Fragmentation node


Can you add a node with the RECAP functionality present in the RDkit? and if is it possible add a   customization by SMART string of the rules to cut the molecules?


There are some practical challenges associated with getting the RECAP (and BRICS) code into a knime node, but nothing that's not solvable.

How should the output table(s) be structured to make it useful? Two obvious possibilities:

  1. the same thing as the current molecule fragmenter and have one table with the fragments and their counts and another with the original molecules and the indices of the fragments
  2. the same thing as the R group decomposition, with a series of output columns


dear Greg,

I think that could be usefull to have a table with original molecules and fragments and the count of them  ... maybe the output colud be an sdf tha could you use to view the chemica space of the fragments.


Dear Greg,

Any updates on this?

FYI if anyone is interested in this you can create a python script taking cli parameters and then call it with the external tools (Labs) node. In my case the script fragments and rebuilds molecules. The external tools node then reads back in the newly generated molecules into a new column (like Molecule#1 or so). You then need to filter the initial source molecules out of the table (eg. everything that has missing value in Molecule#1)