Can jcman be used to import rxnfiles of rdfiles into a mysql

User 1a3b6cd85b

07-02-2011 22:50:06

Is there a way to use jcman to import rdfiles or rxnfiles into a jchem-mysql table (i.e. a rxn database)? If not, is there some commandline utility to help?

ChemAxon e274e1bada

08-02-2011 14:32:40

Hi Steve,


You can import RXN or RDF files to reaction type or any type table. In addition we provide reaction search if you import mapped reactions. Note we have auto-mapper for non mapped reactions, but it is under refactoring.


See the relevant chapter of the admin guide: http://www.chemaxon.com/jchem/doc/admin/#create />and the  guide for reaction search: http://www.chemaxon.com/jchem/doc/user/query_reactionsearch.html


Regards, Edvard

User 1a3b6cd85b

08-02-2011 23:29:50

Thanks! My rdfile was not importing because I had an empty $DATM field. I just added date text and we are good to go!


One variant on the original question - I like the  --nodup option, which seems to report the cd_id of the duplicate structure. Is there a way to get jcman to show the cd_id assigned to the rxn that was loaded?

ChemAxon e274e1bada

10-02-2011 11:55:09

Hi Steve,


unfortunately jcman cannot give back the imported cd_id-s, just the molecules with the --nonduplicates option.
I can add this request to the JChem 5.5 or 5.6 tasks and I will notify you if it is released.


Regards, Edvard

User 1a3b6cd85b

14-02-2011 03:26:58

Thanks - in the meantime, I;ll just run it twice, and get the cd_id report from the second run ;) Not efficient, but effective....

User c1ce6b3d19

14-02-2011 12:19:56

Steve,


I'm glad you could find a way that works for you for now. 


Jon