in the SDF

User c29d691f4a

16-06-2015 20:22:08

Greetings all,

  My name is Chris.  I export the chemical catalog
I manage from Instant Jchem in SDF format and supply the data to third party data hosts.  One of the hosts recently complained "we have received
customer reports of erroneously represented structures in your catalog. We have
found the errors to originate from the bond block sections in the SDF, in most
instances denoting
 four bonds between
atomic members of a molecule," and further "the problem is that by
using bond type 4, which denotes an atom in an aromatic, is that it would force
our system to deduce the bond type [1-3]. It is best to have a defined
structure that way there is no guesswork or additional computation. Whatever
program you are using to export to SDF, does not include these structure
definitions for aromatics and defaults to bond type 4 instead. Can you
please reference or contact support for the software you are using and find out
if you can export using explicit bonds?"

Some of my data I enter manually, some from JChem for Excel where I use
various manipulations to loosely mimic Reactor-type functionality, and some data
comes from outside sources in mixed aromatic/Kekule formats. 
I have Standardizer working so I can easily find duplicates between
the various structural representations when importing data.  I understand Standardizer doesn’t change
the inherent data, only the way it is displayed.  Is there a way I can permanently dearomatize all my data (as the standardizer can aromatize) and/or export it dearomatized?

  Many thanks for your time and effort on my behalf.


ChemAxon 26d92e5dcd

17-06-2015 14:22:26

Dear Chris,

thank you for reporting this to us. You understand correctly. Standartizer in IJC does not modify the data in the database,  Standardizer defines in memory structure representation which is used for searching and displaying the structure. This information is stored elsewhere in the database in the associated metadata. You can see this forum thread.

During export, the structure used, is pulled directly from the database table containing the structure, where it is stored in the same way as it was in the source files used for import. By default, IJC shows the structures in the same way as they are in the database, so to see the structure standartised, you have to select that option in the structure rendering widget, as seen in attached screenshot.

As a workaround, I would suggest using stand alone Standartiser on your exported SDF files as described here. Standartiser can be downloaded as part of JChem Suite, available here

What would probably help, would be a possibility to use Standartisation as an extra option during export. I will file a feature request, but I can not promise a delivery of such feature in the nearest future.


I hope this helps with your problem.

Wishing all the best