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
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
from pathlib import Path
from unittest import TestCase
from shelxfile import Shelxfile
class TestShelxFileIsAtom(TestCase):
def test_is_atom_long_line_true(self):
"""
"""
is_an_atom = Shelxfile.is_atom(atomline='O1 3 0.120080 0.336659 0.494426 11.00000 0.01445 ...')
self.assertEqual(True, is_an_atom)
def test_is_no_atoms_because_type_is_missing(self):
is_an_atom = Shelxfile.is_atom(atomline='O1 0.120080 0.336659 0.494426 11.00000 0.01445 ...')
self.assertEqual(False, is_an_atom)
def test_is_no_atom_because_coordinate_is_missing(self):
is_an_atom = Shelxfile.is_atom(atomline='O1 4 0.120080 0.494426 11.00000 0.01445 ...')
self.assertEqual(False, is_an_atom)
def test_is_no_atom_because_its_a_command(self):
is_atom = Shelxfile.is_atom("AFIX 123")
self.assertEqual(False, is_atom)
def test_is_no_atom_because_its_a_command2(self):
is_atom = Shelxfile.is_atom("AFIX")
self.assertEqual(False, is_atom)
def test_is_an_atom_short(self):
is_atom = Shelxfile.is_atom('O1 3 0.120080 0.336659 0.494426')
self.assertEqual(True, is_atom)
class TestShelxfileElementToSfac(TestCase):
"""
SFAC C H O F Al Ga
"""
def setUp(self) -> None:
self.shx = Shelxfile(debug=True)
self.shx.read_file('tests/resources/p21c.res')
def test_elem2sfac_oxygen(self):
self.assertEqual(3, self.shx.elem2sfac('O'))
def test_elem2sfac_carbon(self):
self.assertEqual(1, self.shx.elem2sfac('c'))
def test_elem2sfac_Argon(self):
self.assertEqual(0, self.shx.elem2sfac('Ar'))
class TestShelxfile(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile(debug=True)
self.shx.read_file('tests/resources/p21c.res')
def test_sfac2elem_C(self):
self.assertEqual('C', self.shx.sfac2elem(1))
def test_sfac2elem_H(self):
self.assertEqual('H', self.shx.sfac2elem(2))
def test_sfac2elem_O(self):
self.assertEqual('O', self.shx.sfac2elem(3))
def test_sfac2elem_Al(self):
self.assertEqual('Al', self.shx.sfac2elem(5))
def test_sfac2elem_not_existent(self):
self.assertEqual('', self.shx.sfac2elem(8))
def test_sfac2elem_zero(self):
self.assertEqual('', self.shx.sfac2elem(0))
def test_sum_formula(self):
self.assertEqual('C0.25 H0.5 O0.75 F1 AL1.25 GA1.5', self.shx.sum_formula)
def test_read_file_to_list(self):
shx = Shelxfile()
shx._reslist = ['Foo']
shx.read_file('tests/resources/p21c.res')
# Make sure read_file() re-initializes the constructor:
self.assertEqual(['TITL p21c in P2(1)/c',
' created by SHELXL-2018/3 at 16:18:25 on 03-May-2018',
'CELL 0.71073 10.5086 20.9035 20.5072 90 94.13 90',
'ZERR 4 0.0003 0.0005 0.0005 0 0.001 0',
'LATT 1'],
[str(x) for x in shx._reslist[:5]])
def test_read_string(self):
self.shx.atoms = 'Foo'
# Make sure read_string re-initializes the constructor:
self.shx.read_string(Path('tests/resources/p21c.res').read_text(encoding='latin1'))
assert self.shx.atoms.number == 148
def test_read_file(self):
shx = Shelxfile()
with self.assertRaises(FileNotFoundError):
shx.read_file('tests/resources/foobar.res')
class TestShelxfileGoodModel(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/model_finished/p21c.res')
def test_atom_representation(self):
a = self.shx._reslist[39]
self.assertEqual(
'C1 1 -0.187504 0.282782 0.527531 11.00000 0.01807 0.02353 0.01797 0.00008 -0.00179 0.00036',
str(a))
def test_atom_object(self):
a = self.shx._reslist[39]
self.assertEqual(
'C1 1 -0.187504 0.282782 0.527531 11.00000 0.01807 0.02353 0.01797 0.00008 -0.00179 0.00036',
a)
def test_qpeak(self):
a = self.shx._reslist[-20]
self.assertEqual('Q1 1 0.0784 0.1310 0.6428 11.00000 0.04 0.10 ', str(a))
def test_r1(self):
assert self.shx.R1 == 0.194
def test_wr2(self):
assert self.shx.wr2 == 0.51
def test_data(self):
assert self.shx.data == 10786
def test_param(self):
assert self.shx.parameters == 551
def test_data_to_param(self):
assert round(self.shx.dat_to_param, 4) == 19.5753
def test_num_restraints(self):
assert self.shx.num_restraints == 0
def test_peak_hole(self):
assert self.shx.highest_peak == 6.395
assert self.shx.deepest_hole == -5.556
def test_peak_goof(self):
assert self.shx.goof == 5.982
assert self.shx.rgoof == 5.982
class TestWriteFile(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/2240189.res')
self.written = Path('tests/resources/2240189-written.res')
self.testwritepath = Path('tests/resources/testwrite.res')
def tearDown(self) -> None:
self.testwritepath.unlink(missing_ok=True)
def test_write_shelx_file(self):
self.shx.write_shelx_file(str(self.testwritepath))
self.assertEqual(self.written.read_bytes(), self.testwritepath.read_bytes())
|
