On the molecule input side:
I believe the V3K mol and SDF files should work using normal cell types (so I don’t think we need to change the typecast node). The KNIME-supplied readers should work fine with v3k mol files or SDF files. Then it would be up to the individual chemistry toolkits to be able to parse V3K.
This works at least with the RDKit nodes, I’ve attached a workflow which demonstrates that:
V3K_Mol.knwf (7.2 KB)
Note that there’s not really any obvious way to see that the RDKit has parsed the V3K features (since the current RDKit renderer in KNIME doesn’t show the extended stereo information here), but hopefully you’ll take my word for it that the information is being read in.
Output is a different story. I’m not aware of a way to force output in V3K format. This is an option that we should add to the RDKit nodes, but it’s not currently there.
If you can share a bit more about exactly what you want to do I can either make suggestions or use the information as feedback for the next time we’re working on the RDKit KNIME nodes.