Improve and Refactor run_alphafold_test.py for Enhanced Robustness

[vivek30117]

This PR addresses improvements in the run_alphafold_test.py unit testing script:

• Refactored mock setup for clarity and maintainability.
• Enhanced docstrings for test functions to meet style requirements.
• Ensured consistent test output structure when models are set to relax or not relax proteins.
• Modernized NumPy usage for compatibility with latest versions.
• Fixed a minor typo and clarified comments for other contributors.

Testing:

• Ran all tests using absltest.
• Verified outputs match expected files and content.
• Confirmed pLDDT scoring correctly appears in the B-factor column.

Related Issues:

Closes #______ (if this relates to a GitHub issue)

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have added tests to cover my changes
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

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