From 96eade3b9f72c5d1fa5bae27ba82a2cd23e1e200 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Fri, 21 Feb 2020 17:16:22 -0700
Subject: Add nuclear charge

---
 ml_exp/compound.py      |  11 ++++
 ml_exp/data.py          | 141 ++++++++++++++++++++++++++++++++++++++++++++++++
 ml_exp/read_qm7_data.py |  11 ++++
 3 files changed, 163 insertions(+)
 create mode 100644 ml_exp/data.py

diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 6fd46fc3a..cfa3e0322 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -21,13 +21,22 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 import numpy as np
+from ml_exp.data import NUCLEAR_CHARGE
 
 
 class Compound:
     def __init__(self, xyz=None):
+        # empty_array = np.asarray([], dtype=float)
+
         self.n = None
         self.atoms = None
+        self.atoms_nc = None
         self.coordinates = None
+        self.energy = None
+
+        self.coulomb_matrix = None
+        self.lennard_jones_matrix = None
+        self.bob = None
 
         if xyz is not None:
             self.read_xyz(xyz)
@@ -42,10 +51,12 @@ class Compound:
 
         self.n = int(lines[0])
         self.atoms = []
+        self.atoms_nc = np.empty(self.n, dtype=int)
         self.coordinates = np.empty((self.n, 3), dtype=float)
 
         for i, atom in enumerate(lines[2:self.n + 2]):
             atom_d = atom.split()
 
             self.atoms.append(atom_d[0])
+            self.atoms_nc[i] = NUCLEAR_CHARGE[atom_d[0]]
             self.coordinates[i] = np.asarray(atom_d[1:4], dtype=float)
diff --git a/ml_exp/data.py b/ml_exp/data.py
new file mode 100644
index 000000000..243aff168
--- /dev/null
+++ b/ml_exp/data.py
@@ -0,0 +1,141 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+NUCLEAR_CHARGE = {
+    '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,
+    'Rf': 104,
+    'Db': 105,
+    'Sg': 106,
+    'Bh': 107,
+    'Hs': 108,
+    'Mt': 109,
+    'Ds ': 110,
+    'Rg ': 111,
+    'Cn ': 112,
+    'Nh': 113,
+    'Fl': 114,
+    'Mc': 115,
+    'Lv': 116,
+    'Ts': 117,
+    'Og': 118}
diff --git a/ml_exp/read_qm7_data.py b/ml_exp/read_qm7_data.py
index 81be05a17..63c48195c 100644
--- a/ml_exp/read_qm7_data.py
+++ b/ml_exp/read_qm7_data.py
@@ -49,6 +49,17 @@ def read_nc_data(data_path):
     return {line[2]: int(line[0]) for line in lines}
 
 
+# For use in the rewriting of the code (from functional programming to object
+# oriented programming-ish)
+def print_nc(nc_data):
+    """
+    Prints the nuclear charge data to the terminal.
+    nc_data: dict of nc.
+    """
+    for key in nc_data.keys():
+        print(f'\'{key}\': {nc_data[key]},')
+
+
 # 'hof_qm7.txt.txt' retrieved from
 # https://github.com/qmlcode/tutorial
 def read_db_data(zi_data,
-- 
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