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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 MDAnalysis as mda
import numpy as np
import pytest
from numpy.testing import assert_equal
from MDAnalysis.lib.mdamath import triclinic_vectors
from MDAnalysisTests.datafiles import DMS
class TestDMSReader(object):
@pytest.fixture()
def universe(self):
return mda.Universe(DMS)
@pytest.fixture()
def ts(self, universe):
return universe.trajectory.ts
def test_global_cell(self, ts):
assert ts.dimensions is None
# cythonised class can no longer raise AttributeError
# so changed to test of has_velocities
def test_velocities(self, ts):
assert_equal(ts.has_velocities, False)
def test_number_of_coords(self, universe):
# Desired value taken from VMD
# Info) Atoms: 3341
assert_equal(len(universe.atoms), 3341)
def test_coords_atom_0(self, universe):
# Desired coordinates taken directly from the SQLite file. Check unit
# conversion
coords_0 = np.array(
[
-11.0530004501343,
26.6800003051758,
12.7419996261597,
],
dtype=np.float32,
)
assert_equal(universe.atoms[0].position, coords_0)
def test_n_frames(self, universe):
assert_equal(
universe.trajectory.n_frames, 1, "wrong number of frames in pdb"
)
def test_time(self, universe):
assert_equal(universe.trajectory.time, 0.0, "wrong time of the frame")
def test_frame(self, universe):
assert_equal(
universe.trajectory.frame,
0,
"wrong frame number "
"(0-based, should be 0 for single frame readers)",
)
def test_frame_index_0(self, universe):
universe.trajectory[0]
assert_equal(
universe.trajectory.ts.frame,
0,
"frame number for frame index 0 should be 0",
)
def test_frame_index_1_raises_IndexError(self, universe):
with pytest.raises(IndexError):
universe.trajectory[1]
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