Conversion of v2000 format to v3000 format

Hi,

We are storing the respective v2000 format for all our compounds in a database column (Oracle), and want to convert all to v3000 format.  Please suggest if there is any utility that can be used or any best practices that should be considered for this conversion.

Regards

RG

Hi Raju,

 

You can either:

1. Export your structures as an SDFile, use molconvert to convert it to MOLV3000 (Extended) SDFile using the "mol:v3" option and import it back. See more details for that here: http://www.chemaxon.com/marvin/help/applications/molconvert.html

or

2. Create a copy of your Structure table, and use Marvin/JChem API to load from the original table and overwrite in the new table in MOLV3000 option. See more details here:

- http://www.chemaxon.com/marvin/help/developer/io/import.html#import_api

- http://www.chemaxon.com/marvin/help/developer/io/export.html#export_options

 

But:

Your stereo flags will not be converted to enhanced stereo flags, so there must be additional steps included that handles those..

 

Best regards,

Akos