Reuse GenBonded parameter lookups

[kierandidi]

Summary

• reuse immutable GenBonded torsion and improper database lookup results across residue types
• cache both matching entries and misses for the lifetime of one energy term
• preserve lookup ordering, offset calculation, output assembly, and all device paths

The default 142 residue types issue 7,574 torsion queries with only 359 unique keys and 562 improper queries with only 47 unique keys. The two small per-term dictionaries remove those repeated hierarchy and permutation searches without global state, device branches, or changes to score-term controls.

Performance

Exact post-#499, alternating three-process medians:

• one-thread CPU block annotation: 28.05 ms to 18.49 ms (1.517x)
• one-thread CPU complete GenBonded setup: 42.52 ms to 32.53 ms (1.307x)
• H200 block annotation: 30.23 ms to 18.98 ms (1.593x)
• H200 complete GenBonded setup: 47.55 ms to 36.94 ms (1.287x)
• complete cold one-thread CPU setup: 682.10 ms to 662.39 ms (1.030x)
• complete cold H200 setup: 747.36 ms to 711.67 ms (1.050x)

H200 peak allocation is unchanged at 41,096,192 bytes.

A follow-up that also cached assembled parameter rows was rejected: it improved CPU complete term setup by only 0.3% and regressed the noisy H200 median. This PR retains the smaller lookup-only cache.

Validation

• all packed GenBonded parameter SHA-256 digests are identical
• the focused reuse test passes on CPU- and CUDA-backed fixture variants
• the complete score-function directory passes 69 tests with 8 device skips
• Black, Flake8, and diff checks pass

Benchmark drivers, profiles, and outputs remain external to the repository.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.42%. Comparing base (05c1d67) to head (bf357dd).
⚠️ Report is 6 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #500       +/-   ##
===========================================
+ Coverage   74.11%   92.42%   +18.30%     
===========================================
  Files         455      456        +1     
  Lines       40173    40255       +82     
===========================================
+ Hits        29775    37204     +7429     
+ Misses      10398     3051     -7347     

Flag	Coverage Δ
cpu	90.97% <100.00%> (?)
cuda	74.11% <100.00%> (+<0.01%)	⬆️

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