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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 mda
from MDAnalysis.transformations import translate, center_in_box
from MDAnalysisTests import make_Universe
@pytest.fixture()
def translate_universes():
# create the Universe objects for the tests
# this universe has no masses and some tests need it as such
reference = make_Universe(trajectory=True)
transformed = make_Universe(["masses"], trajectory=True)
transformed.trajectory.ts.dimensions = np.array(
[372.0, 373.0, 374.0, 90, 90, 90]
)
return reference, transformed
def test_translate_coords(translate_universes):
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
vector = np.float32([1, 2, 3])
ref.positions += vector
trans = translate(vector)(trans_u.trajectory.ts)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
@pytest.mark.parametrize(
"vector",
(
[0, 1],
[0, 1, 2, 3, 4],
np.array([0, 1]),
np.array([0, 1, 2, 3, 4]),
np.array([[0, 1, 2], [3, 4, 5], [6, 7, 8]]),
np.array([[0], [1], [2]]),
),
)
def test_translate_vector(translate_universes, vector):
# what happens if the vector argument is of wrong size?
ts = translate_universes[0].trajectory.ts
with pytest.raises(ValueError):
translate(vector)(ts)
def test_translate_transformations_api(translate_universes):
# test if the translate transformation works when using the
# on-the-fly transformations API
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
vector = np.float32([1, 2, 3])
ref.positions += vector
trans_u.trajectory.add_transformations(translate(vector))
assert_array_almost_equal(
trans_u.trajectory.ts.positions, ref.positions, decimal=6
)
def test_center_in_box_bad_ag(translate_universes):
# this universe has a box size zero
ts = translate_universes[0].trajectory.ts
# what happens if something other than an AtomGroup is given?
bad_ag = 1
with pytest.raises(ValueError):
center_in_box(bad_ag)(ts)
@pytest.mark.parametrize(
"point",
(
[0, 1],
[0, 1, 2, 3, 4],
np.array([0, 1]),
np.array([0, 1, 2, 3, 4]),
np.array([[0, 1, 2], [3, 4, 5], [6, 7, 8]]),
np.array([[0], [1], [2]]),
),
)
def test_center_in_box_bad_point(translate_universes, point):
ts = translate_universes[0].trajectory.ts
ag = translate_universes[0].residues[0].atoms
# what if the box is in the wrong format?
with pytest.raises(ValueError):
center_in_box(ag, point=point)(ts)
def test_center_in_box_bad_pbc(translate_universes):
# this universe has a box size zero
ts = translate_universes[0].trajectory.ts
ag = translate_universes[0].residues[0].atoms
# is pbc passed to the center methods?
# if yes it should raise an exception for boxes that are zero in size
with pytest.raises(ValueError):
center_in_box(ag, wrap=True)(ts)
def test_center_in_box_bad_center(translate_universes):
# this universe has a box size zero
ts = translate_universes[0].trajectory.ts
ag = translate_universes[0].residues[0].atoms
# what if a wrong center type name is passed?
bad_center = " "
with pytest.raises(ValueError):
center_in_box(ag, center=bad_center)(ts)
def test_center_in_box_no_masses(translate_universes):
# this universe has no masses
ts = translate_universes[0].trajectory.ts
ag = translate_universes[0].residues[0].atoms
ts.dimensions = [10, 10, 10, 90, 90, 90]
# if the universe has no masses and `mass` is passed as the center arg
bad_center = "mass"
with pytest.raises(mda.NoDataError):
center_in_box(ag, center=bad_center)(ts)
def test_center_in_box_coords_no_options(translate_universes):
# what happens when we center the coordinates arround the center of geometry of a residue?
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
ref_center = np.float32([6, 7, 8])
box_center = np.float32([186.0, 186.5, 187.0])
ref.positions += box_center - ref_center
ag = trans_u.residues[0].atoms
trans = center_in_box(ag)(trans_u.trajectory.ts)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
def test_center_in_box_coords_with_pbc(translate_universes):
# what happens when we center the coordinates arround the center of geometry of a residue?
# using pbc into account for center of geometry calculation
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
trans_u.dimensions = [363.0, 364.0, 365.0, 90.0, 90.0, 90.0]
ag = trans_u.residues[24].atoms
box_center = np.float32([181.5, 182.0, 182.5])
ref_center = np.float32([75.6, 75.8, 76.0])
ref.positions += box_center - ref_center
trans = center_in_box(ag, wrap=True)(trans_u.trajectory.ts)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
def test_center_in_box_coords_with_mass(translate_universes):
# using masses for calculating the center of the atomgroup
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
ag = trans_u.residues[24].atoms
box_center = np.float32([186.0, 186.5, 187.0])
ref_center = ag.center_of_mass()
ref.positions += box_center - ref_center
trans = center_in_box(ag, center="mass")(trans_u.trajectory.ts)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
def test_center_in_box_coords_with_box(translate_universes):
# using masses for calculating the center of the atomgroup
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
ag = trans_u.residues[0].atoms
newpoint = [1000, 1000, 1000]
box_center = np.float32(newpoint)
ref_center = np.float32([6, 7, 8])
ref.positions += box_center - ref_center
trans = center_in_box(ag, point=newpoint)(trans_u.trajectory.ts)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
def test_center_in_box_coords_all_options(translate_universes):
# what happens when we center the coordinates arround the center of geometry of a residue?
# using pbc into account for center of geometry calculation
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
ag = trans_u.residues[24].atoms
newpoint = [1000, 1000, 1000]
box_center = np.float32(newpoint)
ref_center = ag.center_of_mass(pbc=True)
ref.positions += box_center - ref_center
trans = center_in_box(ag, center="mass", wrap=True, point=newpoint)(
trans_u.trajectory.ts
)
assert_array_almost_equal(trans.positions, ref.positions, decimal=6)
def test_center_transformations_api(translate_universes):
# test if the translate transformation works when using the
# on-the-fly transformations API
ref_u, trans_u = translate_universes
ref = ref_u.trajectory.ts
ref_center = np.float32([6, 7, 8])
box_center = np.float32([186.0, 186.5, 187.0])
ref.positions += box_center - ref_center
ag = trans_u.residues[0].atoms
trans_u.trajectory.add_transformations(center_in_box(ag))
assert_array_almost_equal(
trans_u.trajectory.ts.positions, ref.positions, decimal=6
)
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