|
1
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|
"""
|
|
2
|
|
test_smi2confs.py
|
|
3
|
|
"""
|
|
4
|
0
|
import sys
|
|
5
|
0
|
import os
|
|
6
|
0
|
import pytest
|
|
7
|
|
|
|
8
|
|
# define location of input files for testing
|
|
9
|
0
|
mydir = os.path.dirname(os.path.abspath(__file__))
|
|
10
|
|
|
|
11
|
|
# import functions to aid testing
|
|
12
|
0
|
sys.path.append(os.path.join(os.path.dirname(__file__), 'helpers'))
|
|
13
|
0
|
from helper import *
|
|
14
|
|
|
|
15
|
0
|
from quanformer.initialize_confs import *
|
|
16
|
|
|
|
17
|
|
# -----------------------
|
|
18
|
|
|
|
19
|
0
|
def test_generate_confs():
|
|
20
|
0
|
mol = read_mol(os.path.join(mydir, 'data_tests', 'steric_clash.smi'))
|
|
21
|
0
|
mol_with_confs = generate_confs(mol)
|
|
22
|
0
|
assert mol_with_confs.NumConfs() == 5
|
|
23
|
|
|
|
24
|
|
|
|
25
|
0
|
def test_resolve_clashes():
|
|
26
|
0
|
mol = read_mol(os.path.join(mydir, 'data_tests', 'steric_clash.smi'))
|
|
27
|
0
|
mol = generate_confs(mol)
|
|
28
|
0
|
for conf in mol.GetConfs():
|
|
29
|
0
|
resolve_clashes(conf, os.path.join(mydir, 'clashes.out'))
|
|
30
|
0
|
statinfo = os.stat(os.path.join(mydir, 'clashes.out'))
|
|
31
|
0
|
assert statinfo.st_size == 405
|
|
32
|
0
|
os.remove(os.path.join(mydir, 'clashes.out'))
|
|
33
|
|
|
|
34
|
|
|
|
35
|
0
|
def test_quick_opt():
|
|
36
|
|
# TODO
|
|
37
|
0
|
pass
|
|
38
|
|
|
|
39
|
|
|
|
40
|
0
|
def test_initialize_confs():
|
|
41
|
0
|
os.chdir(mydir)
|
|
42
|
0
|
initialize_confs(os.path.join(mydir, 'data_tests', 'methane.smi'))
|
|
43
|
0
|
statinfo = os.stat(os.path.join(mydir, 'methane.sdf'))
|
|
44
|
0
|
assert statinfo.st_size == 612
|
|
45
|
0
|
os.remove(os.path.join(mydir, 'methane.sdf'))
|
|
46
|
0
|
os.remove(os.path.join(mydir, 'numConfs.txt'))
|
|
47
|
|
|
|
48
|
|
|
|
49
|
0
|
def test_initialize_confs_rename():
|
|
50
|
0
|
initialize_confs(os.path.join(mydir, 'data_tests', 'methane_c2p.sdf'))
|
|
51
|
0
|
statinfo = os.stat(os.path.join(mydir, 'methane_c2p_quanformer.sdf'))
|
|
52
|
0
|
assert statinfo.st_size == 702
|
|
53
|
0
|
os.remove(os.path.join(mydir, 'methane_c2p_quanformer.sdf'))
|
|
54
|
0
|
os.remove(os.path.join(mydir, 'numConfs.txt'))
|
|
55
|
|
|
|
56
|
|
|
|
57
|
|
# test manually without pytest
|
|
58
|
0
|
if 0:
|
|
59
|
|
test_generate_confs()
|
|
60
|
|
test_resolve_clashes()
|
|
61
|
|
test_quick_opt()
|
|
62
|
|
test_initialize_confs()
|
|
63
|
|
test_initialize_confs_rename()
|
vtlim