3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	85fcac09b5	scale_merge: floor the R-free test-set size on small data ... AssignRfreeFlags gains a min_free_reflections floor (default 500): on small data, where the 5% fraction would give too few test reflections for a stable R-free (Brunger's ~500-2000 rule), the fraction is lifted toward ~500 free reflections, capped at 10% so a large test set never steals working data. An explicit rfree_fraction is still honoured; pass 0 to disable. For ordinary data (5% already clears the floor) this is inactive and the fraction stays flat, so the cross-dataset-identical property is preserved; the floor only lifts the fraction on genuinely small datasets, where per-dataset R-free stability outweighs cross-dataset identity (a shared reference set keeps exact identity there). Tests updated to isolate the pure-hash guarantees with the floor off, plus a new small-data floor + cap test. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-13 11:50:28 +02:00
leonarski_fandClaude Opus 4.8	d891551127	rugnux: make model validation batch-consistent for fragment screening ... Reworks the --model / French-Wilson / R-free path so a batch of datasets of one crystal form yields comparable maps and a shared test set, and fixes a French-Wilson prior bug. - French-Wilson: fix inverted centric/acentric prior - the call passed !centric into the selector, swapping the two Wilson forms for every weak reflection. Add a test pinning a centric weak |F| below an acentric one. - R-free flags: assign by a pure per-hkl hash instead of a per-dataset resolution-shell stratification, so every dataset of one crystal form gets the same free set (needed for ensemble refinement / PanDDA). Still a pure function of the Laue-ASU key, so Bijvoet/symmetry mates never split. - R-free flags: import a reference MTZ's FreeR_flag column when present (CCP4 test=0, auto-complement for a phenix-style test=1), so a whole campaign inherits one shared test set. New ApplyReferenceFreeFlags, wired post-merge in both the full-analysis and --scale paths. - Model maps: scale the model with an overall scale, anisotropic B and flat bulk solvent only - drop the free-form per-shell K(1/d^2) rescale, which reshaped each dataset's radial amplitude profile differently and made a batch of maps non-comparable. - Merohedral indexing: model validation resolves the ambiguity by lowest R-free only when there is no reference; with a reference MTZ the indexing is already resolved against it (merge stage / stills scaling) and that authoritative choice is kept. - Remove a stale <algorithm> include; update docs and changelog. Tests: french_wilson, rfree, reference_mtz (new), reindex, hkl_key all pass. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-13 11:31:33 +02:00
leonarski_fandClaude Opus 4.8	9f23976e02	tests: add Catch2 tests for R-free flag assignment and French-Wilson ... RfreeFlagsTest: determinism (pure function of the reflection), ~5% free fraction, Friedel/Bijvoet pairs never split, symmetry equivalents share a flag, resolution stratification (free set spans shells), and fraction=0 flags nothing. FrenchWilsonTest: strong reflections reduce to sqrt(I), weak/negative intensities get a positive amplitude, amplitudes are always finite and non-negative (incl. centric / epsilon>1 reflections in P4(3)2(1)2), and unusable sigma falls back to sqrt(max(I,0)). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-12 22:06:13 +02:00