Adding AlphaFold2 Example

[kimronica]

No description provided.

[sweep-ai]

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• Apply: Leftover TODOs in the code should be handled.
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• Apply: Any clearly inefficient or repeated code should be optimized or refactored.

[kimronica]

updated AF2 notebook: took out dependencies section, because it was not needed when packages were pre-installed into virtual environment. Also added a requirements.txt file manually tracking which packages were installed into a clean virtual environment.

Edited to add: I originally used JupterLab for the CPU notebook, but this time I used VS Code (if that makes a difference)

[kimronica]

For GPU: same notebook will work as long as specific jax and jaxlib are properly installed (see requirements file).

Note: removing dependencies cells that created symbolic links seems to have broken ability for program to find specific files that in fact exist (e.g., hhsearch.py). The simplest inputs for protein alignment work on both CPU and GPU, but this bug needs to be looked into further to enable full capabilities of AF2 using this notebook.

[ktaletsk]

I've got it running after creating a custom conda environment and minor changes to the code