Jungfraujoch/rugnux/WriteModel.h

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#pragma once

#include <string>

#include "gemmi/model.hpp"
#include "gemmi/symmetry.hpp"

#include "../common/UnitCell.h"

class Logger;

// Write `placed` - the atomic model as ValidateAgainstModel left it, re-fractionalized into the data
// 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
// comes with it: chains, residues, ligands, waters, B-factors, occupancies, anisotropic Us.
//
// `cell` and `space_group` must be the ones the reflection files beside it are written in, i.e. the
// unit cell and DiffractionExperiment::GetSpaceGroupOrP1() that WriteReflections is given after
// AdoptModelFrame has settled the enantiomorph. The cell is always taken; the group is taken wherever
// the model's coordinates obey it, which is the ordinary case. Where they do not - data merged in a
// supergroup of the model's group, or in the other hand - the model keeps its own group and a warning
// says the two files disagree, because a label whose operations the coordinates contradict makes a
// refinement program build a different structure and say nothing.
void WritePlacedModel(const gemmi::Structure &placed,
                      const UnitCell &cell,
                      const gemmi::SpaceGroup &space_group,
                      const std::string &output_prefix,
                      Logger &logger);