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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.
*/
#pragma once
#include <filesystem>
#include <map>
#include <set>
#include <stdexcept>
#include <unordered_map>
#include <cif++.hpp>
namespace pdb_redo
{
class BondMapException : public std::runtime_error
{
public:
BondMapException(const std::string &msg)
: runtime_error(msg)
{
}
};
class BondMap
{
public:
BondMap(const cif::mm::structure &structure, std::optional<std::tuple<cif::point,float>> around = {})
: BondMap(structure.get_datablock(), around, structure.get_model_nr())
{
}
BondMap(const cif::datablock &db, std::optional<std::tuple<cif::point,float>> around = {}, std::size_t model_nr = 1);
BondMap(const BondMap &) = delete;
BondMap &operator=(const BondMap &) = delete;
BondMap(BondMap &&);
BondMap &operator=(BondMap &&);
bool operator()(const std::string &atom_1, const std::string &atom_2) const
{
auto aix1 = index.find(atom_1);
auto aix2 = index.find(atom_2);
return aix1 != index.end() and aix2 != index.end() and isBonded(aix1->second, aix2->second);
}
bool operator()(const cif::mm::atom &atom_1, const cif::mm::atom &atom_2) const
{
return operator()(atom_1.id(), atom_2.id());
}
bool is1_4(const std::string &atom_1, const std::string &atom_2) const
{
uint32_t ixa = index.at(atom_1);
uint32_t ixb = index.at(atom_2);
return bond_1_4.count(key(ixa, ixb));
}
bool is1_4(const cif::mm::atom &atom_1, const cif::mm::atom &atom_2) const
{
return is1_4(atom_1.id(), atom_2.id());
}
// links coming from the struct_conn records:
std::vector<std::string> linked(const std::string &atom) const;
// This list of atomID's is comming from either CCD or the CCP4 dictionaries loaded
static std::vector<std::string> atomIDsForCompound(const std::string &compoundID);
private:
bool isBonded(uint32_t ai, uint32_t bi) const
{
return bond.count(key(ai, bi)) != 0;
}
uint64_t key(uint32_t a, uint32_t b) const
{
if (a > b)
std::swap(a, b);
return static_cast<uint64_t>(a) | (static_cast<uint64_t>(b) << 32);
}
std::tuple<uint32_t, uint32_t> dekey(uint64_t k) const
{
return std::make_tuple(
static_cast<uint32_t>(k >> 32),
static_cast<uint32_t>(k));
}
uint32_t dim;
std::unordered_map<std::string, uint32_t> index;
std::set<uint64_t> bond, bond_1_4;
std::map<std::string, std::set<std::string>> link;
};
} // namespace pdbx
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