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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