Error using RDKit One Component Reaction node


I am having an issue using the One Component Rxn Node (on works PC BTW, I havent magically fixed it on the MAC yet).

If I draw a reaction transformation using the Marvin Sketcher node, and then pass this into the RDKit node as a RXN type into the second port it works great, until I use some of the specific query handles. For example using the (u) flag for unsaturated then results in an error in the RDKit node;

ERROR RDKit One Component Reaction Execute failed: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Unable to parse reaction value found in the table.



Hi Simon,

The RDKit's rxn parser isn't able to deal with all query features. You could be hitting that, but I wouldn't necessarily expect it to lead to an error like this.

Can you attach either the .rxn output that's causing the problem or the workflow?


That would be difficult, unfortunately, but I will try and come up with a model system to demonstrate it.


Hmm, since I restarted the PC, the query is now working with these advanced query flags. I will keep an eye on it, and get back to you if this issue resurfaces.