updating plddt and pae loss calculation to consistent with the reported plddt and pae outputs #103
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* Update README.md * Update README.md * typo * typo * Update README.md * adding initial code from Shihao * cleanup (#91) * mpnn: moving decoding_order logic from sample.py/score.py to model.py * mpnn: moving notebook logic to model.py * mpnn: Update proteinmpnn_in_jax.ipynb to avoid recompiling if shapes are the same * increasing default traj_max from 500 to 10000 * adding option to specify custom traj for animate() * Update model.py * adding pandas dataframes :D * typo * Update utils.py * adding option to display any design * Update proteinmpnn_in_jax.ipynb * removing broken code * minor edits to make mpnn standalone * minor edits to avoid recompiling mpnn when rm_aa is updated * cleanup; removing overly complicated option(s) * Update README.md * Update README.md * Update README.md * adding check for blank fix_pos * adding logic to skip alternative amino acids during pdb parsing * model._best moved to model._tmp["best"] * Update README.md
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