element.h

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/**
 * \file IMP/atom/element.h \brief Define the elements used in \imp.
 *
 * Copyright 2007-2020 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPATOM_ELEMENT_H
#define IMPATOM_ELEMENT_H

#include <IMP/atom/atom_config.h>
#include <IMP/base_types.h>

#include <IMP/log.h>
#include <IMP/exception.h>
#include <boost/unordered_map.hpp>

#include <string>

IMPATOM_BEGIN_NAMESPACE

//! The various elements currently supported/known.
enum Element {
  UNKNOWN_ELEMENT = 0,
#ifndef IMP_DOXYGEN
  OH = -1,
  H2O = -2,
#endif
  H = 1,
  He = 2,
  Li = 3,
  Be = 4,
  B = 5,
  C = 6,
  N = 7,
  O = 8,
  F = 9,
  Ne = 10,
  Na = 11,
  Mg = 12,
  Al = 13,
  Si = 14,
  P = 15,
  S = 16,
  Cl = 17,
  Ar = 18,
  K = 19,
  Ca = 20,
  Sc = 21,
  Ti = 22,
  V = 23,
  Cr = 24,
  Mn = 25,
  Fe = 26,
  Co = 27,
  Ni = 28,
  Cu = 29,
  Zn = 30,
  Ga = 31,
  Ge = 32,
  As = 33,
  Se = 34,
  Br = 35,
  Kr = 36,
  Rb = 37,
  Sr = 38,
  Y = 39,
  Zr = 40,
  Nb = 41,
  Mo = 42,
  Tc = 43,
  Ru = 44,
  Rh = 45,
  Pd = 46,
  Ag = 47,
  Cd = 48,
  In = 49,
  Sn = 50,
  Sb = 51,
  Te = 52,
  I = 53,
  Xe = 54,
  Cs = 55,
  Ba = 56,
  La = 57,
  Ce = 58,
  Pr = 59,
  Nd = 60,
  Pm = 61,
  Sm = 62,
  Eu = 63,
  Gd = 64,
  Tb = 65,
  Dy = 66,
  Ho = 67,
  Er = 68,
  Tm = 69,
  Yb = 70,
  Lu = 71,
  Hf = 72,
  Ta = 73,
  W = 74,
  Re = 75,
  Os = 76,
  Ir = 77,
  Pt = 78,
  Au = 79,
  Hg = 80,
  Tl = 81,
  Pb = 82,
  Bi = 83,
  Po = 84,
  At = 85,
  Rn = 86,
  Fr = 87,
  Ra = 88,
  Ac = 89,
  Th = 90,
  Pa = 91,
  U = 92,
  Np = 93,
  Pu = 94,
  Am = 95,
  Cm = 96,
  Bk = 97,
  Cf = 98,
  Es = 99,
  Fm = 100,
  Md = 101,
  No = 102,
  Lr = 103,
  Db = 104,
  Jl = 105,
  Rf = 106
#ifndef IMP_DOXYGEN
  ,
  NUMBER_OF_ELEMENTS = 107
#endif
};

#ifndef IMP_DOXYGEN
inline size_t hash_value(Element e) { return e; }
#endif

/** Class to translate between element symbols, names and masses.*/
class IMPATOMEXPORT ElementTable {
 public:
  ElementTable();

  //! get element from the string name (PDB columns 77-78)
  Element get_element(const std::string& s) const;

  //! get string name for Element
  std::string get_name(Element e) const;

  //! get mass for Element
  Float get_mass(Element e) const { return mass_[e]; }

 private:
  struct ElementString {
    std::string name;
    Element e;
  };

  static ElementString element_strings_[];
  static Float mass_[];
  static boost::unordered_map<std::string, Element> string_2_element_;
  static boost::unordered_map<Element, std::string> element_2_string_;
};

IMPATOMEXPORT ElementTable& get_element_table();

IMPATOM_END_NAMESPACE

#endif /* IMPATOM_ELEMENT_H */