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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 numpy as np
import pytest
from numpy.testing import assert_equal, assert_almost_equal
import MDAnalysis as mda
from MDAnalysisTests.coordinates.reference import RefACHE, RefCappedAla
from MDAnalysisTests.datafiles import PRM, TRJ, TRJ_bz2, PRMpbc, TRJpbc_bz2
class _TRJReaderTest(object):
@pytest.fixture(scope="class")
def universe(self):
return mda.Universe(self.topology_file, self.trajectory_file)
def test_load_prm(self, universe):
assert_equal(
len(universe.atoms),
self.ref_n_atoms,
"load Universe from PRM and TRJ",
)
def test_n_atoms(self, universe):
assert_equal(
universe.trajectory.n_atoms,
self.ref_n_atoms,
"wrong number of atoms",
)
def test_n_frames(self, universe):
assert_equal(
universe.trajectory.n_frames,
self.ref_n_frames,
"wrong number of frames in xyz",
)
def test_periodic(self, universe):
assert_equal(universe.trajectory.periodic, self.ref_periodic)
def test_amber_proteinselection(self, universe):
protein = universe.select_atoms("protein")
assert_equal(
protein.n_atoms,
self.ref_proteinatoms,
"error in protein selection (HIS or termini?)",
)
def test_sum_centres_of_geometry(self, universe):
protein = universe.select_atoms("protein")
total = np.sum(
[protein.center_of_geometry() for ts in universe.trajectory]
)
assert_almost_equal(
total,
self.ref_sum_centre_of_geometry,
self.prec,
err_msg="sum of centers of geometry over the "
"trajectory do not match",
)
def test_initial_frame_is_0(self, universe):
assert_equal(
universe.trajectory.ts.frame,
0,
"initial frame is not 0 but {0}".format(
universe.trajectory.ts.frame
),
)
def test_starts_with_first_frame(self, universe):
"""Test that coordinate arrays are filled as soon as the trajectory
has been opened."""
assert np.any(universe.atoms.positions > 0), (
"Reader does not " "populate positions right away."
)
def test_rewind(self, universe):
trj = universe.trajectory
trj.next()
trj.next() # for readers that do not support indexing
assert_equal(
trj.ts.frame, 2, "failed to forward to frame 2 (frameindex 2)"
)
trj.rewind()
assert_equal(trj.ts.frame, 0, "failed to rewind to first frame")
assert np.any(universe.atoms.positions > 0), (
"Reader does not " "populate positions after rewinding."
)
def test_full_slice(self, universe):
trj_iter = universe.trajectory[:]
frames = [ts.frame for ts in trj_iter]
assert_equal(frames, np.arange(universe.trajectory.n_frames))
def test_random_access(self, universe):
pos1 = universe.atoms[0].position
universe.trajectory.next()
universe.trajectory.next()
pos3 = universe.atoms[0].position
universe.trajectory[0]
assert_equal(universe.atoms[0].position, pos1)
universe.trajectory[2]
assert_equal(universe.atoms[0].position, pos3)
class TestTRJReader(_TRJReaderTest, RefACHE):
topology_file = PRM
trajectory_file = TRJ
prec = 3
def test_read_frame_reopens(self, universe):
# should automatically reopen
u = universe
u.trajectory.close()
u.trajectory[2]
assert u.trajectory.ts.frame == 2
class TestBzippedTRJReader(TestTRJReader):
topology_file = PRM
trajectory_file = TRJ_bz2
prec = 3
class TestBzippedTRJReaderPBC(_TRJReaderTest, RefCappedAla):
topology_file = PRMpbc
trajectory_file = TRJpbc_bz2
prec = 3
def test_trj_no_natoms():
with pytest.raises(ValueError):
mda.coordinates.TRJ.TRJReader("somefile.txt")
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