facebookresearch / esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

MIT License

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fix a bug of undefined Alphabet.toks #106

Closed cutecutecat closed 3 years ago

cutecutecat commented 3 years ago

Fix error attribute 'toks' into 'standard_toks'

  File "/home/xxx/test_esm.py", line 11, in <module>
    print(model_alphabet.to_dict())
  File "/home/xxx/anaconda3/envs/fasthit/lib/python3.9/site-packages/fair_esm-0.3.1-py3.9.egg/esm/data.py", line 129, in to_dict
AttributeError: 'Alphabet' object has no attribute 'toks'

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tomsercu commented 3 years ago

Thanks for finding this and submitting a fix! But actually this method doesn't make too much sense and isn't used in the codebase, maybe you could instead replace it with returning the token to idx mapping: return self.tok_to_idx.copy() Thx!

cutecutecat commented 3 years ago

Thank you for your review！ As I see, self.tok_to_idx is a map from all_toks, which equals prepend_toks+standard_toks. If we use self.tok_to_idx in to_dict, than from_dict can no longer get standard_toks. Therefore, it cannot work any more. I have searched in the project and ensured there is nowhere require Alphabet.from_dict. If from_dict is also deprecated as well? Can I remove from_dict together?

tomsercu commented 3 years ago

Ah now I see where you're coming from - yes you can remove both! Thank you!