I am using RDKit to transform SMILES strings into SDF representations of Molecules. The problem is, that for compounds containing heteroaromatic cycles with one or more Nitrogens the conversion fails.
I tried it with direct conversion from SMILES via the RDKit to Molecule node, there he creates empty input cells.
Using the RDKit from Molecule node he fails to create RDKit Molecules if for the sanitization “reperceive aromaticity” is ticked. Unfortunately the conversion with the RDKit to Molecule node still fails for the 20 molecules.
I am not sure if there is something going wrong in RDKit itself or if its just the KNIME nodes, I would love to use RDKit in the future as it is open source and has amazing functionality, so it would be great to get some advice on how to handle such structures.
I have attached the Structures along with the Error column.
Otherwise I am using KNIME 3.5.2 with Ubuntu 16.04 LTS
Ill gladly provide more information if needed.
RDKIT_error_from_SMILES.txt (2.1 KB)