leonarski_fandClaude Opus 5.5
9ad92b6bfe
A pure move. ModelValidation, RigidBodyRefine, RigidBodyGPU, ModelFFT, ModelGrid, ModelScaling, ModelMaskGPU, ModelScaleGPU and SigmaA - everything that works on an atomic model - become the JFJochStructureRefinement library, linked by JFJochImageAnalysis. WriteModel (the placed-model mmCIF/PDB writer) goes to writer/ as its own small JFJochModelWriter target, so JFJochWriter, which a writer-only build compiles, does not gain a gemmi dependency. Only include paths and CMake lists change. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
43 lines
1.6 KiB
C++
43 lines
1.6 KiB
C++
// SPDX-FileCopyrightText: 2026 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 <vector>
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#include "gemmi/unitcell.hpp"
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// One reflection as the sigma_A estimate sees it: an observed and a calculated amplitude, already on
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// a common scale, plus what the likelihood needs to know about the reflection itself.
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struct SigmaAReflection {
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double f_obs = 0;
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double f_calc = 0;
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double inv_d2 = 0;
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int epsilon = 1;
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bool centric = false;
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bool free = false;
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};
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// The weights of one reflection's map coefficients: 2mFo - DFc and mFo - DFc.
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struct SigmaAWeight {
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double m = 1.0; // figure of merit
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double d = 1.0; // D, carried on the observed amplitudes' scale
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};
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struct SigmaAResult {
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std::vector<SigmaAWeight> weight; // one per input reflection, in the input order
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int shells = 0;
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int free_reflections = 0;
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double mean_fom = 1.0;
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double sigma_a_lowest_shell = 0.0; // for a log line: sigma_A at the low- and high-resolution ends
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double sigma_a_highest_shell = 0.0;
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};
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// Per-resolution-shell sigma_A by maximum likelihood, and from it the figure of merit m and the
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// scale D of each reflection. Estimated on the FREE reflections only - on the working set the model
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// has been fitted to the data, so sigma_A would come out too high and the weighting would under-state
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// the model's error where the map is meant to reveal it.
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//
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// Following Read (1986) Acta Cryst. A42, 140-149
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SigmaAResult EstimateSigmaA(const std::vector<SigmaAReflection> &refl, const gemmi::UnitCell &cell);
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