RDKit Two Component reaction indexes


Is there an easy way to use reactant identifiers supplied with the reagent structures to index the products, instead of the standard ‘0_0’ etc.? So if I supply say A01, A02 etc. for reactant 1 and B01, B02 for reactant 2, the products would be named A01_B01, A01_B02, etc.

Grateful for any tips!


Hi Evert,
This is not currently possible directly from the node. It is possible to make it work by adding a few additional nodes to the workflow, but that solution is pretty ugly. If you’re interested I can post an example.
I’ve created a feature request for the RDKit reaction nodes themselves to enable this option and will try to get it into the next release of the nodes.

Hej Greg,

Being able to select a provided column for each reactant as index would be a nice enhancement to the node.

I can imagine a workaround involving extensive looping right now, but maybe you had something else in mind, so I would certainly appreciate to see your method.



I managed to do a workaround by adding numeric index columns to each list with reactants, several joins, and a Java snippet to generate the product indices. Bit cumbersome admittedly, so having this option built into the RDKit node would be nice.

All the best/Evert

Here’s my workaround;it does the join using canonical SMILES, which is a bit easier than the index column and adds a column that is at least not completely useless. :slight_smile:
Two Component Reaction.knwf (29.5 KB)

1 Like

Very nice solution, thanks for the tip!


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