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/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 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.
*/
/*
Created by: Maarten L. Hekkelman
Date: maandag 07 januari, 2019
Skip list for e.g. pepflip
*/
#pragma once
#include <filesystem>
#include <cif++.hpp>
#if __has_include(<experimental/optional>)
#include <experimental/optional>
using std::experimental::optional;
#else
#include <optional>
using std::optional;
#endif
namespace pdb_redo
{
struct ResidueSpec
{
std::string pdb_asym_id;
std::string pdb_comp_id;
std::string pdb_seq_id;
optional<char> pdbx_PDB_ins_code;
std::string label_asym_id;
std::string label_comp_id;
int label_seq_id;
ResidueSpec() {}
ResidueSpec(const std::string &auth_asym_id,
const std::string &auth_comp_id,
const std::string &auth_seq_id,
const std::string &pdbx_PDB_ins_code,
const std::string &label_asym_id,
const std::string &label_comp_id,
int label_seq_id)
: pdb_asym_id(auth_asym_id)
, pdb_comp_id(auth_comp_id)
, pdb_seq_id(auth_seq_id)
#if __has_include(<experimental/optional>)
, pdbx_PDB_ins_code(pdbx_PDB_ins_code.empty() ? optional<char>{} : std::experimental::make_optional(pdbx_PDB_ins_code.c_str()[0]))
#else
, pdbx_PDB_ins_code(pdbx_PDB_ins_code.empty() ? optional<char>{} : std::make_optional(pdbx_PDB_ins_code.c_str()[0]))
#endif
, label_asym_id(label_asym_id)
, label_comp_id(label_comp_id)
, label_seq_id(label_seq_id)
{
}
ResidueSpec(const ResidueSpec &rhs) = default;
ResidueSpec &operator=(const ResidueSpec &rhs) = default;
ResidueSpec(const cif::mm::residue &res)
: pdb_asym_id(res.get_pdb_strand_id())
, pdb_comp_id(res.get_compound_id())
, pdb_seq_id(res.get_pdb_seq_num())
, label_asym_id(res.get_asym_id())
, label_comp_id(res.get_compound_id())
, label_seq_id(res.get_seq_id())
{
char ins_code = res.get_pdb_ins_code().c_str()[0];
if (ins_code != 0 and ins_code != ' ')
pdbx_PDB_ins_code = ins_code;
}
ResidueSpec(const cif::mm::atom &atom)
: pdb_asym_id(atom.get_auth_asym_id())
, pdb_comp_id(atom.get_label_comp_id())
, pdb_seq_id(atom.get_auth_seq_id())
, label_asym_id(atom.get_label_asym_id())
, label_comp_id(atom.get_label_comp_id())
, label_seq_id(atom.get_label_seq_id())
{
char ins_code = atom.get_pdb_ins_code().c_str()[0];
if (ins_code != 0 and ins_code != ' ')
pdbx_PDB_ins_code = ins_code;
}
bool operator==(const ResidueSpec &rhs) const
{
return pdb_asym_id == rhs.pdb_asym_id and
pdb_comp_id == rhs.pdb_comp_id and
pdb_seq_id == rhs.pdb_seq_id and
pdbx_PDB_ins_code == rhs.pdbx_PDB_ins_code and
label_asym_id == rhs.label_asym_id and
label_comp_id == rhs.label_comp_id and
label_seq_id == rhs.label_seq_id;
}
};
using SkipList = std::vector<ResidueSpec>;
enum class SkipListFormat
{
OLD,
CIF
};
// --------------------------------------------------------------------
SkipList readSkipList(const std::filesystem::path &file);
SkipList readSkipList(std::istream &is);
void writeSkipList(std::ostream &os, const SkipList &list, SkipListFormat format);
void writeSkipList(const std::filesystem::path &file, const SkipList &list, SkipListFormat format);
} // namespace pdb_redo
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