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.