Program Listing for File pdb.hpp

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/*-
 * SPDX-License-Identifier: BSD-2-Clause
 *
 * Copyright (c) 2023 NKI/AVL, Netherlands Cancer Institute
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include "cif++/file.hpp"

#include <system_error>

namespace cif::pdb
{

// PDB to mmCIF

file read(const std::filesystem::path &file);

file read(std::istream &is);

file read_pdb_file(std::istream &pdbFile);

// mmCIF to PDB

void write(std::ostream &os, const datablock &db);

inline void write(std::ostream &os, const file &f)
{
    write(os, f.front());
}

void write(const std::filesystem::path &file, const datablock &db);

inline void write(const std::filesystem::path &p, const file &f)
{
    write(p, f.front());
}

// --------------------------------------------------------------------

bool reconstruct_pdbx(file &pdbx_file, std::string_view dictionary = "mmcif_pdbx");

bool is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary = "mmcif_pdbx");

bool is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec);

bool is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary,
    std::error_code &ec);

// --------------------------------------------------------------------
// Other I/O related routines

std::string get_HEADER_line(const datablock &data, std::string::size_type truncate_at = 127);
std::string get_COMPND_line(const datablock &data, std::string::size_type truncate_at = 127);
std::string get_SOURCE_line(const datablock &data, std::string::size_type truncate_at = 127);
std::string get_AUTHOR_line(const datablock &data, std::string::size_type truncate_at = 127);

} // namespace cif::pdb