Chemical Transformation not working as expected


I'm using your Chemical Transformation node and using the same reaction files that I have successfully used for the Indigo nodes but they don't work for RDKit.

I am trying to transform R-O-Na into R-O- Na+ and I have Rxn/RD Reader attached to Molecule Type Cast going into Chemical Transformation node.

I get no reaction but yet when I have this same Rxn file linked to Indigo a transformation successfully occurs.

Maybe I am doing something wrong but I've done what the node description says.




Oh and when I create daylight smarts from this exact rxn, instead of getting Na+ and -OR, all I get as the output is Na+! I lose the other half of the compound. 


Hi Louisa,

There are a couple of things going on here.

1) The Chemical Transformation node is really expecting the products to have a single molecule. You should use unbalanced reactions and leave the Na out of the products.

2) There may be a bug when I use the RXN output coming from Marvin Sketch in the Chemical Transformation node (there is certainly something I don't understand). This is demonstrated in the attached workflow, which shows that the RXN works using the One Component Reaction node, but not using the Chemical Transformation Node. We'll look into that.

Note that if you ask the Marvin Sketch node to provid SMARTS instead of a RXN, the Chemical Transformation node works fine (at least it seems to).



Hi Greg, I used SMARTS and got the same. I have found a (not very good) workaround for now.