HPuntu/DynaMode ? reverse-engineered prompt

Build me this protein dynamics project so I can train and run inference on protein structures from a checkpoint.

I want to be able to give it a PDB file and a temperature, then have it generate a 256 frame trajectory and save the aligned first frame plus the trajectory output. It should also support training from mdCATH data, with Hydra style config files for the model, data, diffusion, training, sampling, and inference settings. Please make the default model the spectral diffusion one from the README, and keep the transformer baseline and the SHAKE variant available too.

If it helps, you can look up any current docs online while wiring up the training and inference commands. I also want the project to be easy to install in editable mode, run on one GPU or multiple GPUs, and resume from the latest checkpoint in a run directory.