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

#pragma once

#include <string>

#include "../image_analysis/structure_refinement/RugnuxModel.h"

// The atomic model of a run from the bytes of its file: PDB or mmCIF, gzipped or not, the format taken from
// the content, never from a name. `pae_json` is the AlphaFold DB's predicted-aligned-error JSON of a
// prediction, empty where there is none; one that cannot be read is left out, as one never given. `name` is
// what the report calls the model, and what gemmi names a PDB structure after. Throws where the bytes hold no
// atomic model.
RugnuxModel ParseRugnuxModel(const std::string &bytes, const std::string &name, const std::string &pae_json = {});

// The model file at `path`, with the predicted aligned error the AlphaFold DB puts beside it where it is there
// (PaePathFor). Named by `path`.
RugnuxModel ReadRugnuxModelFile(const std::string &path);

// The PAE file the AlphaFold DB puts beside a model: AF-<id>-F1-model_v<n>.cif ->
// AF-<id>-F1-predicted_aligned_error_v<n>.json in the same directory; empty where the name does not follow it.
std::string PaePathFor(const std::string &model_path);