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
|
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Jeremy MG Leung
# Contributors:
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
import numpy as np
import pytest
from mdtraj.utils.unitcell import check_valid_unitcell_angles
class Test_Unitcell:
@pytest.mark.parametrize(["alpha", "beta", "gamma"], [[90, 90, 90], [70, 90, 30]], ids=["orthogonal", "triclinic"])
def test_valid(self, alpha, beta, gamma):
"""Test for valid unitcell angles, single frame"""
unitcell_angles = np.array([alpha, beta, gamma], dtype=np.float32)
assert check_valid_unitcell_angles(*unitcell_angles) # True
@pytest.mark.parametrize(
["alpha", "beta", "gamma"],
[[126.96979, 54.83003, 178.20027], [44.82802, 110.52171, 65.693695]],
ids=["over360", "close"],
)
def test_invalid_over360(self, alpha, beta, gamma):
"""Test for invalid unitcell angles, single frame"""
unitcell_angles = np.array([alpha, beta, gamma], dtype=np.float32)
assert not check_valid_unitcell_angles(*unitcell_angles) # False
def test_valid_array(self):
"""test for valid unitcell angles, input being an array"""
unitcell_angles = np.array([[90.0, 90.0, 90], [70, 90, 30], [40, 20, 30]], dtype=np.float32)
assert np.all(check_valid_unitcell_angles(*unitcell_angles.T) == [True, True, True])
def test_invalid_over360_array(self):
"""Test for invalid unitcell angles that sum up to over 360˚, input being an array"""
unitcell_angles = np.array([[90, 90, 90], [126.96979, 54.83003, 178.20027], [70, 90, 30]], dtype=np.float32)
assert np.all(check_valid_unitcell_angles(*unitcell_angles.T) == [True, False, True])
def test_invalid_angles_close_array(self):
"""Test for invalid unitcell angles where angles 1 and 3 sum up to more than angle 2"""
unitcell_angles = np.array([[44.82802, 110.52171, 65.693695], [90, 90, 90], [70, 90, 30]], dtype=np.float64)
assert np.all(check_valid_unitcell_angles(*unitcell_angles.T) == [False, True, True])
|
