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# -*- 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 os
import pytest
from numpy.testing import assert_almost_equal
import MDAnalysis as mda
from MDAnalysis.coordinates.GSD import GSDReader, HAS_GSD
from MDAnalysisTests.datafiles import GSD
@pytest.mark.skipif(HAS_GSD, reason="gsd is installed")
def test_no_gsd_u_raises():
with pytest.raises(ImportError, match="please install gsd"):
_ = mda.Universe(GSD)
@pytest.mark.skipif(HAS_GSD, reason="gsd is installed")
def test_gsd_reader_raises():
with pytest.raises(ImportError, match="please install gsd"):
_ = GSDReader("foo")
@pytest.mark.skipif(not HAS_GSD, reason="gsd is not installed")
class TestGSDReader:
@pytest.fixture(scope="class")
def GSD_U(self):
return mda.Universe(GSD)
def test_gsd_positions(self, GSD_U):
# first frame first particle
GSD_U.trajectory[0]
assert_almost_equal(
GSD_U.atoms.positions[0], [-5.4000001, -10.19999981, -10.19999981]
)
# second frame first particle
GSD_U.trajectory[1]
assert_almost_equal(
GSD_U.atoms.positions[0], [-5.58348083, -9.98546982, -10.17657185]
)
def test_gsd_n_frames(self, GSD_U):
assert len(GSD_U.trajectory) == 2
def test_gsd_dimensions(self, GSD_U):
ts = GSD_U.trajectory[0]
assert_almost_equal(
ts.dimensions,
[21.60000038, 21.60000038, 21.60000038, 90.0, 90.0, 90.0],
)
def test_gsd_data_step(self, GSD_U):
assert GSD_U.trajectory[0].data["step"] == 0
assert GSD_U.trajectory[1].data["step"] == 500
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