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1
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"""
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2
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test_pipeline.py
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3
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"""
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4
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0
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import sys
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5
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0
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import os
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6
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0
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import pytest
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7
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0
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import shutil
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8
|
|
|
|
9
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|
# define location of input files for testing
|
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10
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0
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mydir = os.path.dirname(os.path.abspath(__file__))
|
|
11
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|
|
|
12
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|
# import functions to aid testing
|
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13
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0
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sys.path.append(os.path.join(os.path.dirname(__file__), 'helpers'))
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14
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0
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from helper import *
|
|
15
|
|
|
|
16
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0
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from quanformer.pipeline import *
|
|
17
|
|
|
|
18
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|
# -----------------------
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|
19
|
|
|
|
20
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0
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def test_name_manager_pass():
|
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21
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0
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curr_dir, checked_infile, prefix, ext, no_path_infile = name_manager(
|
|
22
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|
os.path.join(mydir, 'data_tests', 'two_alkanes.smi'))
|
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23
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0
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assert prefix == 'two_alkanes'
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|
24
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0
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assert ext == '.smi'
|
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25
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0
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assert no_path_infile == 'two_alkanes.smi'
|
|
26
|
|
|
|
27
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0
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def test_name_manager_fail():
|
|
28
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0
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with pytest.raises(FileNotFoundError):
|
|
29
|
0
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curr_dir, checked_infile, prefix, ext, no_path_infile = name_manager(
|
|
30
|
|
os.path.join(mydir, 'data_tests', 'blah.sdf'))
|
|
31
|
0
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assert True
|
|
32
|
|
|
|
33
|
0
|
def test_setup_conformers():
|
|
34
|
0
|
setup_conformers(os.path.join(mydir, 'data_tests', 'two_alkanes.smi'))
|
|
35
|
|
|
|
36
|
|
# check pre-filtered file
|
|
37
|
0
|
mols = read_mol(os.path.join(mydir, 'two_alkanes.sdf'), True)
|
|
38
|
0
|
mol = next(mols)
|
|
39
|
0
|
assert mol.NumConfs() == 9
|
|
40
|
0
|
mol = next(mols)
|
|
41
|
0
|
assert mol.NumConfs() == 3
|
|
42
|
|
|
|
43
|
|
# check post-filtered file
|
|
44
|
0
|
mols = read_mol(os.path.join(mydir, 'two_alkanes-200.sdf'), True)
|
|
45
|
0
|
mol = next(mols)
|
|
46
|
0
|
assert mol.NumConfs() == 3
|
|
47
|
0
|
mol = next(mols)
|
|
48
|
0
|
assert mol.NumConfs() == 3
|
|
49
|
0
|
os.remove(os.path.join(mydir, 'two_alkanes.sdf'))
|
|
50
|
0
|
os.remove(os.path.join(mydir, 'two_alkanes-200.sdf'))
|
|
51
|
0
|
os.remove(os.path.join(mydir, 'numConfs.txt'))
|
|
52
|
|
|
|
53
|
0
|
def test_setup_conformers_ext():
|
|
54
|
0
|
with pytest.raises(ValueError):
|
|
55
|
0
|
setup_conformers(os.path.join(mydir, 'data_tests', 'methane_c2p.sdf'))
|
|
56
|
0
|
assert True
|
|
57
|
|
|
|
58
|
0
|
def test_setup_calculations_true():
|
|
59
|
0
|
setup_calculations(
|
|
60
|
|
os.path.join(mydir, 'data_tests', 'methane_c2p.sdf'),
|
|
61
|
|
'mp2',
|
|
62
|
|
'def2-sv(p)',
|
|
63
|
|
'spe')
|
|
64
|
|
# check file byte size (this line should be updated if confs_to_psi changes)
|
|
65
|
0
|
assert os.path.getsize(os.path.join('methane', '1', 'input.dat')) == 370
|
|
66
|
0
|
shutil.rmtree('methane')
|
|
67
|
|
|
|
68
|
0
|
def test_setup_calculations_false():
|
|
69
|
0
|
with pytest.raises(ValueError):
|
|
70
|
0
|
setup_calculations(
|
|
71
|
|
os.path.join(mydir, 'data_tests', 'methane_c2p.sdf'),
|
|
72
|
|
'mp2',
|
|
73
|
|
'def2-sv(p)',
|
|
74
|
|
'blah')
|
|
75
|
0
|
assert True
|
|
76
|
|
|
|
77
|
0
|
def test_process_results():
|
|
78
|
0
|
process_results(os.path.join(mydir, 'data_tests', 'gbi-200.sdf'), 'opt')
|
|
79
|
0
|
os.remove(os.path.join(os.getcwd(), 'gbi-210.sdf'))
|
|
80
|
0
|
os.remove(os.path.join(os.getcwd(), 'gbi-220.sdf'))
|
|
81
|
|
|
|
82
|
0
|
def test_filter_results():
|
|
83
|
0
|
filter_results(os.path.join(mydir, 'data_tests', 'gbi_prefilt.sdf'),
|
|
84
|
|
os.path.join(mydir, 'data_tests', 'output.sdf'),
|
|
85
|
|
'mp2','def2-SV(P)')
|
|
86
|
0
|
os.remove(os.path.join(mydir, 'data_tests', 'output.sdf'))
|
|
87
|
0
|
os.remove(os.path.join(os.getcwd(), 'numConfs.txt')) # don't use mydir here
|
|
88
|
|
|
|
89
|
|
# test manually without pytest
|
|
90
|
0
|
if 0:
|
|
91
|
|
sys.path.insert(0, '/home/limvt/Documents/quanformer/quanformer')
|
|
92
|
|
from pipeline import *
|
|
93
|
|
test_name_manager_pass()
|
|
94
|
|
test_name_manager_fail()
|
|
95
|
|
test_setup_conformers()
|
|
96
|
|
test_setup_calculations_true()
|
|
97
|
|
test_setup_calculations_false()
|
vtlim