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
|
# fmt: off
# flake8: noqa
from io import StringIO
import numpy as np
import pytest
from ase.io.proteindatabank import read_proteindatabank
header1 = """
CRYST1 2.000 2.000 2.000 90.00 90.00 90.00 P 1
MODEL 1
"""
header2 = """
REMARK Step 83, E = -55.02388312121
CRYST1 2.000 2.000 2.000 90.00 90.00 90.00 P 1
"""
body1 = """
ATOM 1 C MOL 1 0.443 1.409 1.905 1.00 0.00 C
ATOM 2 O MOL 1 1.837 1.409 1.373 1.00 0.00 O
"""
body2 = """
ATOM 1 C 0.443 1.409 1.905 1.00 0.00 C
ATOM 2 O 1.837 1.409 1.373 1.00 0.00 O
"""
body3 = """
ATOM 0.443 1.409 1.905 C
ATOM 1.837 1.409 1.373 O
"""
cellref = pytest.approx(np.array([[2., 0., 0.], [0., 2., 0.], [0., 0., 2.]]))
posref = pytest.approx(np.array([[0.443, 1.409, 1.905], [1.837, 1.409, 1.373]]))
@pytest.mark.parametrize('body', [body1, body2, body3])
def test_pdb_optional_tag_body_without_header(body):
atoms = read_proteindatabank(StringIO(body))
assert all(atoms.numbers == [6, 8])
assert not any(atoms.pbc)
assert atoms.get_positions() == posref
@pytest.mark.parametrize('body', [body1, body2, body3])
def test_pdb_optional_tag_body(body):
txt = header1 + body
atoms = read_proteindatabank(StringIO(txt))
assert all(atoms.numbers == [6, 8])
assert all(atoms.pbc)
assert atoms.cell[:] == cellref
assert atoms.get_positions() == posref
@pytest.mark.parametrize('header', [header1, header2])
def test_pdb_optional_heading(header):
txt = header + body1
atoms = read_proteindatabank(StringIO(txt))
assert all(atoms.numbers == [6, 8])
assert all(atoms.pbc)
assert atoms.cell[:] == cellref
assert atoms.get_positions() == posref
def test_pdb_filled_optional_fields():
atoms = read_proteindatabank(StringIO(body1))
assert all(atoms.get_array('occupancy') == np.array([1., 1.]))
assert all(atoms.get_array('bfactor') == np.array([0., 0.]))
assert all(atoms.get_array('atomtypes') == np.array(['C', 'O']))
assert all(atoms.get_array('residuenames') == np.array(['MOL', 'MOL']))
assert all(atoms.get_array('residuenumbers') == np.array([1, 1]))
def test_pdb_unfilled_optional_fields():
atoms = read_proteindatabank(StringIO(body3))
assert 'occupancy' not in atoms.__dict__['arrays']
assert all(atoms.get_array('bfactor') == np.array([0., 0.]))
assert all(atoms.get_array('atomtypes') == np.array(['', '']))
assert all(atoms.get_array('residuenames') == np.array(['', '']))
assert all(atoms.get_array('residuenumbers') == np.array([1, 1]))
|
