I have a set of protein fragments (peptides in PDB format). When I use the node Rdkit from molecule, I get the error:
WARN RDKit From Molecule 0:264 Failed to process data due to SDF Parsing Error (GenericRDKitException) - Generating empty result cells. [All rows]
Is there a way to preprocess the input molecule to let the Rdkit node works properly.
NB: I already tried to convert the PDB as input (RDkit Canon smiles and MOE smiles from molecule), but both failed giving this error :
WARN RDKit Canon SMILES 0:266 Auto conversion in column ‘PDB File’ failed: SDF Parsing Error (GenericRDKitException) - Using empty cell. [All rows]
Encountered empty input cell. [All rows]
I am doing this work to be able to generate the RDkit descriptors for my peptides.