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Improve steric-clash repair and add placement/repair tuning knobs - #549
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Adds explicit control over beam-search placement, force-field repair steps, and ring-piercing retry behavior in generate_complex, and consolidates bad-state detection (overlap/ordering/ring-piercing) into shared helpers. run_sterics_check gains make_figure to skip plotting when only the clash/severity data is needed.
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Replace `float | None` (requires Python 3.10) with Optional[float] -- this also broke doctest collection under Python 3.8 (TypeError at import time). Also initialize per_atom_ff_force/optimized2 with safe fallbacks in enforce_metal_ligand_distances_and_optimize so the return statement is always well-defined even when constrain/final_relax are disabled, per CodeQL's possibly-unbound-variable alerts.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #549 +/- ##
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+ Coverage 40.26% 40.65% +0.38%
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Files 93 93
Lines 30325 30349 +24
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+ Hits 12211 12339 +128
+ Misses 18114 18010 -104
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Summary
generate_complexinto shared_bad_state_summary/_hopelesshelpersplacement_beam_topk,placement_early_exit_score) and repair behavior (repair_ff_steps,max_ring_piercing_retries,bail_if_still_bad_after_repair)run_sterics_checkgainsmake_figureto skip plotting when only clash/severity data is needed__main__block to correctly unpack the tuple returned bygenerate_complexTest plan
run_sterics=Trueandmake_figure=False