Jungfraujoch/image_analysis/structure_refinement/MonomerLibrary.cpp

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

#include "MonomerLibrary.h"

#include <algorithm>
#include <cstring>
#include <vector>

#include "gemmi/numb.hpp"       // as_number
#include "gemmi/read_cif.hpp"   // read_cif_from_memory

// Generated by CMakeLists.txt from monomers/*.cif (MonomerLibraryData.cpp in the build tree).
extern const EmbeddedMonomerFile embedded_monomer_files[];
extern const size_t embedded_monomer_file_count;

namespace {

struct MetalRow {
    gemmi::El metal, ligand;
    int coordination;
    double distance, std;
    int count;
};

struct EmbeddedLibrary {
    gemmi::MonLib monlib;
    std::vector<MetalRow> metals;   // metals.cif
};

EmbeddedLibrary ReadEmbeddedMonomerLibrary() {
    EmbeddedLibrary lib;
    gemmi::MonLib &monlib = lib.monlib;
    for (size_t i = 0; i < embedded_monomer_file_count; i++) {
        const EmbeddedMonomerFile &f = embedded_monomer_files[i];
        std::string text;
        for (size_t k = 0; k < f.n_pieces; k++)
            text += f.pieces[k];
        gemmi::cif::Document doc = gemmi::read_cif_from_memory(text.data(), text.size(), f.name);
        if (std::strcmp(f.name, "ener_lib.cif") == 0)
            monlib.ener_lib.read(doc);
        else if (std::strcmp(f.name, "metals.cif") == 0) {
            for (const auto &row : doc.blocks.at(0).find("_metal_coordination.",
                                                         {"metal", "ligand", "coordination", "distance", "std", "count"}))
                lib.metals.push_back({gemmi::find_element(row[0].c_str()), gemmi::find_element(row[1].c_str()),
                                      gemmi::cif::as_int(row[2]), gemmi::cif::as_number(row[3]),
                                      gemmi::cif::as_number(row[4]), gemmi::cif::as_int(row[5])});
        } else
            monlib.read_monomer_doc(doc);
    }
    return lib;
}

const EmbeddedLibrary &Library() {
    static const EmbeddedLibrary lib = ReadEmbeddedMonomerLibrary();
    return lib;
}

}  // namespace

const gemmi::MonLib &EmbeddedMonomerLibrary() {
    return Library().monlib;
}

bool EmbeddedMetalDistance(gemmi::El metal, gemmi::El ligand, int coordination, double &distance, double &sigma) {
    // the rows of the pair resting on enough sites: the nearest at or below the coordination and above it
    const MetalRow *lo = nullptr, *hi = nullptr;
    for (const MetalRow &r : Library().metals) {
        if (r.metal != metal || r.ligand != ligand || r.count < METAL_MIN_SITES)
            continue;
        if (r.coordination <= coordination && (lo == nullptr || r.coordination > lo->coordination))
            lo = &r;
        if (r.coordination > coordination && (hi == nullptr || r.coordination < hi->coordination))
            hi = &r;
    }
    if (lo == nullptr && hi == nullptr)
        return false;
    if (lo != nullptr && (lo->coordination == coordination || hi == nullptr)) {
        distance = lo->distance;
        sigma = lo->std;
    } else if (lo == nullptr) {
        distance = hi->distance;
        sigma = hi->std;
    } else {
        // between two coordination numbers: linear in the coordination
        const double t = static_cast<double>(coordination - lo->coordination) / (hi->coordination - lo->coordination);
        distance = lo->distance + t * (hi->distance - lo->distance);
        sigma = lo->std + t * (hi->std - lo->std);
    }
    sigma = std::max(sigma, METAL_MIN_SIGMA);
    return true;
}

bool InEmbeddedMonomerLibrary(const std::string &code) {
    return EmbeddedMonomerLibrary().monomers.count(code) > 0;
}