Substructure Match node - reaction handling?

Hi,

First of all, apologies if this has already been covered somewhere - but if it has, I couldn't see it!

I have been very impressed so far with the reaction capabilities in Indigo, which have started to appear in the KNIME nodes.  It looks like everything is almost in place to do reaction searching in KNIME - is the plan to allow the current "Substructure Matcher" node to handle Indigo Reactions and Indigo Query Reactions in the same way as the Indigo.substructurematcher and IndigoObject.match methods work in the toolkit via eg python?

I guess along the same lines, it would make sense for the Substructure Match Counter to handle reaction objects / reaction queries as well(?)

Kind regards

James

Hello James,

We will definitely add a support of reactions in Substructure Matcher and Substructure Match Counter node. This task didn't get high priority, because we didn't understand if it is interseting for the community or not. Because there was even no default readers for the reactions in KNIME. But after your request, we will add it soon. Thank you for the interest.

With best regards,
Mikhail

That's great news, Mikhail - thanks!  On your point about the lack of default readers - I completely agree that these are required.  Thanks to the Erl Wood 'Chemical Reactions File Reader', it is possible to read in RD files and RXN files using open source tools.

However, as the RXN data type is now supported within KNIME, I think it would be good to settle on 'standard' RDF reader and writer nodes - analogous to the SDF reader and writer.  At the moment, there is no easy way to export an RDF file - so this would be VERY useful functionality for the community as well.

Certainly all of the necessary functionality appears to already be there in the Indigo toolkit for reading / writing RD files!

It may be that the Lilly guys have already worked on this(?), or that there are plans already underway with the KNIME developers for standard RDF reader and writer nodes(?)

 

Kind regards

James

Hello James,

We have added a reaction support to the Substructure Match node! And to other manipulators nodes like aromatizer, hydrogen adder, and etc.

You can update Indigo nodes from the nightly builds.

PS: Substructure Match Counter node doesn't support reactions in this version, but we are working in this direction too.

Best regards,
Mikhail