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Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

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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
This commit is contained in:
leonarski_f
2026-10-07 14:05:37 +02:00
co-authored by Claude Opus 5.5
parent 08ca1d5764
commit 9ad92b6bfe
34 changed files with 73 additions and 69 deletions
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tests/ModelScaleGPUTest.cpp
+6 -6
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@@ -23,12 +23,12 @@
#include "gemmi/unitcell.hpp"
#include "../common/Logger.h"
#include "../rugnux/ModelFFT.h"
#include "../rugnux/ModelGrid.h"
#include "../rugnux/ModelScaling.h"
#include "../rugnux/ModelScaleGPU.h"
#include "../rugnux/ModelValidation.h"
#include "../rugnux/RigidBodyRefine.h"
#include "../image_analysis/structure_refinement/ModelFFT.h"
#include "../image_analysis/structure_refinement/ModelGrid.h"
#include "../image_analysis/structure_refinement/ModelScaling.h"
#include "../image_analysis/structure_refinement/ModelScaleGPU.h"
#include "../image_analysis/structure_refinement/ModelValidation.h"
#include "../image_analysis/structure_refinement/RigidBodyRefine.h"
namespace {