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

#pragma once

#include <cstddef>
#include <string>

#include "gemmi/monlib.hpp"

// The restraint dictionary refinement uses: the subset of the CCP4 Monomer Library (Vagin et al. 2004,
// LGPL-3.0) carried in the binary - the standard amino acids and nucleotides, the common modified RNA nucleotides,
// their links and modifications, the common cofactors (NAD(P)(H), FAD, FMN, hemes, SAM/SAH), a few other ligands
// and additives, water and ions; monomers/update_monomers.py holds the list. Parsed from memory once per process;
// no file is read.
const gemmi::MonLib &EmbeddedMonomerLibrary();

// The ideal distance and its sigma of a bond from a metal ion to a donor atom (O, N, S) at a site of `coordination`
// donors, from the library's statistics of metal sites (metals.json, embedded as monomers/metals.cif). Only rows
// resting on at least METAL_MIN_SITES sites count: the row of that coordination number, else the two nearest
// below and above it interpolated linearly, else the nearest one; the sigma is the row's standard deviation, at
// least METAL_MIN_SIGMA. False where the pair has no such row.
constexpr int METAL_MIN_SITES = 20;
constexpr double METAL_MIN_SIGMA = 0.02;   // A
bool EmbeddedMetalDistance(gemmi::El metal, gemmi::El ligand, int coordination, double &distance, double &sigma);

// Whether `code` (a residue name) has a description in it.
bool InEmbeddedMonomerLibrary(const std::string &code);

// One .cif of monomers/, as CMakeLists.txt embeds it: its name and its text in pieces.
struct EmbeddedMonomerFile {
    const char *name;
    const char *const *pieces;
    size_t n_pieces;
};