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

KNIME Analytics Platform
1

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

 

1 Like
2

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.

2 Likes
3

Thanks BTW,

that helped!

4

This post helped me as well.

Thanks!

5

This really helped. Thanks a lot.

1 Like