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
|
import pytest
import glob
import MDAnalysis as mda
from MDAnalysis.analysis.dssp import DSSP, translate
from MDAnalysisTests.datafiles import DSSP as DSSP_FOLDER
from MDAnalysisTests.datafiles import TPR, XTC
# Files that match glob pattern '????.pdb.gz' and matching '????.pdb.dssp' files,
# containing the secondary structure assignment string, will be tested automatically.
@pytest.mark.parametrize(
"pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")
)
def test_file_guess_hydrogens(pdb_filename, client_DSSP):
u = mda.Universe(pdb_filename)
with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin:
correct_answ = fin.read().strip().split()[0]
run = DSSP(u, guess_hydrogens=True).run(**client_DSSP)
answ = "".join(run.results.dssp[0])
assert answ == correct_answ
def test_trajectory(client_DSSP):
u = mda.Universe(TPR, XTC).select_atoms("protein").universe
run = DSSP(u).run(**client_DSSP, stop=10)
first_frame = "".join(run.results.dssp[0])
last_frame = "".join(run.results.dssp[-1])
avg_frame = "".join(translate(run.results.dssp_ndarray.mean(axis=0)))
assert (
first_frame[:10] != last_frame[:10] == avg_frame[:10] == "-EEEEEE---"
)
protein = mda.Universe(TPR, XTC).select_atoms("protein")
run = DSSP(protein).run(**client_DSSP, stop=10)
def test_atomgroup(client_DSSP):
protein = mda.Universe(TPR, XTC).select_atoms("protein")
run = DSSP(protein).run(**client_DSSP, stop=10)
first_frame = "".join(run.results.dssp[0])
last_frame = "".join(run.results.dssp[-1])
avg_frame = "".join(translate(run.results.dssp_ndarray.mean(axis=0)))
assert (
first_frame[:10] != last_frame[:10] == avg_frame[:10] == "-EEEEEE---"
)
def test_trajectory_with_hydrogens(client_DSSP):
u = mda.Universe(TPR, XTC).select_atoms("protein").universe
run = DSSP(u, guess_hydrogens=False).run(**client_DSSP, stop=10)
first_frame = "".join(run.results.dssp[0])
last_frame = "".join(run.results.dssp[-1])
avg_frame = "".join(translate(run.results.dssp_ndarray.mean(axis=0)))
assert (
first_frame[:10] == last_frame[:10] == avg_frame[:10] == "-EEEEEE---"
)
@pytest.mark.parametrize(
"pdb_filename", glob.glob(f"{DSSP_FOLDER}/2xdgA.pdb.gz")
)
def test_trajectory_without_hydrogen_fails(pdb_filename, client_DSSP):
u = mda.Universe(pdb_filename)
with pytest.raises(ValueError):
DSSP(u, guess_hydrogens=False).run(**client_DSSP)
@pytest.mark.parametrize(
"pdb_filename", glob.glob(f"{DSSP_FOLDER}/1mr1D_failing.pdb.gz")
)
def test_trajectory_with_uneven_number_of_atoms_fails(
pdb_filename, client_DSSP
):
u = mda.Universe(pdb_filename)
with pytest.raises(ValueError):
DSSP(u, guess_hydrogens=True).run(**client_DSSP)
@pytest.mark.parametrize(
"pdb_filename", glob.glob(f"{DSSP_FOLDER}/wrong_hydrogens.pdb.gz")
)
def test_exception_raises_with_atom_index(pdb_filename, client_DSSP):
u = mda.Universe(pdb_filename)
with pytest.raises(
ValueError,
match="Residue <Residue SER, 298> contains*",
):
DSSP(u, guess_hydrogens=False).run(**client_DSSP)
|
