/*-
 * 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: dinsdag 22 mei, 2018
*/

#pragma once

#include <cif++/cif++.hpp>

#include "pdb-redo/BondMap.hpp"
#include "pdb-redo/Compound.hpp"
#include "pdb-redo/Restraints.hpp"

// --------------------------------------------------------------------

namespace pdb_redo
{

class AtomLocationProvider
{
  public:
	AtomLocationProvider(const AtomLocationProvider &) = delete;
	AtomLocationProvider &operator=(const AtomLocationProvider &) = delete;

	AtomLocationProvider(std::vector<cif::mm::atom> &atoms)
		: mAtoms(atoms)
	{
	}
	virtual ~AtomLocationProvider() = default;

	virtual DPoint operator[](AtomRef atomID) const;
	[[nodiscard]] virtual std::string atom(AtomRef atomID) const;

  protected:
	std::vector<cif::mm::atom> &mAtoms;
};

// --------------------------------------------------------------------

class DFCollector
{
  public:
	DFCollector(const DFCollector &) = delete;
	DFCollector &operator=(const DFCollector &) = delete;

	DFCollector() = default;
	virtual ~DFCollector() = default;

	virtual void add(AtomRef atom, double dx, double dy, double dz) = 0;
	void add(AtomRef atom, DPoint &&d)
	{
		add(atom, d.m_x, d.m_y, d.m_z);
	}
};

// --------------------------------------------------------------------

class Minimizer
{
  public:
	using XMap = clipper::Xmap<float>;

	Minimizer(const Minimizer &) = delete;
	Minimizer &operator=(const Minimizer &) = delete;

	virtual ~Minimizer() = default;

	// factory method:
	static Minimizer *create(const cif::crystal &crystal, const cif::mm::polymer &poly, int first, int last, const XMap &xMap);

	static Minimizer *create(const cif::crystal &crystal, cif::mm::structure &structure, const std::vector<cif::mm::atom> &atoms, const XMap &xMap)
	{
		return create(crystal, structure, atoms, &xMap);
	}

	// factory method for minimizer without density:
	static Minimizer *create(const cif::crystal &crystal, cif::mm::structure &structure, const std::vector<cif::mm::atom> &atoms)
	{
		return create(crystal, structure, atoms, nullptr);
	}

	// Drop all torsion restraints
	void dropTorsionRestraints();

	// Filter based on result of callback
	// Signature of callback should be: bool (*filter)(cif::mm::atom a1, cif::mm::atom a2, cif::mm::atom a3, cif::mm::atom a4)
	template <typename F>
	void filterTorsionRestraints(F &&cb)
	{
		auto e = std::remove_if(mTorsionRestraints.begin(), mTorsionRestraints.end(),
			[this, cb = std::forward<F>(cb)](TorsionRestraint &r)
			{
				return r.mA >= mAtoms.size() or r.mB >= mAtoms.size() or r.mC >= mAtoms.size() or r.mD >= mAtoms.size() or
					cb(mAtoms[r.mA], mAtoms[r.mB], mAtoms[r.mC], mAtoms[r.mD]);
			});
		
		for (auto i = e; i != mTorsionRestraints.end(); ++i)
			mRestraints.erase(std::remove(mRestraints.begin(), mRestraints.end(), &*i), mRestraints.end());

		mTorsionRestraints.erase(e, mTorsionRestraints.end());
	}

	// Set the map weight, default is 60
	void setMapWeight(float mapWeight);

	// Set the chiral volume ESD, default is 0.2
	void setChiralVolumeESD(float chiralityESD);

	// Set the planarity ESD, default is 0.11
	void setPlanarityESD(float planarityESD);

	void printStats();

	virtual double refine(bool storeAtoms) = 0;
	double score();
	[[nodiscard]] virtual std::vector<std::pair<std::string, cif::point>> getAtoms() const = 0;
	virtual void storeAtomLocations() = 0;

  protected:

	Minimizer(const cif::mm::structure &structure);

	static Minimizer *create(const cif::crystal &crystal, cif::mm::structure &structure, const std::vector<cif::mm::atom> &atoms, const XMap *xMap);

	virtual void addResidue(const cif::mm::residue &res);
	virtual void addPolySection(const cif::mm::polymer &poly, int first, int last);
	virtual void addDensityMap(const XMap &xMap, float mapWeight);
	virtual void Finish(const cif::crystal &crystal);

	double score(const AtomLocationProvider &loc);

	void addLinkRestraints(const cif::mm::residue &a, const cif::mm::residue &b,
		const std::string &atom_id_a, const std::string &atom_id_b, const std::string &linkName)
	{
		auto link = CompoundFactory::instance().createLink(linkName);
		if (not link)
			throw std::runtime_error("Failed to load link data for " + linkName);

		addLinkRestraints(a, b, atom_id_a, atom_id_b, *link);
	}

	void addLinkRestraints(const cif::mm::residue &a, const cif::mm::residue &b,
		const std::string &atom_id_a, const std::string &atom_id_b, const Link &link);

	void addSimpleBondRestraint(const cif::mm::residue &a, const cif::mm::residue &b,
		const std::string &atom_id_a, const std::string &atom_id_b);

	template <typename R>
	[[nodiscard]] std::tuple<double, double> rmsz(const AtomLocationProvider &atoms, const std::vector<R> &a) const
	{
		double z = 0, sum = 0;

		if (not a.empty())
		{
			sum = accumulate(a.begin(), a.end(),
				0.0, [&atoms](double s, const R &r)
				{ double z = r.f(atoms); return s + z; });

			z = std::sqrt(sum / a.size());
		}

		return { z, sum };
	}

	AtomRef ref(const cif::mm::atom &atom);

	BondMap createBondMap();

	bool mElectronScattering = false; // TODO: use!

	const cif::mm::structure &mStructure;

	std::vector<cif::mm::atom> mAtoms, mReferencedAtoms;
	std::vector<std::size_t> mRef2AtomIndex;
	std::map<std::string, AtomRef> mRefIndex;

	std::vector<BondRestraint> mBondRestraints;
	std::vector<AngleRestraint> mAngleRestraints;
	std::vector<TorsionRestraint> mTorsionRestraints;
	std::vector<TransPeptideRestraint> mTransPeptideRestraints;
	std::vector<ChiralVolumeRestraint> mChiralVolumeRestraints;
	std::vector<PlanarityRestraint> mPlanarityRestraints;
	std::vector<NonBondedContactRestraint> mNonBondedContactRestraints;
	std::unique_ptr<DensityRestraint> mDensityRestraint;

	std::vector<Restraint *> mRestraints;
};

} // namespace pdb_redo