dear all,


how can cluter the murcko scaffold and remove the duplicate?

Convert structures to Canon Smiles (Canonicalised or Unique Smiles) and then use the GroupBy node and group by smiles,and aggregate on all the other columns as "First Value" and choose to keep original column names.

To get Canon Smiles,you can use the RDKit Canon Smiles or also use Indigo to Molecule node.

Hope that helps,


For completenesses sake: the RDKit to Molecule node also creates canonical smiles if you ask it to generate smiles as the output format.


How to you get from smiles back to an SDFile. Smiles were generated with RDKit Canon Smiles?  I tried OpenBabel and a SDFWriter, but could not get it to work.


Well you can go back to RDKit again with Mol to RDKit, and then from RDKit to Mol and specify SDF.

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