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
31 lines
1.5 KiB
C++
31 lines
1.5 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 <string>
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#include "gemmi/model.hpp"
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#include "gemmi/symmetry.hpp"
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#include "../common/UnitCell.h"
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class Logger;
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// Write `placed` - the atomic model as ValidateAgainstModel left it, re-fractionalized into the data
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// cell and moved by the rigid-body step - to `output_prefix`_model.cif, and to `_model.pdb` as well where a PDB can express the cell. Everything the input carried
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// comes with it: chains, residues, ligands, waters, B-factors, occupancies, anisotropic Us.
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//
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// `cell` and `space_group` must be the ones the reflection files beside it are written in, i.e. the
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// unit cell and DiffractionExperiment::GetSpaceGroupOrP1() that WriteReflections is given after
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// AdoptModelFrame has settled the enantiomorph. The cell is always taken; the group is taken wherever
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// the model's coordinates obey it, which is the ordinary case. Where they do not - data merged in a
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// supergroup of the model's group, or in the other hand - the model keeps its own group and a warning
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// says the two files disagree, because a label whose operations the coordinates contradict makes a
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// refinement program build a different structure and say nothing.
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void WritePlacedModel(const gemmi::Structure &placed,
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const UnitCell &cell,
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const gemmi::SpaceGroup &space_group,
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const std::string &output_prefix,
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Logger &logger);
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