Error Converting Excel file to SDF file

How do I convert the attached excel file “sample_data.xlsx” to a sdf file. I keep getting the following error when I try converting my excel file to an sdf file.

sample_data.xlsx (10.0 KB)

Thank you,
Anas Hussain.

In the MolConverter node are you making sure to set an output format of MDL SDfile as shown here? The SDF Writer is complaining because it’s not finding expected column types in its input port.

2020-09-21 14_23_10-Dialog - 0_391 - MolConverter


It’s really impossible to say without seeing the way you’ve configured the nodes, or the seeing the outputs of the previous nodes.

I just uploaded my knime workflow(kinme_project14) to the knime public server. Could you help me out.

Thank you.

  1. You didn’t tell the Excel Reader node that the first row of the table contains table headers. This will be a problem later downstream.
  2. The Molecule Type Cast node is currently set to lookup the string in Col2, which has no SMILES data, and therefore results in an empty column
  3. The MolConverter node must be set to output SD formatted data, as @ScottF mentioned

In the future, please provide a Hub link to the workflow.


thank you, that solved the problem

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