Refactor all_atom_test.py for clarity, reusability, and modular structure

[Vruddhi18]

• Extracted helpers for Vecs and Rigids creation
• Simplified test logic using named parameters and reusable transforms
• Improved test case readability and naming consistency
• Preserved original logic with clearer structure

[Vruddhi18]

I would like to request the merging of the pull request I submitted. All checks have been successfully validated, and there are no errors present. The changes have been reviewed and approved.

Thank you for your attention to this matter.