Using IJC for conversion

User d2950aa5e4

22-02-2010 08:23:44

I need to convert large reaction databases into flat ones (RDF to SDF), I need to get each individual structure from the RDF with its label and flag where it belongs (reactant, product). I was encouraged by the fact that when I point a MarvinView on RDF, I see exactly the result I would like to get - table with columns for structures and their IDs together with the ID that identifies the record. Indeed it is impossible to export this beautiful arrangement. I hoped that IJC might be suitable tool and tried to create an import template following the fields of my RDF file(s). However, I repeatedly failed to use this template for correct import of the file. I can describe the steps I made but do not know if it is worth bothering the whole audience ? I also tried to create a template considering the input is flat SDF but just text fields were respected, no structures. Questions: is IJC in general suitable tool for this purpose and how shall I specify the steps I made to eventually identify the mistakes ? Thanks.

ChemAxon fa971619eb

22-02-2010 12:51:45

Yes, IJC might well be of use here.

The import of RDF files is problematical as the RDF format is so open, and its very difficult to find a generic way to import any RDF file as they can differ so much in their content.

Would you be able to send a very small sample file that we can examine? With that we should be able to provide some more substantive feedback. Either attach file to this topic, or if it contains data you would prefer not to public then email it directly to me: tdudgeon at chemaxon dot com



ChemAxon fa971619eb

24-02-2010 14:59:01

This subject is being followed up privately.

Essentially IJC is able to import the RDF file into a database, but there is no simple way to export the data to SDF in the required way. This is probably only possible by means of scripts tailored specifically for the task.