sokrypton / sokrypton/ColabFold

ESMFold Notebook fails with "No module named openfold" error message

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Jupyter Notebook
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Description

I simply opened the ESMFold notebook and clicked on Runtime > Run all. When the execution reaches the cell titled "run ESMFold", it fails and displays the following error message:

ModuleNotFoundError                       Traceback (most recent call last)
<timed exec> in <module>

[/usr/local/lib/python3.10/dist-packages/torch/serialization.py](https://localhost:8080/#) in load(f, map_location, pickle_module, weights_only, **pickle_load_args)
    787                     except RuntimeError as e:
    788                         raise pickle.UnpicklingError(UNSAFE_MESSAGE + str(e)) from None
--> 789                 return _load(opened_zipfile, map_location, pickle_module, **pickle_load_args)
    790         if weights_only:
    791             try:

2 frames
[/usr/local/lib/python3.10/dist-packages/esm/esmfold/v1/esmfold.py](https://localhost:8080/#) in <module>
      9 import torch.nn as nn
     10 from omegaconf import MISSING
---> 11 from openfold.data.data_transforms import make_atom14_masks
     12 from openfold.np import residue_constants
     13 from openfold.utils.loss import compute_predicted_aligned_error, compute_tm

ModuleNotFoundError: No module named 'openfold'

This bug might be similar to #509.

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by opening the ESMFold notebook, running Runtime > Run all, and inspecting the setup cells and the cell titled "run ESMFold" where the openfold import fails. Compare the issue with #509 and verify the notebook completes without the ModuleNotFoundError.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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