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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_array_almost_equal
import MDAnalysis as mdanalysis
from MDAnalysis.transformations import set_dimensions
from MDAnalysisTests import make_Universe
@pytest.fixture()
def boxdimensions_universe():
# create Universe objects for tests
new_u = make_Universe(trajectory=True)
return new_u
@pytest.fixture()
def variable_boxdimensions_universe():
# create Universe objects for tests
n_atoms = 1
n_frames = 3
u = mdanalysis.Universe.empty(n_atoms, trajectory=True)
coordinates = np.zeros((n_frames, u.atoms.n_atoms, 3))
u.load_new(coordinates, order="fac")
return u
def test_boxdimensions_dims(boxdimensions_universe):
new_dims = np.float32([2, 2, 2, 90, 90, 90])
set_dimensions(new_dims)(boxdimensions_universe.trajectory.ts)
assert_array_almost_equal(
boxdimensions_universe.dimensions, new_dims, decimal=6
)
@pytest.mark.parametrize(
"dim_vector_shapes",
(
[1, 1, 1, 90, 90],
[1, 1, 1, 1, 90, 90, 90],
np.array([[1], [1], [90], [90], [90]]),
np.array([1, 1, 1, 90, 90]),
np.array([1, 1, 1, 1, 90, 90, 90]),
[1, 1, 1, 90, 90],
111909090,
),
)
def test_dimensions_vector(boxdimensions_universe, dim_vector_shapes):
# wrong box dimension vector shape
ts = boxdimensions_universe.trajectory.ts
with pytest.raises(ValueError, match="valid box dimension shape"):
set_dimensions(dim_vector_shapes)(ts)
@pytest.mark.parametrize(
"dim_vector_forms_dtypes",
(
["a", "b", "c", "d", "e", "f"],
np.array(["a", "b", "c", "d", "e", "f"]),
"abcd",
),
)
def test_dimensions_vector_asarray(
boxdimensions_universe, dim_vector_forms_dtypes
):
# box dimension input type not convertible into array
ts = boxdimensions_universe.trajectory.ts
with pytest.raises(ValueError, match="cannot be converted"):
set_dimensions(dim_vector_forms_dtypes)(ts)
def test_dimensions_transformations_api(boxdimensions_universe):
# test if transformation works with on-the-fly transformations API
new_dims = np.float32([2, 2, 2, 90, 90, 90])
transform = set_dimensions(new_dims)
boxdimensions_universe.trajectory.add_transformations(transform)
for ts in boxdimensions_universe.trajectory:
assert_array_almost_equal(
boxdimensions_universe.dimensions, new_dims, decimal=6
)
def test_varying_dimensions_transformations_api(
variable_boxdimensions_universe,
):
"""
Test if transformation works with on-the-fly transformations API
when we have varying dimensions.
"""
new_dims = np.float32(
[
[2, 2, 2, 90, 90, 90],
[4, 4, 4, 90, 90, 90],
[8, 8, 8, 90, 90, 90],
]
)
transform = set_dimensions(new_dims)
variable_boxdimensions_universe.trajectory.add_transformations(transform)
for ts in variable_boxdimensions_universe.trajectory:
assert_array_almost_equal(
variable_boxdimensions_universe.dimensions,
new_dims[ts.frame],
decimal=6,
)
def test_varying_dimensions_no_data(
variable_boxdimensions_universe,
):
"""
Check error is raised when dimensions are missing for a frame
in a trajectory.
"""
# trjactory has three frames
new_dims = np.float32(
[
[2, 2, 2, 90, 90, 90],
[4, 4, 4, 90, 90, 90],
]
)
transform = set_dimensions(new_dims)
with pytest.raises(
ValueError, match="Dimensions array has no data for frame 2"
):
variable_boxdimensions_universe.trajectory.add_transformations(
transform
)
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