Join fragments to template


I am looking for a node that allows to combine molecules and fragments.

For example, to build a librarie of compounds out of some small fragments.

Interesting would be a possibility to give a template with some rest groups, like:


and then add the fragments to this template.

Do you know nodes/extentions that can do that?

best regards




Rdkit one and two component reaction nodes should be sufficient.

i'm not sure if it will work with R1 and R2 groups, you may need to change them to real atoms like I, Br, or At for instance, but may be worth a try initially.

you will then use the Marvin sketcher node to draw a reaction showing this template and two reagents going to the product with atom mapping. Feed this reaction into the rdkit one or two component reaction node. 

Hope it helps


Thats of course very interesting!

Are there example reaction files?

Or files with common reaction patterns?

It works! Thank you.

Can you only use one reaction per node?

"Table with reaction values; if there are multiple rows only the first row is considered"


What if you have 100 reactions? Would you genereate 100 nodes?

It only processes one reaction row.

however you can process each reaction row by inserting a chunk loop start node just prior to the rdkit reaction component node where the reactions are fed into the node and a loop end node just after.

hope it helps simon.