Embedding molecules with fixed coords seems to be broken #1
Description
This may be an upstream bug in RDKit.
Embedding molecules using convenience_structures.pdb_to_mol does not seem to work properly. Specified coordinates are ignored, and are not fixed.
Currently, this code works by creating an RDKit EmbedParams struct and adding a coordMap argument. Replacing the EmbedMolecule call with the alternative function signature (using arguments vs supplying a struct) enables fixed coords, but I'm unsure of the implications for coordinate generation - can ETKDGv2 still be used?