Jungfraujoch/tests/LoadReferenceSfCifTest.cpp

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

#include <catch2/catch_all.hpp>

#include <filesystem>
#include <fstream>
#include <string>

#include <zlib.h>

#include "../image_analysis/LoadFCalcFromMtz.h"

namespace {
    // A synthetic structure-factor mmCIF in the layout of a PDB deposition: an unmerged block first
    // (which the loader must pass over), then the merged block with intensities, sigmas and the
    // _refln.status test-set marks ('f' free, 'o' working, '-' neither). Cell and space group are
    // synthetic.
    const char* SF_CIF = R"(data_r0testsf_unmerged
_cell.length_a 50.0
_cell.length_b 60.0
_cell.length_c 70.0
_cell.angle_alpha 90.0
_cell.angle_beta 90.0
_cell.angle_gamma 90.0
_symmetry.space_group_name_H-M 'P 21 21 21'
loop_
_diffrn_refln.index_h
_diffrn_refln.index_k
_diffrn_refln.index_l
_diffrn_refln.intensity_net
_diffrn_refln.intensity_sigma
1 0 0 5.0 1.0
1 0 0 6.0 1.0
#
data_r0testsf
_cell.length_a 50.0
_cell.length_b 60.0
_cell.length_c 70.0
_cell.angle_alpha 90.0
_cell.angle_beta 90.0
_cell.angle_gamma 90.0
_symmetry.space_group_name_H-M 'P 21 21 21'
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.intensity_meas
_refln.intensity_sigma
0 0 2 o 100.0 5.0
0 1 1 f 200.0 6.0
1 1 1 o 300.0 7.0
1 2 3 f 400.0 8.0
2 2 2 - 500.0 9.0
3 1 4 o ? ?
)";

    std::string WriteFile(const std::string& name, const std::string& content) {
        const auto path = (std::filesystem::temp_directory_path() / name).string();
        std::ofstream(path) << content;
        return path;
    }

    std::string WriteGzFile(const std::string& name, const std::string& content) {
        const auto path = (std::filesystem::temp_directory_path() / name).string();
        gzFile f = gzopen(path.c_str(), "wb");
        gzwrite(f, content.data(), static_cast<unsigned>(content.size()));
        gzclose(f);
        return path;
    }

    void CheckSyntheticReference(const ReferenceMtzData& ref) {
        CHECK(ref.source == "SF-mmCIF block r0testsf");
        CHECK(ref.used_column == "IMEAN");
        CHECK_FALSE(ref.squared);
        REQUIRE(ref.cell.has_value());
        CHECK(ref.cell->a == Catch::Approx(50.0));
        CHECK(ref.cell->b == Catch::Approx(60.0));
        CHECK(ref.cell->c == Catch::Approx(70.0));
        REQUIRE(ref.space_group_number.has_value());
        CHECK(*ref.space_group_number == 19);

        // The reflection with no intensity ('?') is not a reference reflection.
        REQUIRE(ref.reflections.size() == 5);
        CHECK(ref.reflections[1].h == 0);
        CHECK(ref.reflections[1].k == 1);
        CHECK(ref.reflections[1].l == 1);
        CHECK(ref.reflections[1].I == Catch::Approx(200.0));
        CHECK(ref.reflections[4].I == Catch::Approx(500.0));

        // 'f' is the test set; 'o' and '-' are not.
        REQUIRE(ref.has_free_flags);
        CHECK(ref.n_free == 2);
        CHECK_FALSE(ref.reflections[0].rfree_flag);
        CHECK(ref.reflections[1].rfree_flag);
        CHECK_FALSE(ref.reflections[2].rfree_flag);
        CHECK(ref.reflections[3].rfree_flag);
        CHECK_FALSE(ref.reflections[4].rfree_flag);
    }
}

TEST_CASE("LoadReferenceMtz reads a structure-factor mmCIF", "[reference_mtz][portable]") {
    // Named without a .cif extension: the format is recognised by content.
    const auto path = WriteFile("rugnux_ref_sf.dat", SF_CIF);
    const auto ref = LoadReferenceMtz(path);
    std::filesystem::remove(path);
    CheckSyntheticReference(ref);
}

TEST_CASE("LoadReferenceMtz reads a gzipped structure-factor mmCIF", "[reference_mtz]") {
    const auto path = WriteGzFile("rugnux_ref_sf.cif.gz", SF_CIF);
    const auto ref = LoadReferenceMtz(path);
    std::filesystem::remove(path);
    CheckSyntheticReference(ref);
}

TEST_CASE("LoadReferenceMtz SF-mmCIF: amplitudes and pdbx_r_free_flag when status marks no test set", "[reference_mtz]") {
    // Only amplitudes: FP is squared to an intensity. The status column has no 'f', so the free set
    // comes from pdbx_r_free_flag (here 1 marks free, as phenix writes it - the minority value).
    const auto path = WriteFile("rugnux_ref_sf_fp.cif", R"(data_r0testsf
_cell.length_a 50.0
_cell.length_b 60.0
_cell.length_c 70.0
_cell.angle_alpha 90.0
_cell.angle_beta 90.0
_cell.angle_gamma 90.0
_symmetry.space_group_name_H-M 'P 21 21 21'
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.pdbx_r_free_flag
_refln.F_meas_au
_refln.F_meas_sigma_au
0 0 2 o 0 10.0 1.0
0 1 1 o 1 20.0 1.0
1 1 1 o 0 30.0 1.0
1 2 3 o 0 40.0 1.0
2 2 2 o 0 50.0 1.0
)");
    const auto ref = LoadReferenceMtz(path);
    std::filesystem::remove(path);

    CHECK(ref.used_column == "FP");
    CHECK(ref.squared);
    REQUIRE(ref.reflections.size() == 5);
    CHECK(ref.reflections[2].I == Catch::Approx(900.0));
    REQUIRE(ref.has_free_flags);
    CHECK(ref.n_free == 1);
    CHECK(ref.reflections[1].rfree_flag);
}