ENH: Add PDB reader benchmark to track parsing performance

[Dreamstick9]

Changes made in this Pull Request:

• Contributes to performance benchmarks #1023
• Added PDBReaderBench class to benchmarks/benchmarks/traj_reader.py.
• it benchmarks PDB format reading and parsing across different number of frames ([10, 100, 500]) using the standard PDB test file.

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[read-the-docs-community]

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📚 MDAnalysis | 🛠️ Build #32994886 | 📁 Comparing 625961e against latest (941d679)

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2 files changed

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± documentation_pages/analysis/wbridge_analysis.html

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.85%. Comparing base (b05a84b) to head (625961e).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

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  Files          182      182           
  Lines        22509    22509           
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[tylerjereddy]

Maybe I'm mistaken, but won't this nested loop do something weird?

• for each integer in n_frames range
• loop over the entire trajectory--all frames, since u.trajectory isn't sliced

Now, it may be the case that after the first outer loop iteration there's no rewind so you don't redo the full iteration each time, but I'm pretty sure the way this is expressed isn't quite right yet.

Even if you fix that, I'm not entirely certain this is benchmarking what we want on the "reading" side.

[Dreamstick9]

Well the standard PDB file only contains 1 frame, but for a better approach i could use PDB_multiframe (which is an NMR) and MDAnalysis treats all the 3d models in this file as a different frame, which removes the need for the outer loop totally, So @tylerjereddy if this approach seems to be better, shall I go ahead?

[Dreamstick9]

I made the change and the benchmarks for this updated reader come out to be 5.13 ms

[Dreamstick9]

Also added time_read to separately benchmark the initial parse, let me know if this approach is the right direction to move forward with.