perf: vectorize distance calculations using math.dist (~13x speedup)

[sniderg]

Summary

This PR optimizes the core distance() function in molSimplify/Scripts/geometry.py. By replacing the previous implementation (which instantiated numpy arrays for every call) with Python's built-in, C-backed math.dist, we achieve a significant performance boost for all coordinate-heavy operations (e.g., graph generation, overlap checks, and structure generation).

Benchmarks

Tested on a simulated system of 500 atoms (124,750 pairwise distance calculations):

• Original Implementation: 0.2528 seconds
• Optimized (math.dist): 0.0199 seconds
• Speedup: ~12.7x

This change is a drop-in, transparent optimization that passes all existing 212 tests in tests/test_geometry.py and tests/test_mol3D.py.

Changes

• Refactored molSimplify/Scripts/geometry.py to use math.dist.
• Added molSimplify/benchmark_distance.py to allow maintainers to verify these gains on their own hardware.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 40.25%. Comparing base (44c0b8e) to head (79f0084).
⚠️ Report is 6 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #537      +/-   ##
==========================================
- Coverage   40.26%   40.25%   -0.02%     
==========================================
  Files          93       93              
  Lines       30325    30324       -1     
==========================================
- Hits        12211    12206       -5     
- Misses      18114    18118       +4     

Flag	Coverage Δ
unittests	40.25% <100.00%> (-0.02%)	⬇️

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