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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
import MDAnalysis.analysis.diffusionmap as diffusionmap
import numpy as np
import pytest
from MDAnalysisTests.datafiles import PDB, XTC
from numpy.testing import assert_array_almost_equal, assert_allclose
@pytest.fixture(scope="module")
def u():
return MDAnalysis.Universe(PDB, XTC)
@pytest.fixture(scope="module")
def dist(u):
return diffusionmap.DistanceMatrix(u, select="backbone")
@pytest.fixture(scope="module")
def dmap(dist):
d_map = diffusionmap.DiffusionMap(dist)
d_map.run()
return d_map
def test_eg(dist, dmap):
eigvals = dmap.eigenvalues
# number of frames is trajectory is now 10 vs. 98
assert eigvals.shape == (dist.n_frames,)
# makes no sense to test values here, no physical meaning
def test_dist_weights(u):
backbone = u.select_atoms("backbone")
weights_atoms = np.ones(len(backbone.atoms))
dist = diffusionmap.DistanceMatrix(
u, select="backbone", weights=weights_atoms
)
dist.run(step=3)
dmap = diffusionmap.DiffusionMap(dist)
dmap.run()
assert_array_almost_equal(dmap.eigenvalues, [1, 1, 1, 1], 4)
assert_array_almost_equal(
dmap._eigenvectors,
(
[
[0, 0, 1, 0],
[0, 0, 0, 1],
[-0.707, -0.707, 0, 0],
[0.707, -0.707, 0, 0],
]
),
2,
)
def test_dist_weights_frames(u):
backbone = u.select_atoms("backbone")
weights_atoms = np.ones(len(backbone.atoms))
dist = diffusionmap.DistanceMatrix(
u, select="backbone", weights=weights_atoms
)
frames = np.arange(len(u.trajectory))
dist.run(frames=frames[::3])
dmap = diffusionmap.DiffusionMap(dist)
dmap.run()
assert_array_almost_equal(dmap.eigenvalues, [1, 1, 1, 1], 4)
assert_array_almost_equal(
dmap._eigenvectors,
(
[
[0, 0, 1, 0],
[0, 0, 0, 1],
[-0.707, -0.707, 0, 0],
[0.707, -0.707, 0, 0],
]
),
2,
)
def test_distvalues_ag_universe(u):
dist_universe = diffusionmap.DistanceMatrix(u, select="backbone").run()
ag = u.select_atoms("backbone")
dist_ag = diffusionmap.DistanceMatrix(ag).run()
assert_allclose(
dist_universe.results.dist_matrix, dist_ag.results.dist_matrix
)
def test_distvalues_ag_select(u):
dist_universe = diffusionmap.DistanceMatrix(u, select="backbone").run()
ag = u.select_atoms("protein")
dist_ag = diffusionmap.DistanceMatrix(ag, select="backbone").run()
assert_allclose(
dist_universe.results.dist_matrix, dist_ag.results.dist_matrix
)
def test_different_steps(u):
dmap = diffusionmap.DiffusionMap(u, select="backbone")
dmap.run(step=3)
assert dmap._eigenvectors.shape == (4, 4)
def test_transform(u, dmap):
eigvects = dmap._eigenvectors
n_eigenvectors = 4
dmap = diffusionmap.DiffusionMap(u)
dmap.run()
diffusion_space = dmap.transform(n_eigenvectors, 1)
assert diffusion_space.shape == (eigvects.shape[0], n_eigenvectors)
def test_long_traj(u):
with pytest.warns(UserWarning, match="The distance matrix is very large"):
dmap = diffusionmap.DiffusionMap(u)
dmap._dist_matrix.run(stop=1)
dmap._dist_matrix.n_frames = 5001
dmap.run()
def test_updating_atomgroup(u):
with pytest.warns(UserWarning, match="U must be a static AtomGroup"):
resid_select = "around 5 resname ALA"
ag = u.select_atoms(resid_select, updating=True)
dmap = diffusionmap.DiffusionMap(ag)
dmap.run()
def test_not_universe_atomgroup_error(u):
trj_only = u.trajectory
with pytest.raises(ValueError, match="U is not a Universe or AtomGroup"):
diffusionmap.DiffusionMap(trj_only)
def test_DistanceMatrix_attr_warning(u):
dist = diffusionmap.DistanceMatrix(u, select="backbone").run(step=3)
wmsg = f"The `dist_matrix` attribute was deprecated in MDAnalysis 2.0.0"
with pytest.warns(DeprecationWarning, match=wmsg):
assert getattr(dist, "dist_matrix") is dist.results.dist_matrix
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