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
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
|
#!/usr/bin/env python
import os
import sys
import subprocess
import unittest
import gemmi
TOP_DIR = os.path.join(os.path.dirname(__file__), "..")
# Skip tests if the program is not installed,
# or the installed version doesn't match the library.
def has_gemmi():
try:
v = subprocess.check_output(['gemmi', '--version'], cwd=TOP_DIR)
except OSError:
return False
return v.split()[1].decode() == gemmi.__version__
@unittest.skipIf(not has_gemmi(), "Program gemmi not found.")
class TestProg(unittest.TestCase):
def do(self, example):
cmd, _, rest = example.partition('\n')
assert cmd.startswith('$ gemmi ')
output = subprocess.check_output(cmd[2:], shell=True, cwd=TOP_DIR,
stderr=subprocess.STDOUT)
expected_lines = rest.splitlines()
output_lines = output.decode().splitlines()
if expected_lines[0].startswith('[...]'):
t = expected_lines.pop(0)
if len(t) > 8:
n1, n2 = t[5:].split()
output_lines = output_lines[int(n1):int(n2)]
else:
output_lines = output_lines[-len(expected_lines):]
self.assertEqual(expected_lines, output_lines)
def test_fprime1(self):
# example from utils.rst
self.do('''\
$ gemmi fprime --wavelength=1.2 Se
Element E[eV] Wavelength[A] f' f"
Se 10332.0 1.2 -1.4186 0.72389
''')
def test_fprime2(self):
self.do('''\
$ gemmi fprime --energy=12345 Se
Element E[eV] Wavelength[A] f' f"
Se 12345.0 1.00433 -3.1985 0.52258
''')
def test_sfcalc1(self):
self.do('''\
$ gemmi sfcalc --compare=tests/2242624.hkl tests/2242624.cif
RMSE=0.019256 0.2252% max|dF|=0.04784 R=0.191% sum(F^2)_ratio=1.00094
''')
def test_sfcalc2(self):
self.do('''\
$ gemmi sfcalc --wavelength=0 --compare=tests/2242624.hkl tests/2242624.cif
RMSE=0.10942 1.295% max|dF|=0.1498 R=1.279% sum(F^2)_ratio=1.01019
''')
def test_sfcalc3(self):
self.do('''\
$ gemmi sfcalc --ciffp --compare=tests/2242624.hkl tests/2242624.cif
RMSE=0.019724 0.2307% max|dF|=0.04863 R=0.196% sum(F^2)_ratio=1.00101
''')
def test_sfcalc4(self):
self.do('''\
$ gemmi sfcalc -w0 --hkl=4,9,0 --hkl=5,6,4 --hkl=1,1,1 tests/2013551.cif
(4 9 0) 1.12314668 180.000000
(5 6 4) 1.49089619 180.000000
(1 1 1) 11.22159034 360.000000
''')
@unittest.skipIf(sys.platform == 'win32', 'with MSVC it differs slightly')
def test_sfcalc_5wkd(self):
self.do('''\
$ gemmi sfcalc --blur=12 --dmin=2.5 --rate=2.5 --rcut=1e-7 --test -v tests/5wkd.pdb
[...]
RMSE=3.3342e-05 4.703e-05% max|dF|=0.0001706 R=0.000% <dPhi>=4.718e-06
''') # noqa: E501
@unittest.skipIf(sys.platform == 'win32', 'with MSVC it differs slightly')
def test_sfcalc_1pfe(self):
self.do('''\
$ gemmi sfcalc --dmin=9 --rate=4 --blur=60 --rcut=1e-7 --test -v tests/1pfe.cif.gz
[...]
RMSE=0.0010414 0.0001639% max|dF|=0.003530 R=0.000% <dPhi>=8.067e-06
''') # noqa: E501
# example from utils.rst
def test_align_text(self):
self.do('''\
$ gemmi align -p --match=0 --gapo=0 --text-align Saturday Sunday
Score: -3 CIGAR: 1M2I5M
Saturday
| |.|||
S--unday
''')
def test_cif2mtz_5e5z(self):
self.do('''\
$ gemmi mtz2cif tests/5e5z.mtz -
[...] -158 -155
1 2 0 46.859 0.6285 68.443 0.4591 o
1 2 1 ? ? ? ? x
1 2 2 38.249 0.3855 61.841 0.3117 f
''')
def test_contacts_4oz7(self):
self.do('''\
$ gemmi contact --maxdist=2.5 --ignore=4 tests/4oz7.pdb
metalc5 N 22Q A 1 CU CU1 B 101 1555 6345 2.05
metalc6 S 22Q A 1 CU CU1 B 101 1555 6345 2.26
metalc7 N 22Q B 1 CU CU1 A 101 1555 6344 2.07
metalc8 S 22Q B 1 CU CU1 A 101 1555 6344 2.22
''')
if __name__ == '__main__':
unittest.main()
|
