* 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

* speedup alphafold weight download