Error: module 'rdkit.Chem' has no attribute 'Mol'


I´m using Flare Docking node (Cresset) to perform some dockings. However, it halts with the following message:

ERROR Flare Docking 4:6 Execute failed: Error (exit code 255) : Error (exit code 255) running
Error (exit code 255) running

Error: module ‘rdkit.Chem’ has no attribute ‘Mol’

---- Exception Information For Developers ----

Traceback (most recent call last):
File “/apps/cresset/Flare/bin/…/pyflare-scripts/”, line 68, in main
project, ligands_to_dock_role = _configure_process(docking, args)
File “/apps/cresset/Flare/bin/…/pyflare-scripts/”, line 379, in _configure_process
role.ligands.extend(flare.read_file(args.reference, _find_format(args.reference, args)))
AttributeError: module ‘rdkit.Chem’ has no attribute ‘Mol’

I got Knime 4.7.5 and RDKit 2022.09.3. Linux LT 20.04 as OS

Any ideas of what can cause this situation and how to sort it?

Thanks a lot,



can you send a Community Hub link to that node? I don’t find it.
Additionally it is quite unclear what you are doing, could you provide an example workflow please? Is that part of the Schroedinger extension? Maybe @Schroedinger has a clue?


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I´m trying to run a docking experiment, providing a ligand line (sdf) a docking grid (based in the previous ligand, sdf) and a receptor (pdb). Node halts with aforementioned message. Attached wf image.

Ah, Schrödinger is not the maintainer. I suggest contacting the maintainers of that extension.

Best regards

Thanks @steffen_KNIME.

Maintainers were unable to provide a satisfactory solution via knime. Thta´s why I´m consulting it here…

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