Reaction Automapper and Combinatorial Node Bug

Hi Mikhail,

Many thanks for the continuing development of the Indigo nodes, its very much appreciated, and they are coming along really well, and quite exciting with the increased reaction support.

I have noticed a bug in the Reaction Automapper node in that selecting the "Highlight Reacting Centre" doesnt appear to do anything when I view the output, nothing appears to be highlighted.

In the Combinatorial Reaction Enumeration node, I have input a reaction of Benzoic Acid and Methyl Amine producing the corresponding Amide product which first went through the Reaction Automapper node, the Automapper looks good. In the two reagent input ports, I have 3 benzoic acids and 3 amines, so theoretically I should see 9 products, however the output from the enumeration node gives 18, everything appears to be doubled up.




Hi Simon,

The new option 'Highlight Reacting Centers' in the Reaction Automapper changes the reacting centers (Make/Break, Change, Make/Break/Change). Therefore, you should see only single lines (bond was changed) or double lines (bond was made or broken) intersected bonds. There are no centers if a bond was not changed. Could you specify the reactions which were tested.

Thanks for the notes about the Combinatorial Reaction Enumeration node. We will check the issue and will try to resolve it ASAP.

With best regards,


Hi Alexander,

The reaction I was using was; PhCO2H + EtNH2 going to PhCONHEt.

The Reaction Automapper correctly labels all the atom numbers but it does not show which bonds are being broken/created with a double line.

I am using the latest nightly build of Indigo nodes.