FROM CSV TO SDF

Groups Cheminformatics
1

Hello,

I've obtained a csv file from Chembl containing molecular smiles, molecule name  and activity information and I would like to convert it in an sdf file. Is there a more rapid method than extracting smiles --> converting them into sdf --> append columns with name and activity? 

Thanks a lot

2

One way to do this would be to use the OpenBabel node to convert SMILES input to SDF/MDL Mol format.  The workflow would consist of CSV Reader -> OpenBabel -> SDF Writer.

Hope this helps.

 

Tim

3

Ok, thanks a lot.

4

Another option would be to send the SMILES cell into an RDKit coordinate generator node, select whether you want 2D or 3D coordinates, and then use the RDKit to Molecule node to convert the RDKit molecule cell to an SDF cell.

Best,

-greg