Refactor files

1 files changed, 0 insertions, 144 deletions

diff --git a/read_qm7_data.py b/read_qm7_data.py
deleted file mode 100644
index 068ea1a42..000000000
--- a/read_qm7_data.py
+++ /dev/null
@@ -1,144 +0,0 @@
-"""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.
-"""
-import os
-import time
-import numpy as np
-import random
-from misc import printc
-
-
-# 'periodic_table_of_elements.txt' retrieved from
-# https://gist.github.com/GoodmanSciences/c2dd862cd38f21b0ad36b8f96b4bf1ee
-def read_nc_data(data_path):
-    """
-    Reads nuclear charge data from file and returns a dictionary.
-    data_path: path to the data directory.
-    """
-    fname = 'periodic_table_of_elements.txt'
-    with open(''.join([data_path, '\\', fname]), 'r') as infile:
-        temp_lines = infile.readlines()
-
-    del temp_lines[0]
-
-    lines = []
-    for temp_line in temp_lines:
-        new_line = temp_line.split(sep=',')
-        lines.append(new_line)
-
-    # Dictionary of nuclear charge.
-    return {line[2]: int(line[0]) for line in lines}
-
-
-# 'hof_qm7.txt.txt' retrieved from
-# https://github.com/qmlcode/tutorial
-def reas_db_data(zi_data,
-                 data_path,
-                 r_seed=111):
-    """
-    Reads molecule database and extracts
-    its contents as usable variables.
-    zi_data: dictionary containing nuclear charge data.
-    data_path: path to the data directory.
-    r_seed: random seed.
-    """
-    os.chdir(data_path)
-
-    fname = 'hof_qm7.txt'
-    with open(fname, 'r') as infile:
-        lines = infile.readlines()
-
-    # Temporary energy dictionary.
-    energy_temp = dict()
-
-    for line in lines:
-        xyz_data = line.split()
-
-        xyz_name = xyz_data[0]
-        hof = float(xyz_data[1])
-        dftb = float(xyz_data[2])
-        # print(xyz_name, hof, dftb)
-
-        energy_temp[xyz_name] = np.array([hof, hof - dftb])
-
-    # Use a random seed.
-    random.seed(r_seed)
-
-    et_keys = list(energy_temp.keys())
-    random.shuffle(et_keys)
-
-    # Temporary energy dictionary, shuffled.
-    energy_temp_shuffled = dict()
-    for key in et_keys:
-        energy_temp_shuffled.update({key: energy_temp[key]})
-
-    mol_data = []
-    mol_nc_data = []
-    # Actual reading of the xyz files.
-    for i, k in enumerate(energy_temp_shuffled.keys()):
-        with open(k, 'r') as xyz_file:
-            lines = xyz_file.readlines()
-
-        len_lines = len(lines)
-        mol_temp_data = []
-        mol_nc_temp_data = np.array(np.zeros(len_lines-2))
-        for j, line in enumerate(lines[2:len_lines]):
-            line_list = line.split()
-
-            mol_nc_temp_data[j] = float(zi_data[line_list[0]])
-            line_data = np.array(np.asarray(line_list[1:4], dtype=float))
-            mol_temp_data.append(line_data)
-
-        mol_data.append(mol_temp_data)
-        mol_nc_data.append(mol_nc_temp_data)
-
-    # Convert everything to a numpy array.
-    molecules = np.array([np.array(mol) for mol in mol_data])
-    nuclear_charge = np.array([nc_d for nc_d in mol_nc_data])
-    energy_pbe0 = np.array([energy_temp_shuffled[k][0]
-                            for k in energy_temp_shuffled.keys()])
-    energy_delta = np.array([energy_temp_shuffled[k][1]
-                             for k in energy_temp_shuffled.keys()])
-
-    return molecules, nuclear_charge, energy_pbe0, energy_delta
-
-
-def read_qm7_data():
-    """
-    Reads all the qm7 data.
-    """
-    tic = time.perf_counter()
-    printc('Data reading started.', 'CYAN')
-
-    init_path = os.getcwd()
-    os.chdir('data')
-    data_path = os.getcwd()
-
-    zi_data = read_nc_data(data_path)
-    molecules, nuclear_charge, energy_pbe0, energy_delta = \
-        reas_db_data(zi_data, data_path)
-
-    os.chdir(init_path)
-    toc = time.perf_counter()
-    printc('\tData reading took {:.4f} seconds.'.format(toc-tic), 'GREEN')
-
-    return zi_data, molecules, nuclear_charge, energy_pbe0, energy_delta