CDK still supported? Molecule to cdk node fails to convert

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1

Using Molecule to CDK node always just returns:

WARN Molecule to CDK 3:14 Format conversion failed.

For all rows and these are all valid molecules. Same happens when using the Molecular Properties node directly.

This is all with newest versions. KNIME 5.4.4

EDIT:

this is what I get for all rows:

image

Data is loaded from database as molfile and converted to molecules with Molecule type cast.

When I create a trivial test workflow like Table Creator → Molecule to CDK it works but not in my actual use-case. I can load say 10 molecules from the database, convert them to smiles in knime and the Molecule to CDK node fails. when I copy these 10 exact same SMILES into a table creator node, then it works (in a different workflow, just realized it fails as well in this same workflow)

2

It seems cdk can’t deal with molfile v3000 and once the node breaks due to this, it fails to recover even when changing input to SMILES. the only fix is to delete the node and add it back 100% fresh wthout any state

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