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
|
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
import pytest
import pickle
import MDAnalysis as mda
from numpy.testing import TestCase, assert_equal
import gc
from MDAnalysisTests.datafiles import PDB_small
class TestAtomGroupPickle(object):
"""Set up hopefully unique universes."""
# _n marks named universes/atomgroups/pickled strings
@staticmethod
@pytest.fixture()
def universe():
return mda.Universe(PDB_small, PDB_small, PDB_small)
@staticmethod
@pytest.fixture()
def ag(universe):
return universe.atoms[:20]
@staticmethod
@pytest.fixture()
def ag_2(universe):
return universe.atoms[10:20]
@staticmethod
@pytest.fixture()
def pickle_str(ag):
return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
@staticmethod
@pytest.fixture()
def pickle_str_two_ag(ag, ag_2):
return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL)
@staticmethod
@pytest.fixture()
def pickle_str_ag_with_universe_f(ag, universe):
return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL)
@staticmethod
@pytest.fixture()
def pickle_str_ag_with_universe(ag, universe):
return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL)
def test_unpickle(self, pickle_str, ag, universe):
"""Test that an AtomGroup can be unpickled (Issue 293)"""
newag = pickle.loads(pickle_str)
# Can unpickle
assert_equal(ag.indices, newag.indices)
def test_pickle_unpickle_empty(self, universe):
"""Test that an empty AtomGroup can be pickled/unpickled (Issue 293)"""
ag = universe.atoms[[]]
pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
newag = pickle.loads(pickle_str)
assert len(newag) == 0
def test_unpickle_two_ag(self, pickle_str_two_ag):
newag, newag2 = pickle.loads(pickle_str_two_ag)
assert (
newag.universe is newag2.universe
), "Two AtomGroups are unpickled to two different Universes"
def test_unpickle_ag_with_universe_f(self, pickle_str_ag_with_universe_f):
newu, newag = pickle.loads(pickle_str_ag_with_universe_f)
assert newag.universe is newu, (
"AtomGroup is not unpickled to the bound Universe"
"when Universe is pickled first"
)
def test_unpickle_ag_with_universe(self, pickle_str_ag_with_universe):
newag, newu = pickle.loads(pickle_str_ag_with_universe)
assert newag.universe is newu, (
"AtomGroup is not unpickled to the bound Universe"
"when AtomGroup is pickled first"
)
class TestPicklingUpdatingAtomGroups(object):
@staticmethod
@pytest.fixture()
def u():
return mda.Universe(PDB_small)
def test_pickling_uag(self, u):
ag = u.atoms[:100]
uag = ag.select_atoms("name C", updating=True)
pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL)
new_uag = pickle.loads(pickle_str)
assert_equal(uag.indices, new_uag.indices)
def test_pickling_uag_of_uag(self, u):
uag1 = u.select_atoms("name C or name H", updating=True)
uag2 = uag1.select_atoms("name C", updating=True)
pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL)
new_uag2 = pickle.loads(pickle_str)
assert_equal(uag2.indices, new_uag2.indices)
|
