mirror of
https://github.com/PDB-REDO/libcifpp.git
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269 lines
9.0 KiB
C++
269 lines
9.0 KiB
C++
/*-
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* SPDX-License-Identifier: BSD-2-Clause
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*
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* Copyright (c) 2023 NKI/AVL, Netherlands Cancer Institute
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice, this
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* list of conditions and the following disclaimer
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
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* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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#pragma once
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#include "cif++/file.hpp"
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#include "cif++/validate.hpp"
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#include <system_error>
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/**
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* @file pdb.hpp
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*
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* This file presents the API to read and write files in the
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* legacy and ancient PDB format.
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*
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* The code works on the basis of best effort since it is
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* impossible to have correct round trip fidelity.
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*
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*/
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namespace cif::pdb
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{
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/// --------------------------------------------------------------------
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// PDB to mmCIF
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/** @brief Read a file in either mmCIF or PDB format from file @a file,
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* compressed or not, depending on the content.
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*/
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file read(const std::filesystem::path &file);
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/** @brief Read a file in either mmCIF or PDB format from std::istream @a is,
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* compressed or not, depending on the content.
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*/
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file read(std::istream &is);
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/**
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* @brief Read a file in legacy PDB format from std::istream @a is and
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* put the data into @a cifFile
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*/
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void read_pdb_file(std::istream &pdbFile, cif::file &cifFile);
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// mmCIF to PDB
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/** @brief Write out the data in @a db in legacy PDB format
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* to std::ostream @a os
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*/
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void write(std::ostream &os, const datablock &db);
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/** @brief Write out the data in @a f in legacy PDB format
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* to std::ostream @a os
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*/
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inline void write(std::ostream &os, const file &f)
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{
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write(os, f.front());
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}
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/** @brief Write out the data in @a db to file @a file
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* in legacy PDB format or mmCIF format, depending on the
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* filename extension.
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*
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* If extension of @a file is *.gz* the resulting file will
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* be written in gzip compressed format.
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*/
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void write(const std::filesystem::path &file, const datablock &db);
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/** @brief Write out the data in @a f to file @a file
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* in legacy PDB format or mmCIF format, depending on the
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* filename extension.
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*
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* If extension of @a file is *.gz* the resulting file will
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* be written in gzip compressed format.
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*/
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inline void write(const std::filesystem::path &p, const file &f)
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{
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write(p, f.front());
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}
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// --------------------------------------------------------------------
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/**
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* @brief Quickly fix a PDB file that lacks some often needed categories
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*
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* This differs from reconstruct_pdbx which does a much more thorough job
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*
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* \param pdbx_file The cif::file that hopefully contains some valid data
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*/
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void fixup_pdbx(file &pdbx_file);
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/**
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* @brief Quickly fix a PDB file that lacks some often needed categories
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*
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* This differs from reconstruct_pdbx which does a much more thorough job
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*
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* \param pdbx_file The cif::file that hopefully contains some valid data
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* \param v The validator to use
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*/
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void fixup_pdbx(file &pdbx_file, const validator &v);
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/** \brief Reconstruct all missing categories for an assumed PDBx file.
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*
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* Some people believe that simply dumping some atom records is enough.
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*
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* This version uses the audit_conform information and falls back to
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* using mmcif_pdbx.dic if not specified.
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*
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* \param pdbx_file The cif::file that hopefully contains some valid data
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* \result Returns true if the resulting file is valid
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*/
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bool reconstruct_pdbx(file &pdbx_file);
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/** \brief Reconstruct all missing categories for an assumed PDBx file.
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*
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* Some people believe that simply dumping some atom records is enough.
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*
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* \param pdbx_file The cif::file that hopefully contains some valid data
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* \param v The validator to use
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* \result Returns true if the resulting file is valid
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*/
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bool reconstruct_pdbx(file &pdbx_file, const validator &v);
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/** \brief This is an extension to cif::validator, use the logic in common
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* PDBx files to see if the file is internally consistent.
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*
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* This function for now checks if the following categories are consistent:
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*
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* atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
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*
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* Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
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*
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* This function throws a std::system_error in case of an error
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*
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* \param pdbx_file The input file
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* \result Returns true if the file was valid and consistent
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*/
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bool is_valid_pdbx_file(const file &pdbx_file);
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/** \brief This is an extension to cif::validator, use the logic in common
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* PDBx files to see if the file is internally consistent.
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*
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* This function for now checks if the following categories are consistent:
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*
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* atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
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*
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* Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
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*
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* This function throws a std::system_error in case of an error
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*
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* \param pdbx_file The input file
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* \param v The validator to use
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* \result Returns true if the file was valid and consistent
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*/
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bool is_valid_pdbx_file(const file &pdbx_file, const validator &v);
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/** \brief This is an extension to cif::validator, use the logic in common
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* PDBx files to see if the file is internally consistent.
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*
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* This function for now checks if the following categories are consistent:
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*
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* atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
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*
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* Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
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*
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* The dictionary is assumed to be specified in the file or to be the
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* default mmcif_pdbx.dic dictionary.
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*
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* \param pdbx_file The input file
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* \param ec In case of error, this will contain what went wrong
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* \result Returns true if the file was valid and consistent
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*/
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bool is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec);
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/** \brief This is an extension to cif::validator, use the logic in common
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* PDBx files to see if the file is internally consistent.
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*
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* This function for now checks if the following categories are consistent:
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*
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* atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
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*
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* Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
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*
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* \param pdbx_file The input file
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* \param v The validator to use
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* \param ec The error_code in case something was wrong
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* \result Returns true if the file was valid and consistent
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*/
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bool is_valid_pdbx_file(const file &pdbx_file, const validator &v,
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std::error_code &ec);
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// --------------------------------------------------------------------
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// Other I/O related routines
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/** @brief Return the HEADER line for the data in @a data
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*
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* The line returned should be compatible with the legacy PDB
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* format and is e.g. used in the DSSP program.
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*
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* @param data The datablock to use as source for the requested data
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* @param truncate_at The maximum length of the line returned
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*/
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std::string get_HEADER_line(const datablock &data, std::string::size_type truncate_at = 127);
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/** @brief Return the COMPND line for the data in @a data
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*
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* The line returned should be compatible with the legacy PDB
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* format and is e.g. used in the DSSP program.
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*
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* @param data The datablock to use as source for the requested data
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* @param truncate_at The maximum length of the line returned
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*/
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std::string get_COMPND_line(const datablock &data, std::string::size_type truncate_at = 127);
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/** @brief Return the SOURCE line for the data in @a data
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*
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* The line returned should be compatible with the legacy PDB
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* format and is e.g. used in the DSSP program.
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*
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* @param data The datablock to use as source for the requested data
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* @param truncate_at The maximum length of the line returned
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*/
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std::string get_SOURCE_line(const datablock &data, std::string::size_type truncate_at = 127);
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/** @brief Return the AUTHOR line for the data in @a data
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*
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* The line returned should be compatible with the legacy PDB
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* format and is e.g. used in the DSSP program.
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*
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* @param data The datablock to use as source for the requested data
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* @param truncate_at The maximum length of the line returned
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*/
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std::string get_AUTHOR_line(const datablock &data, std::string::size_type truncate_at = 127);
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} // namespace cif::pdb
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