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Tier-2 test evidence: budgets, timings and reference checks (WP45 item 25)

Tier-2 test evidence: budgets, timings and reference checks (WP45 item 25)

  • [tested: tests/tier2/test_density_2wcd.py::test_ver49_2wcd_budget] The WP19/WP20 plan predicted stages 2 and 3 on the 2WCD structure at 0.05 nm to take at most 60 s and under 1.5 GB peak RSS (plan, Design §5). The budget test records the wall clock and ru_maxrss (kB on Linux) in a fresh interpreter and never gates on them. Source: tests/tier2/test_density_2wcd.py (test_ver49_2wcd_budget).
  • [verified]1 Example 05's frozen solve on the ClyA reference mesh took 2,512 s on one core (WP16 D11 Outcome); its Tier-2 wrapper is slow and records rather than gates, and the budget assumes about twice that [tested: tests/tier2/test_examples_05_clya_reference.py::test_ver46_the_frozen_case_solves_on_the_reference_mesh]. Source: tests/tier2/test_examples_05_clya_reference.py.
  • [tested: tests/tier2/test_examples_06_pdb_to_mesh.py::test_ver46_06_the_exported_map_overlays_the_aligned_structure] A PDB coordinate column is written to 0.001 Å, so a written atom lies at most half of that from the true one; the map bound of example 06 therefore allows √3 times that rounding. For a single Gaussian frame the map at distance d from an atom is at least exp(−d²/(σR)²); the grid node nearest the written atom lies within √3h/2 of it. R is the smallest shipped radius of any heavy atom, which gives 0.928 at h = 0.05 nm (WP25 plan, Design §2), so a map in nm or with transposed axes fails. Source: tests/tier2/test_examples_06_pdb_to_mesh.py (test_ver46_06_the_exported_map_overlays_the_aligned_structure).
  • [tested: tests/tier2/test_examples_06_pdb_to_mesh.py::test_ver46_06_the_exported_map_overlays_the_aligned_structure] A residue table names some hydrogens without a leading H (NAD's NH2T), so a radius looked up by name filtered on H takes a hydrogen's radius and makes a bound vacuous; the lookup goes through the set's own table. Source: test_examples_06_pdb_to_mesh.py (comment at the bound).
  • [verified]2 Example 07's ePNP-NS solve at size_scale 4 (chosen for runtime) takes a few minutes on one core (WP32 D9) [tested: tests/tier2/test_examples_07_pdb_to_charged_run.py::test_ver46_07_the_prepared_entry_walks_every_stage_to_a_charged_solve]. Source: tests/tier2/test_examples_07_pdb_to_charged_run.py.

  1. git show 3782c43:tests/tier2/test_examples_05_clya_reference.py, module docstring (WP16 D11 Outcome). ↩

  2. git show 3782c43:tests/tier2/test_examples_07_pdb_to_charged_run.py, module docstring (WP32 D9). ↩