RDKit One Component Reaction


I seem unable to get this "RDKit One Component Reaction" node to work.

If I input an RDKit column of structures to the top port and Rxn column to the bottom port, when I run the node I get the error "ERROR RDKit One Component Reaction Execute failed: No such column in input table: Molecule (RDKit Mol)"

I dont understand this, as the column is there in the input table. If I change the column name of the RDkit structures to "Molecule A" then the same error appears only now the error says "Molecule A" at the end.

Also instead of inputing a Rxn column to the bottom port, if I generate a SMARTS reaction cell and convert this to a variable and insert it via the variable port, and then select this column in the flow variables tab under "Reactionsmarts" the node also fails reporting "No reaction smarts provided".

Am I doing something wrong ?


Also when using the "Two Component Reaction node", this works better but there still seems to be issues.

1. If I use the Marvin Sketcher and output as a Rxn cell format, the node works as expected.

2. If I use Marvin Sketcher and output as a Smarts cell, and then use "TableRow To Variable" and input this into the node via the flow variables tab, I get the error "Reaction Should Have One Reactant, It has: 2"

I must be doing something wrong!


Hi Simon,

As you've discovered, there's a pretty serious bug in the version of the One Component Reaction node that's in svn. Thanks for pointing it out; we'll get it fixed.

With the Two Component Reaction node: Marvin will not generate Reaction SMARTS correctly (it's an RDKit format), so the approach using the flow variable doesn't work. To use the Marvin node, you should ask it to generate Rxn format and use the optional third input port.


Thanks, I look forward to the fix.


I have also noticed that if I uninstall RDKit, and put on the stable release of RDKit, the bug is present in that release also. So I guess the stable release version will need fixing too.



Hi Simon,

Thanks for reporting this issue. This was my fault (in fact a very stupid one). Unfortunately at the same time we also changed the procedure for stable releases this is why the error ended up in the stable branch. The good news: everything should be fixed by tomorrow morning.



Hi Greg,

Many thanks for the quick bugfix, the One Component Reaction node is now working as expected.



Thanks Thorsten!

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