sokrypton / sokrypton/ColabFold

AlphaFold2_advanced.ipynb is resulting error not able to complete run alphafold

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Jupyter Notebook
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Description

Expected Behavior

Should output a zip file

Current Behavior

Does not output a zip file. Results an error:

AttributeError Traceback (most recent call last)
in <cell line: 67>()
65 # run alphafold
66 ###########################
---> 67 outs, model_rank = cf_af.run_alphafold(feature_dict, opt, runner, num_models, num_samples, subsample_msa,
68 rank_by=rank_by, show_images=show_images)

39 frames
[... skipping hidden 12 frame]

[... skipping hidden 9 frame]

[... skipping hidden 8 frame]

/content/alphafold/alphafold/model/utils.py in mask_mean(mask, value, axis, drop_mask_channel, eps)
54 elif axis is None:
55 axis = list(range(len(mask_shape)))
---> 56 assert isinstance(axis, collections.Iterable), (
57 'axis needs to be either an iterable, integer or "None"')
58

AttributeError: module 'collections' has no attribute 'Iterable'

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.
Use of all default settings hit runtime run all

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

Context

Providing context helps us come up with a solution and improve our documentation for the future.
Using online version

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used
  • If you run it on a local system. Please add the server specifications
  • Operating system and version:
    Windows 11

Contributor guide

Open the contributing guide

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 AlphaFold2_advanced.ipynb and reproducing the default run in the online Colab environment after a factory reset. Trace the run from the run_alphafold call into alphafold/model/utils.py, especially mask_mean where the collections.Iterable error occurs. Done means the notebook completes and produces the expected zip file.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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