test(domain): hinge-joined two-domain receptor integration smoke test (Phase 4 task 5)

[transfix]

Lands Phase 4 task 5 of the F3Dock migration matrix: a deterministic integration regression that exercises the f3-mode scoring cross-product loop on a hinge-joined two-domain receptor.

What

• ests/integration/inputs/1A2K_domain_smoke.inp splits the 1A2K receptor (3895 atoms) at atom 1948 into two domains and joins them with a z-axis hinge through the origin (
  eceptorJointHinge 0 1 0 0 0 0 0 1 0.0).

eceptorJointHingeSweep 0 1 0.0 0.0872664626 2 produces two domain states (0 rad and ~5 deg).

• The f3-mode loop therefore iterates n_flex_states x n_domain_states = 1 x 2 = 2.
• The committed 307-line baseline at ests/integration/expected/1A2K_domain_smoke_out.txt was generated by the same dockingMain path the production binary uses and reproduces bit-for-bit on re-run.
• New 1A2K_domain case is registered in ests/integration/CMakeLists.txt via the existing �dd_f2dock_integration_case helper (ROWS=50, ABS_TOL=1e-3, REL_TOL=1e-5, label integration, 1800 s timeout).

Verification

• Local re-run on Ubuntu-24.04 (WSL): compare_f2dock_outputs.py --rows 50 --abs-tol 1e-3 --rel-tol 1e-5 -> 50 rows compared, PASS.
• F2Dock stdout shows Receptor domain partition: 2 domain(s) and the per-state banners === Flex state 1 / 1, domain state 1 / 2 === and === Flex state 1 / 1, domain state 2 / 2 === confirming the cross-product loop fires.

Docs

• doc/F3DOCK_MIGRATION_MATRIX.md Task 5 marked Landed with details; Phase 4 risk note updated to reflect that all five Phase 4 tasks have landed (PRs style(windows): silence final MSVC C4305/C4244 warnings (3rd pass) #24, feat(domain): per-domain atom partition + libcvc 3.2.1 prebuilt fetch (Phase 4 task 2) #27, feat(domain): hinge-state sampler + cross-product scoring loop (Phase 4 task 3) #28, feat(icp): point-to-plane refinement on top-N final poses (Phase 4 task 4) #29, and this one).

Risk

• Test-only change. No production code is modified. Other integration cases (1A2K, 1ACB, 1A2K_flex) are untouched.