Reaction Vector data structure

Could you tell me what the data structure is required to be for the database for the reaction vector nodes?



Hi Steve,

Not sure if you are after the db schema or just information about what Db was used, how to configure and what molecule formats?

I have attached a zipped workflow that should help.

The DB we use is the freebie java H2 db from

You need to install the H2 build and tell knime where to find it using file > preferences > knime > db driver > new then add the full path to the jar file. 


Reactions reader (rdf, rxn, smiles)> RV Db Writer > Reaction generator (this node also needs starting material( sketch/smiles)  and reagents (smiles/sdf) if required).

To configure the RV db writer node you need:

db driver : org.h2.Driver                                      protocol: jdbc:h2:

input a name for the create db file. No username or passwd is required.

Take a look at the attached example or I can add a screen shot.


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