1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
import os
import numpy as np
import random
# 'hof_qm7.txt.txt' retrieved from
# https://github.com/qmlcode/tutorial
def read_db_edata(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
|
