baker-laboratory/rf_diffusion_all_atom ? reverse-engineered prompt

Build me a working inference app for the RFDiffusion AA project so I can generate new protein backbone designs around a ligand or a short protein motif from a PDB file.

I want to be able to point it at an input structure, choose a ligand or residue range to keep fixed, set the output length, number of designs, and number of diffusion steps, then get back PDB files for the final design plus the intermediate denoising trajectory. Please make it easy to run from the command line with a simple one line command, and keep it compatible with the container based setup described in the repo. If anything depends on current setup details, check the latest docs online and make it work cleanly. Also include clear example commands for a ligand only binder and a ligand plus protein motif binder, using the sample inputs already in the repo.