forked from tchaney97/IsoScatter
-
Notifications
You must be signed in to change notification settings - Fork 0
/
RunIsoScatter.py
78 lines (65 loc) · 2.5 KB
/
RunIsoScatter.py
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
77
78
import numpy as np
import glob
import os
import argparse
import time
from utilities import parse_config_file, save_config_to_txt
from IsoScatter import xyz_simulation
def main(config):
# Input Parameters
input_folder = config.get('input_folder', None)
input_filepath = config.get('input_filepath', None)
filetype = config.get('filetype', 'xyz')
gen_name = config.get('gen_name')
q_min = float(config.get('q_voxel_size', 0.01))
q_max = float(config.get('q_voxel_size', 0.01))
num_qs = float(config.get('q_voxel_size', 0.01))
logspace_q = config.get('log_q', False)
energy = float(config.get('energy', 1))
output_dir = config.get('output_dir', os.getcwd())
hull_method = config.get('hull_method', False)
vol_pct = float(config.get('vol_pct', 0))
solvent_edens = float(config.get('solvent_edens', 0))
if input_folder:
input_paths = glob.glob(f'{input_folder}/*{filetype}')
elif input_filepath:
input_paths = [input_filepath]
else:
raise Exception('Either input_folder or input_path must be specified')
if logspace_q:
q_min = np.log10(q_min)
q_max = np.log10(q_max)
qs = np.logspace(q_min, q_max, num_qs)
else:
qs = np.linspace(q_min, q_max, num_qs)
for i, input_path in enumerate(input_paths):
iq, q_vals = xyz_simulation(input_path,
qs,
vol_pct,
solvent_edens,
energy,
hull_method=hull_method)
if i==0:
iq_avg = iq
else:
iq_avg += iq
iq_avg /= len(input_paths)
# Save
save_path = f'{output_dir}/{gen_name}_output_files'
if not os.path.exists(save_path):
os.mkdir(save_path)
np.save(f'{save_path}/{gen_name}_iq.npy', iq_avg)
np.save(f'{save_path}/{gen_name}_q_vals.npy', q_vals)
#add some plotting later?
save_config_to_txt(config, f'{save_path}/{gen_name}_config.txt')
if __name__ == "__main__":
start = time.time()
parser = argparse.ArgumentParser(description="Process a configuration file.")
parser.add_argument('--config', type=str, required=True, help='Path to the configuration file')
args = parser.parse_args()
config_path = args.config
config = parse_config_file(config_path)
main(config)
end = time.time()
runtime = end-start
print(f'\nTotal Time: {str(runtime)}')