I was on my to convert my molecules to SDF I noticed something strange:
Going from Indigo smiles to SDF using BABEL, there seems to be a problem with valencies. Now, the weird thing is, that converting it back with BABEL to smiles it looks ok again.
This does not occur if I convert my input molecules with Babel directly, or when using e.g. RDKIT and then Babel.
I tried different renderers within Knime, also imported the new sdf file to external viewers confirming incorrect sdf structure.
See the enclosed workflow, check column "IndigoCanon_to_BABEL_SDF" (or see picture).
So somewhere, something seems to be off?
