Molfile with haptic bond causes error


I'm reading a set of molfiles into KNIME and calling RDKit from molecule.

An error appears in the UI (Failed to process data due to SDF Parsing Error (GenericRDKitException) - Generating empty result cells. [2 of 8 rows]), plus the associated log message.

A molfile is attached.



That's correct. The RDKit does not correctly support haptic bonds and is unable to parse this particular way of expressing them. The RDKit's support for organometallics is quite rudimentary.

Adding support that would at least allow the files to be parsed without generating an error should be possible, but it's still unlikely that the the code will actually be able to do anything sensible with the molecules.