leonarski_fandClaude Opus 4.8
d891551127
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>
62 lines
3.4 KiB
C++
62 lines
3.4 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <optional>
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#include <string>
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#include <vector>
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#include "../common/Reflection.h"
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#include "../common/UnitCell.h"
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// A column an MTZ offers as reference intensities/structure factors (type 'J' mean intensity or
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// 'F' amplitude). Surfaced so the caller (CLI flag / viewer combo) can pick which one to scale
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// against and report the choice, rather than the loader silently guessing.
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struct ReferenceMtzColumn {
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std::string label;
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char type = '\0'; // 'J' = mean intensity, 'F' = structure-factor amplitude
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};
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// Reference reflections loaded from an MTZ, plus the metadata a user needs to judge whether the
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// reference matches the data being scaled: which column was used, the cell / space group it was
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// recorded in, its resolution range and reflection count.
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struct ReferenceMtzData {
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std::vector<MergedReflection> reflections; // h,k,l,I,d set (sigma stays NaN)
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std::optional<UnitCell> cell;
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std::optional<int> space_group_number;
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std::string space_group_name; // Hermann-Mauguin short symbol, for display
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std::string point_group; // point-group symbol, for the consistency check
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std::string used_column;
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char used_column_type = '\0';
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bool squared = false; // an 'F' column was squared to an intensity
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bool default_column = true; // column was auto-selected, not user-specified
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std::vector<ReferenceMtzColumn> candidate_columns;
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double d_min = 0.0;
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double d_max = 0.0;
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// Cross-validation (free-R) flags, if the MTZ carried a FreeR_flag column. When present, the
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// per-reflection rfree_flag above is set from it and a whole campaign can inherit one test set.
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bool has_free_flags = false;
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std::string free_column; // the FreeR column label used, for display
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int n_free = 0; // number of reflections flagged free (test set)
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};
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// Load reference reflections from an MTZ. With no column requested the smart default is used:
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// a calculated structure factor F-model (squared to an intensity), else a merged/observed
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// intensity column (IMEAN/I/IOBS/...), else any mean-intensity (J) column - this also lets
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// reference-based scaling be self-seeded from the data's own previous merge. A requested column overrides
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// the default (an 'F'-type column is squared, a 'J'-type used directly). Throws if the requested
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// column is missing or no usable column exists.
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ReferenceMtzData LoadReferenceMtz(const std::string& path,
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const std::optional<std::string>& column = std::nullopt);
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// Compare a loaded reference against the data it will scale. Returns an empty string when they are
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// consistent (or when the data cell / space group is unknown, so nothing can be said); otherwise a
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// one-line, human-readable description of the mismatch to warn the user about. Reference intensities
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// keyed in a different point group or cell do not correspond to the data, so this is the check that
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// makes reference-based scaling and CCref trustworthy.
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std::string ReferenceConsistencyWarning(const ReferenceMtzData& reference,
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const std::optional<UnitCell>& data_cell,
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std::optional<int> data_space_group_number);
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