The dialog cannot be opened for the following reason: No column in spec compatible to "RDKitMolValue" "SdfValue" or "SmilesValue

Hey,

I try to generate 3D coordinates from SMILES string, but neither "RDKit Generate Coords" nor "Molconvert" from Marvin works. Both nodes claim, there is no compatible columns, although there is a propper column.

Here a minimal workflow to reproduce the error:

Take "ChEMBLdb Connector" search for CHEMBL25 search type "compoud".

The search gives you Aspirin:

CHEMBL25    ASPIRIN    Aspirin,Bayer Extra Strength,8-Hour Bayer,Ecotrin, ...... No    C9H8O4    CC(=O)Oc1ccccc1C(=O)O ...

so, the table contains the field smiles with a simles code of Aspirin.

Now, linking it with the above-mentioned nodes gives and trying to configure it gives :

The dialog cannot be opened for the following reason: No column in spec compatible to "RDKitMolValue" "SdfValue" or "SmilesValue"

I tried to rename the column smiles to SmilesValue, but this did not solve the problem.

 

Any idea what could go wrong here?

thanks

 

The column is of type string even if it contains Smiles. You need to user the Molecule Type Cast node in order to change the column's type to Smiles.

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Thanks BTW,

that helped!

This post helped me as well.

Thanks!

This really helped. Thanks a lot.

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