RDKIT from molecule note does not recognize my smiles codes

Hi There,

New to the platform (tried to find if this question was posted before)
I used CSV reader to inport my Smiles codes and looked that that worked fine.
Now I want to use on of the RDKIT nodes to analyze the data. But the smiles codes are not recognized.
The Error from RDKIT descriptor Calculation → The dialog cannot be opened for the following reason: No column in spec compatiple to “RDKTMolValue”, SdfValue of SmilesValue

I got my smiles from the EPA CompTox Chemicals Dashboard
below a screenshot of the CVS reader output

Hi @nienke_R

Welcome to the KNIME forum.

Since your SMILES are coded as strings when reading them using the CSV node, you need to add an extra node called -Molecule Type Cast- to cast the SMILES before using the -RDKit Descriptors Calculation- node, so that RDKit recognizes them as “molecules” rather than strings.

Hope this helps.

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Thanks. Is this the exact name of the node? because I cannot find it? Does it belong to the RDKit?

Yes, it is the exact node name.

It does not belong to RDKit. It belongs to the “KNIME base Chemistry types & nodes” :

Super will look it up. I hope new things to discover here

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I had to instal the Basic chemical notes first


If you have the types installed you can also use the transformation tab of the CSV Reader to directly read it in as SMILES, which should spare you the typecast node.

Sidenote: With the RDKit extension installed you can change the renderer to show the molecule rather than the string. (You can also change the default in the KNIME preferences under “preferred renderers”)


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