For a project I was really in need of a clean way to convert a RDKit Chem.Mol object to a params file as the way I was making params files was horrid.
So I ended up writing a MIT-licenced python module that can load and save params files and do "surgery" on them or create one from a RDKit Mol object, which can include the dummy atom (*) which becomes a connect entry. It can be used without either rdkit installed (surgery only!) or pyrosetta installed (no testing method).
It was fairly straightforward, so I won't be devastated if someone tells me that you can load a mol file directly in pyrosetta... (I seriously suspect I am doing it wrong given the PDB components library and the chemical submodule in pyrosetta) —is there?
I had to make several guesses with the AtomType allocation, but I think they are mostly right —in the repo's example folder there is a params file generated as a ligand. I did not copy from the mol_to_params.py file because I didn't really want to get into licencing issues. I was actually unaware that there were two forms (aa and generic), so I wrote generic first, found it did not work, and re-did it with the aa form — is there a tag for a params file with generic atom types or a different way to add them to a pose?
I have not released it to pip yet and there are some tweaks needed and I need to do some minor changes (as listed in the repo).
But I thought I best ask in case I get some good suggestions. Thanks!