sokrypton / sokrypton/ColabFold
ESMFold Notebook fails with "No module named openfold" error message
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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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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