Reintroduce .cif file handling, change fixed residue rotamer sampling behavior

Fixes a small bug that prevented using .cif files as inputs to LASErMPNN.run_batch_inference mode.

Updates the way residues that are fixed with the --fixed_betas flag are handled. Previously, a torch.nan_to_num call would convert any missing dihedral angles to 0.0 to avoid crashing. Now, any available dihedral angles are fixed and new ones are sampled according to their predicted probabilities.