Jungfraujoch/writer/WriteRugnuxFiles.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 "../common/JFJochMessages.h"

class Logger;

// The files rugnux writes beside its merged output, made from the structured END-message blocks
// (common/JFJochMessages.h), so that jfjoch_writer can write them with no analysis library. rugnux
// writes its own MTZ files through the same function.

// An MTZ file from its table. Throws where the table does not describe one: a column with another number
// of rows than the first, a column or a batch naming a dataset the table does not have, a batch header that
// is not 29 + 156 long, or a space group gemmi does not know.
void WriteMtz(const MtzTable &table, const std::string &filename);

// The model the block describes, for WritePlacedModel (writer/WriteModel.h). Throws where the block
// describes none: a per-atom field with another number of entries than atom_name, or aniso neither empty
// nor six per atom.
gemmi::Structure PlacedModelStructure(const PlacedModelMessage &model);

// The three files above, from whichever blocks `end` carries, at <file_prefix>.mtz, _maps.mtz and
// _model.cif (WritePlacedModel adds _model.pdb where a PDB can hold the cell). Each is written under a
// temporary name and renamed into place. An existing file is replaced only with `overwrite`; otherwise
// it is kept and the new one is not written.
void WriteRugnuxResultFiles(const EndMessage &end, const std::string &file_prefix, bool overwrite,
                            Logger &logger);