Fix off-by-one in 1-indexed loops in docking/membrane/misc (split 4/4 of #707) - #733
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lyskov merged 1 commit intoJul 23, 2026
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…tch / loops / misc) Split from RosettaCommons#707. Off-by-one in 1-indexed loops (< -> <=), last element was silently skipped: - docking/DockingEnsemblePrepackProtocol.cc x2 (chain identity validation) - docking/metrics.cc x2 (cutpoint scan in Fnonnat) - membrane/MPLipidAccessibility.cc x2 (slice iteration) - antibody/residue_selector/CDRResidueSelector.cc - match/output/UpstreamDownstreamCollisionFilter.cc - loops/util.cc x3 (non-protein-chunk and per-loop accounting) - cartesian/md.cc x2 (per-atom state save / derivative check) - cutoutdomain/CutOutDomain.cc (find_nearest_res) - enzdes/EnzRepackMinimize.cc (movable-residue collection for backrub) - moves/PyMOLMover.cc (relevant_residues mask init -- last entry left default false despite the intent of 'all relevant') membrane/util.cc: comment-only. This documents WHY a nearby loop intentionally stays '< chains.size()' (the trailing MEM virtual chain must be excluded); no behavior change. Note: this batch changes the output of several regression tests -- enzdes, inverse_rotamer_remodel, ligand_dock_cholesterol, mp_f19_relax, mpil_load_implicit_lipids. The changes are intentional but results-affecting and warrant scientific sign-off before merge.
roccomoretti
approved these changes
Jul 6, 2026
lyskov
approved these changes
Jul 23, 2026
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Summary
One of four PRs splitting #707 (originally a single 35-file off-by-one batch) into coherent, per-subsystem pieces, so each can be reviewed and its regression-test impact assessed independently. #707 is being closed in favor of these four. The split is deliberate — the individual diffs are below the usual bundling threshold — because the changes are behavior-affecting and the maintainer asked to isolate regression-test impact per subsystem.
This PR: docking / membrane / antibody / match / loops / misc movers (11 files).
Off-by-one in 1-indexed loops (
<→<=)The last element was silently skipped:
docking/DockingEnsemblePrepackProtocol.cc×2 — chain identity validationdocking/metrics.cc×2 — cutpoint scan incalc_Fnonnatmembrane/MPLipidAccessibility.cc×2 — slice iterationantibody/residue_selector/CDRResidueSelector.ccmatch/output/UpstreamDownstreamCollisionFilter.ccloops/util.cc×3 — non-protein-chunk and per-loop accountingcartesian/md.cc×2 — per-atom state save / derivative checkcutoutdomain/CutOutDomain.cc—find_nearest_resenzdes/EnzRepackMinimize.cc— movable-residue collection for backrubmoves/PyMOLMover.cc—relevant_residuesmask init (last entry left defaultfalsedespite the intent of "all relevant")Comment-only
membrane/util.cc— documents why a nearby loop intentionally stays< chains.size()(the trailing MEM virtual chain must be excluded). No behavior change.Regression tests
This PR carries most of #707's results-affecting changes:
enzdesandinverse_rotamer_remodel(enzdes/EnzRepackMinimize.cc),ligand_dock_cholesterol(docking/),mp_f19_relaxandmpil_load_implicit_lipids(membrane/MPLipidAccessibility.cc). These output changes are intentional but results-affecting and warrant scientific sign-off before merge.