/*-
 * 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;
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 * 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.
 */

// Lib for working with structures as contained in mmCIF and PDB files

#pragma once

#include <cstdint>
#include <stdexcept>
#include <string>

namespace cif
{

enum atom_type : uint8_t
{
	Nn = 0, // Unknown

	H = 1,  // Hydro­gen
	He = 2, // He­lium

	Li = 3,  // Lith­ium
	Be = 4,  // Beryl­lium
	B = 5,   // Boron
	C = 6,   // Carbon
	N = 7,   // Nitro­gen
	O = 8,   // Oxy­gen
	F = 9,   // Fluor­ine
	Ne = 10, // Neon

	Na = 11, // So­dium
	Mg = 12, // Magne­sium
	Al = 13, // Alumin­ium
	Si = 14, // Sili­con
	P = 15,  // Phos­phorus
	S = 16,  // Sulfur
	Cl = 17, // Chlor­ine
	Ar = 18, // Argon

	K = 19,  // Potas­sium
	Ca = 20, // Cal­cium
	Sc = 21, // Scan­dium
	Ti = 22, // Tita­nium
	V = 23,  // Vana­dium
	Cr = 24, // Chrom­ium
	Mn = 25, // Manga­nese
	Fe = 26, // Iron
	Co = 27, // Cobalt
	Ni = 28, // Nickel
	Cu = 29, // Copper
	Zn = 30, // Zinc
	Ga = 31, // Gallium
	Ge = 32, // Germa­nium
	As = 33, // Arsenic
	Se = 34, // Sele­nium
	Br = 35, // Bromine
	Kr = 36, // Kryp­ton

	Rb = 37, // Rubid­ium
	Sr = 38, // Stront­ium
	Y = 39,  // Yttrium
	Zr = 40, // Zirco­nium
	Nb = 41, // Nio­bium
	Mo = 42, // Molyb­denum
	Tc = 43, // Tech­netium
	Ru = 44, // Ruthe­nium
	Rh = 45, // Rho­dium
	Pd = 46, // Pallad­ium
	Ag = 47, // Silver
	Cd = 48, // Cad­mium
	In = 49, // Indium
	Sn = 50, // Tin
	Sb = 51, // Anti­mony
	Te = 52, // Tellurium
	I = 53,  // Iodine
	Xe = 54, // Xenon
	Cs = 55, // Cae­sium
	Ba = 56, // Ba­rium
	La = 57, // Lan­thanum

	Hf = 72, // Haf­nium
	Ta = 73, // Tanta­lum
	W = 74,  // Tung­sten
	Re = 75, // Rhe­nium
	Os = 76, // Os­mium
	Ir = 77, // Iridium
	Pt = 78, // Plat­inum
	Au = 79, // Gold
	Hg = 80, // Mer­cury
	Tl = 81, // Thallium
	Pb = 82, // Lead
	Bi = 83, // Bis­muth
	Po = 84, // Polo­nium
	At = 85, // Asta­tine
	Rn = 86, // Radon
	Fr = 87, // Fran­cium
	Ra = 88, // Ra­dium
	Ac = 89, // Actin­ium

	Rf = 104, // Ruther­fordium
	Db = 105, // Dub­nium
	Sg = 106, // Sea­borgium
	Bh = 107, // Bohr­ium
	Hs = 108, // Has­sium
	Mt = 109, // Meit­nerium
	Ds = 110, // Darm­stadtium
	Rg = 111, // Roent­genium
	Cn = 112, // Coper­nicium
	Nh = 113, // Nihon­ium
	Fl = 114, // Flerov­ium
	Mc = 115, // Moscov­ium
	Lv = 116, // Liver­morium
	Ts = 117, // Tenness­ine
	Og = 118, // Oga­nesson

	Ce = 58, // Cerium
	Pr = 59, // Praseo­dymium
	Nd = 60, // Neo­dymium
	Pm = 61, // Prome­thium
	Sm = 62, // Sama­rium
	Eu = 63, // Europ­ium
	Gd = 64, // Gadolin­ium
	Tb = 65, // Ter­bium
	Dy = 66, // Dyspro­sium
	Ho = 67, // Hol­mium
	Er = 68, // Erbium
	Tm = 69, // Thulium
	Yb = 70, // Ytter­bium
	Lu = 71, // Lute­tium

	Th = 90,  // Thor­ium
	Pa = 91,  // Protac­tinium
	U = 92,   // Ura­nium
	Np = 93,  // Neptu­nium
	Pu = 94,  // Pluto­nium
	Am = 95,  // Ameri­cium
	Cm = 96,  // Curium
	Bk = 97,  // Berkel­ium
	Cf = 98,  // Califor­nium
	Es = 99,  // Einstei­nium
	Fm = 100, // Fer­mium
	Md = 101, // Mende­levium
	No = 102, // Nobel­ium
	Lr = 103, // Lawren­cium

	D = 129, // Deuterium
};

// --------------------------------------------------------------------
// atom_type_info

enum class radius_type
{
	calculated,
	empirical,
	covalent_empirical,

	single_bond,
	double_bond,
	triple_bond,

	van_der_waals,

	type_count
};

constexpr size_t kRadiusTypeCount = static_cast<size_t>(radius_type::type_count);

enum class ionic_radius_type
{
	effective, crystal
};

struct atom_type_info
{
	atom_type type;
	std::string name;
	std::string symbol;
	float weight;
	bool metal;
	float radii[kRadiusTypeCount];
};

extern const atom_type_info kKnownAtoms[];

// --------------------------------------------------------------------
// AtomTypeTraits

class atom_type_traits
{
  public:
	atom_type_traits(atom_type a);
	atom_type_traits(const std::string &symbol);

	atom_type type() const { return m_info->type; }
	std::string name() const { return m_info->name; }
	std::string symbol() const { return m_info->symbol; }
	float weight() const { return m_info->weight; }

	bool is_metal() const { return m_info->metal; }

	static bool is_element(const std::string &symbol);
	static bool is_metal(const std::string &symbol);

	float radius(radius_type type = radius_type::single_bond) const
	{
		if (type >= radius_type::type_count)
			throw std::invalid_argument("invalid radius requested");
		return m_info->radii[static_cast<size_t>(type)] / 100.f;
	}

	/// \brief Return the radius for a charged version of this atom in a solid crystal
	///
	/// \param charge  The charge of the ion
	/// \return        The radius of the ion
	float crystal_ionic_radius(int charge) const;

	/// \brief Return the radius for a charged version of this atom in a non-solid environment
	///
	/// \param charge  The charge of the ion
	/// \return        The radius of the ion
	float effective_ionic_radius(int charge) const;

	/// \brief Return the radius for a charged version of this atom, returns the effective radius by default
	///
	/// \param charge  The charge of the ion
	/// \return        The radius of the ion
	float ionic_radius(int charge, ionic_radius_type type = ionic_radius_type::effective) const
	{
		return type == ionic_radius_type::effective ? effective_ionic_radius(charge) : crystal_ionic_radius(charge);
	}

	// data type encapsulating the Waasmaier & Kirfel scattering factors
	// in a simplified form (only a and b).
	// Added the electrion scattering factors as well
	struct SFData
	{
		double a[6], b[6];
	};

	// to get the Cval and Siva values, use this constant as charge:
	enum
	{
		kWKSFVal = -99
	};

	const SFData &wksf(int charge = 0) const;
	const SFData &elsf() const;

  private:
	const struct atom_type_info *m_info;
};

} // namespace pdbx
