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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 <cif++.hpp>
#include <unordered_map>
#ifdef near
#undef near
#endif
namespace pdb_redo
{
class DistanceMap
{
public:
DistanceMap(const cif::mm::structure &p, const cif::crystal &crystal, float maxDistance);
DistanceMap(const cif::mm::structure &p, float maxDistance)
: DistanceMap(p, cif::crystal(p.get_datablock()), maxDistance)
{
}
DistanceMap(const DistanceMap &) = delete;
DistanceMap &operator=(const DistanceMap &) = delete;
float operator()(const std::string &a, const std::string &b) const;
std::vector<cif::mm::atom> near(const cif::mm::atom &atom, float maxDistance = 3.5f) const;
private:
using DistKeyType = std::tuple<std::size_t, std::size_t>;
using DistValueType = std::tuple<float, cif::sym_op, bool>;
using DistMap = std::map<DistKeyType, DistValueType>;
void AddDistancesForAtoms(const std::vector<std::tuple<std::size_t,cif::point>> &a,
const std::vector<std::tuple<std::size_t,cif::point>> &b, DistMap &dm);
void AddDistancesForAtoms(const std::vector<std::tuple<std::size_t,cif::point>> &a,
const std::vector<std::tuple<std::size_t,cif::point>> &b, DistMap &dm, cif::sym_op symop);
cif::point offsetToOrigin(const cif::point &p) const;
const cif::mm::structure &mStructure;
cif::crystal crystal;
std::size_t dim;
std::unordered_map<std::string, std::size_t> index;
std::map<std::size_t, std::string> rIndex;
float mMaxDistance, mMaxDistanceSQ;
std::vector<std::tuple<float, cif::sym_op, bool>> mA;
std::vector<std::size_t> mIA, mJA;
};
} // namespace pdb_redo
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