notebooks/1_plot_pn_vs_eneg.ipynb

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    "\n",
    "Short intro: basic plotting using the periodic table\n",
    "==========\n",
    "\n",
    "- **Complexity level**: novice\n",
    "- **Requirements**: basic knowledge of chemistry and Python\n",
    "\n",
    "The reader would probably agree, that the periodic table is crucially important. The **chemical elements**, as well as the **chemical formulae** are introduced here. Let's explore this a bit.\n",
    "\n",
    "We know the inorganic chemical formulae are constructed according to the electronegativities of the chemical elements. Generally, **the more** the electronegativity value, **the more** to the right the chemical element in the formula. Although there are some details, concerned with the exact definition of the electronegativity.\n",
    "\n",
    "Let's plot the Pauling electronegativities _vs._ periodic numbers of the chemical elements using the popular `matplotlib` Python library.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "plt.switch_backend('agg')\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Now we define the periodic table and electronegativities.\n",
    "\n",
    "Note that there are several electronegativity scales (see _e.g._ those given in the [mendeleev database](http://mendeleev.readthedocs.io/en/stable/data.html#electronegativities)). And here we use the Pauling's scale.\n",
    "\n",
    "The **periodic numbers** reflect the periodic table proposed by Julius-Lothar Meyer in 1870. How is that different from the well-known one by Dmitry Mendeleev? The rows and columns are exchanged!\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "chemical_elements = [\n",
    "'H',                                                                                                                                                                                      'He',\n",
    "'Li', 'Be',                                                                                                                                                 'B',  'C',  'N',  'O',  'F',  'Ne',\n",
    "'Na', 'Mg',                                                                                                                                                 'Al', 'Si', 'P',  'S',  'Cl', 'Ar',\n",
    "'K',  'Ca',                                                                                     'Sc', 'Ti', 'V',  'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr',\n",
    "'Rb', 'Sr',                                                                                     'Y',  'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I',  'Xe',\n",
    "'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W',  'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn',\n",
    "'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U',  'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']\n",
    "\n",
    "periodic_numbers = [\n",
    "1,                                                                                                                                                                                        112,\n",
    "2,    8,                                                                                                                                                     82,   88,   94,  100,  106,  113,\n",
    "3,    9,                                                                                                                                                     83,   89,   95,  101,  107,  114,\n",
    "4,   10,                                                                                        14,    46,   50,   54,   58,   62,   66,   70,   74,   78,   84,   90,   96,  102,  108,  115,\n",
    "5,   11,                                                                                        15,    47,   51,   55,   59,   63,   67,   71,   75,   79,   85,   91,   97,  103,  109,  116,\n",
    "6,   12,    16,    18,   20,  22,   24,    26,   28,   30,   32,   34,   36,   38,  40,   42,   44,    48,   52,   56,   60,   64,   68,   72,   76,   80,   86,   92,   98,  104,  110,  117,\n",
    "7,   13,    17,    19,   21,  23,   25,    27,   29,   31,   33,   35,   37,   39,  41,   43,   45,    49,   53,   57,   61,   65,   69,   73,   77,   81,   87,   93,   99,  105,  111,  118]\n",
    "\n",
    "electronegativities = [\n",
    "2.2,                                                                                                                                                                                      0,\n",
    "0.98, 1.57,                                                                                                                                                 2.04, 2.55, 3.04, 3.44, 3.98, 0,\n",
    "0.93, 1.31,                                                                                                                                                 1.61, 1.90, 2.19, 2.58, 3.16, 0,\n",
    "0.82, 1.00,                                                                                     1.36, 1.54, 1.63, 1.66, 1.55, 1.83, 1.88, 1.91, 1.9,  1.65, 1.81, 2.01, 2.18, 2.55, 2.96, 3,\n",
    "0.82, 0.95,                                                                                     1.22, 1.33, 1.60, 2.16, 1.90, 2.20, 2.28, 2.20, 1.93, 1.69, 1.78, 1.96, 2.05, 2.10, 2.66, 2.6,\n",
    "0.79, 0.89, 1.1,  1.12, 1.13, 1.14, 1.13, 1.17,  1.2,  1.2,  1.1, 1.22, 1.23, 1.24, 1.25, 1.1,  1.27, 1.30, 1.50, 2.36, 1.90, 2.20, 2.20, 2.28, 2.54, 2.00, 1.62, 2.33, 2.02, 2.00, 2.20, 2.20,\n",
    "0.70, 0.90, 1.1,  1.30, 1.50, 1.38, 1.36, 1.28,  1.3,  1.3,  1.3, 1.3,  1.3,  1.3,  1.3,  1.3,  1.3,  0,    0,    0,    0,    0,    0,    0,    0,    0,    0,    0,    0,    0,    0,    0]"
   ]
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   "cell_type": "markdown",
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   "source": [
    "\n",
    "Then we _massage_ our data a little bit adding a summary trend line.\n",
    "\n",
    "We're good to go:\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "\n",
    "points = [pair for pair in zip(electronegativities, periodic_numbers) if pair[0] > 0]\n",
    "x, y = zip(*points)\n",
    "\n",
    "fitted_coeffs = np.polyfit(x, y, 1)\n",
    "fitted_fn = np.poly1d(fitted_coeffs)\n",
    "\n",
    "fig, ax = plt.subplots(figsize=(15, 10))\n",
    "\n",
    "ax.set_xlabel('Electronegativity')\n",
    "ax.set_ylabel('Periodic Number')\n",
    "\n",
    "ax.scatter(x, y, c='b', s=2, label='Chem. elements')\n",
    "plt.plot(x, fitted_fn(x), c='g', linewidth=0.5, label='Linear fit')\n",
    "plt.legend()\n",
    "\n",
    "for i, label in enumerate(chemical_elements):\n",
    "    ax.annotate(\n",
    "        label,\n",
    "        (electronegativities[i], periodic_numbers[i]),\n",
    "        size=10\n",
    "    )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n",
    "Look, the whole chemistry is encoded in the resulted figure :)\n",
    "\n",
    "Were you able to follow everything? Please, try to explain the plot: why it looks specifically like this?\n"
   ]
  }
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