/*-
 * 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 <unordered_map>

#include <clipper/clipper.h>

#include "cif++/Structure.hpp"

namespace mmcif
{

class DistanceMap
{
  public:
	DistanceMap(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell,
		float maxDistance);

	// simplified version for subsets of atoms (used in refining e.g.)
//	DistanceMap(const Structure& p, const std::vector<Atom>& atoms);
	
	DistanceMap(const DistanceMap&) = delete;
	DistanceMap& operator=(const DistanceMap&) = delete;

	float operator()(const Atom& a, const Atom& b) const;

	std::vector<Atom> near(const Atom& a, float maxDistance = 3.5f) const;
	std::vector<Atom> near(const Point& p, float maxDistance = 3.5f) const;

	static std::vector<clipper::RTop_orth>
		AlternativeSites(const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);

  private:

	typedef std::map<std::tuple<size_t,size_t>,std::tuple<float,int32_t>> DistMap;

	void AddDistancesForAtoms(const Residue& a, const Residue& b, DistMap& dm, int32_t rtix);

	const Structure&						structure;
	clipper::Cell							cell;
	clipper::Spacegroup						spacegroup;
	size_t									dim;
	std::unordered_map<std::string,size_t>	index;
	std::map<size_t,std::string>			rIndex;
	
	float									mMaxDistance, mMaxDistanceSQ;
	
	std::vector<std::tuple<float,int32_t>>	mA;
	std::vector<size_t>						mIA, mJA;
	Point									mD;			// needed to move atoms to center
	std::vector<clipper::RTop_orth>			mRtOrth;
};

}
