sdf > lipinskis

I am doing Chemistry > IO > SDF Reader which reads my file and is happy.

I then send it to Chemistry > cdk > lipinski’s Rof5 which complains:
No CDK compatible column in input table

If I click Configure for Rof5 I get – The dialog cannot be opened for the following reason:
No column in spec compatible to “CDKValue”

Any hints about what tool to read SDFs and send to Lipinski?
Any friendly manual to read?


Hello Margaret,

We obviously need to improve on the error messages. You need to process the output of the SD reader with the “Molecule to CDK” node, which will parse the structures into an appropriate format for the Lipinski node. Reason is that the Lipinski node is contributed from the CDK plugin, so it needs its desired input format.

Let us know if you have further questions.


Thanks for the help. I find: schrodinger > Converters > Molecule to MAE
but can’t find a Molecule to CDK anywhere.

Not under Chemistry > CDK > translators
Chemistry > translators has Molecule Type Cast and OpenBabel

Where should I look? What do I need to add?


Ooops, I found it. Running now.