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	4c95a289b6	scale_merge: harden R-free flag assignment (Bijvoet-safe, deterministic, stratified) ... The R-free flags were drawn with a per-reflection std::bernoulli_distribution off a shared std::mt19937(12345). Two problems: in anomalous mode I(+) and I(-) are separate merged rows, so a Bijvoet pair could be split across the work and free sets (biasing R-free); and the draw order depended on merge/call order, so it was not reproducible or parallel-safe. The resolution-shell grouping was cosmetic — it still drew an independent Bernoulli per row, so it neither tied mates together nor guaranteed a per-shell quota. New AssignRfreeFlags() (own file RfreeFlags.{h,cpp}) replaces both call sites (stills MergeOnTheFly, rotation RotationScaleMerge). It: - keys each reflection by its Friedel-merged (Laue) ASU index, so all symmetry- and Friedel-equivalent reflections (including a Bijvoet pair) share one flag and are never split; - selects the free set by a deterministic splitmix64 hash of that key (same idiom as the CC1/2 half-set split), so it is reproducible run-to-run and order-independent; - stratifies by resolution: exactly round(fraction * n) of the distinct reflections in each of 20 shells is flagged free. Verified on an anomalous lyso merge (29536 refl, 5% free): 13548 Bijvoet pairs, 0 split; free fraction 4.6-5.4% in every resolution shell. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-12 21:27:44 +02:00