Two-Component Reaction: Empty table or weird enumeration

I'm trying out the 2-component reaction but it seems I have a lack of understand how it works. 

Please see the attached workflow.

I draw a reaction in Marvin Sketch with proper mapping and as Rxn column type. I also have 1 primary reactant (scaffold) and as an example 3 r-groups as SMILES. They are also drawn in a Marvin sketch node. Connecting them to the 2-Component reaction leads to an empty table.

What am I doing wrong?

 

Second point:

On the right side of the attached example workflow, I copy & pasted above node and made some minor changes. First the primary reactant is exported as SMARTS and then converted with the RDKit from Molecule node. Now the Reaction node actually does some reactions. Why? It's the exact same molecule???

Third Point:

 

If I use the products that are created in second point for a second reaction, I get Problem 1 again: Empty table.

How can I resolve this?

 

Hi,

There are a number of problems with the workflow.

  1. The reaction needs to be fully mapped (i.e. all atoms from the reactants that you plan to have in the products should be mapped.
  2. The Marvin nodes need to be configured to provide standard data types like RXN cells (for the reaction) and MOL or SDF cells for the reactants

There's also something wrong with the way the reaction itself is drawn, but this is more difficult for me to fix because I'm not really sure what you're trying to accomplish.

Can you please provide a simple example that has a single set of reactants for the reaction and what you expect the products to be? That may help diagnose things further.

Best,

-greg

Hi Greg,

thanks. I was able to fix part issue one using the Indigo Automapper and changing the reaction.

Can you please provide a simple example that has a single set of reactants for the reaction and what you expect the products to be? That may help diagnose things further.

The goal is a simple enumeration of all the structures. Simple example see attached screenshot how it would be done in ChemDraw.