Jungfraujoch/rugnux/WriteModel.cpp

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

#include "WriteModel.h"

#include <fstream>

#include <gemmi/to_mmcif.hpp>  // make_mmcif_document
#include <gemmi/to_cif.hpp>    // write_cif_to_stream
#include <gemmi/to_pdb.hpp>    // write_pdb
#include <gemmi/polyheur.hpp>  // setup_entities

#include "../common/Logger.h"

void WritePlacedModel(const gemmi::Structure &placed,
                      const UnitCell &cell,
                      const gemmi::SpaceGroup &space_group,
                      const std::string &output_prefix,
                      Logger &logger) {
    const std::string cif_path = output_prefix + "_model.cif";
    // PDB as well as mmCIF, because the fragment-screening tools this file exists for take a PDB:
    // PanDDA's per-dataset input is <name>.pdb beside <name>.mtz, and dimple produces the same pair.
    // Same coordinates, same frame, both formats - a PDB cannot hold every cell, so it is written
    // when it can be and skipped, with a line saying so, when it cannot.
    const std::string pdb_path = output_prefix + "_model.pdb";

    gemmi::Structure st = placed;
    // Not the model's own cell and group but the data's, taken from the same two values the reflection
    // files are written from. The coordinates already sit in this cell; what is set here is the label
    // the file carries, which must match the .mtz beside it - the enantiomorph in particular, since
    // --model can adopt the model's and that is neither the data's original label nor, necessarily,
    // the one the input model arrived with.
    st.cell = cell;
    st.spacegroup_hm = space_group.xhm();
    st.setup_cell_images();
    // Fills in entity types and label_asym_id for a model read from a PDB, which carries neither.
    // Both are no-ops where the input already had them, i.e. for an mmCIF input.
    // setup_entities and make_mmcif_document can both throw, and this runs BEFORE the reflection files
    // are written: a convenience deliverable must not be able to take the run's actual output with it.
    // The map writer does the same.
    try {
        gemmi::setup_entities(st);
        std::ofstream os(cif_path);
        gemmi::cif::write_cif_to_stream(os, gemmi::make_mmcif_document(st));
        if (!os) {
            logger.Error("Model validation: cannot write the placed model to {}", cif_path);
            return;
        }
    } catch (const std::exception &e) {
        logger.Warning("Model validation: could not write the placed model to {} ({})",
                       cif_path, e.what());
        return;
    }
    bool pdb_written = false;
    try {
        std::ofstream os(pdb_path);
        gemmi::write_pdb(st, os);
        pdb_written = static_cast<bool>(os);
    } catch (const std::exception &e) {
        logger.Warning("Model validation: the placed model could not also be written as PDB ({}); "
                       "{} has it", e.what(), cif_path);
    }
    logger.Info("Model validation: the model as placed against these data written to {}{} "
                "(cell and space group {} as in the reflection files)",
                cif_path, pdb_written ? " and " + pdb_path : "", space_group.short_name());
}