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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
#
from __future__ import absolute_import
import numpy as np
from numpy.testing import assert_equal, assert_allclose
import pytest
import copy
import MDAnalysis as mda
from MDAnalysisTests.datafiles import (
PSF,
DCD,
mol2_comments_header,
XYZ_mini,
BATArray,
TPR,
XTC,
)
from MDAnalysis.analysis.bat import BAT
class TestBAT(object):
@pytest.fixture()
def selected_residues(self):
u = mda.Universe(mol2_comments_header)
ag = u.select_atoms("all")
return ag
@pytest.fixture()
def bat(self, selected_residues, client_BAT):
R = BAT(selected_residues)
R.run(**client_BAT)
return R.results.bat
@pytest.fixture
def bat_npz(self, tmpdir, selected_residues, client_BAT):
filename = str(tmpdir / "test_bat_IO.npy")
R = BAT(selected_residues)
R.run(**client_BAT)
R.save(filename)
return filename
def test_bat_root_selection(self, selected_residues):
R = BAT(selected_residues)
assert_equal(
R._root.indices,
[8, 2, 1],
err_msg="error: incorrect root atoms selected",
)
def test_bat_number_of_frames(self, bat):
assert_equal(
len(bat), 2, err_msg="error: list is not length of trajectory"
)
def test_bat_coordinates(self, bat):
test_bat = np.load(BATArray)
assert_allclose(
bat,
test_bat,
rtol=0,
atol=1.5e-5,
err_msg="error: BAT coordinates should match test values",
)
def test_bat_coordinates_single_frame(self, selected_residues, client_BAT):
bat = (
BAT(selected_residues)
.run(start=1, stop=2, **client_BAT)
.results.bat
)
test_bat = [np.load(BATArray)[1]]
assert_allclose(
bat,
test_bat,
rtol=0,
atol=1.5e-5,
err_msg="error: BAT coordinates should match test values",
)
def test_bat_reconstruction(self, selected_residues, bat):
R = BAT(selected_residues)
XYZ = R.Cartesian(bat[0])
assert_allclose(
XYZ,
selected_residues.positions,
rtol=0,
atol=1.5e-5,
err_msg="error: Reconstructed Cartesian coordinates "
+ "don't match original",
)
def test_bat_IO(self, bat_npz, selected_residues, bat):
R2 = BAT(selected_residues, filename=bat_npz)
test_bat = R2.results.bat
assert_allclose(
bat,
test_bat,
rtol=0,
atol=1.5e-5,
err_msg="error: Loaded BAT coordinates should match test values",
)
def test_bat_nobonds(self):
u = mda.Universe(XYZ_mini)
errmsg = "AtomGroup has no attribute bonds"
with pytest.raises(AttributeError, match=errmsg):
Z = BAT(u.atoms)
def test_bat_bad_initial_atom(self, selected_residues):
errmsg = "Initial atom is not a terminal atom"
with pytest.raises(ValueError, match=errmsg):
R = BAT(selected_residues, initial_atom=selected_residues[0])
def test_bat_disconnected_atom_group(self):
u = mda.Universe(PSF, DCD)
selected_residues = u.select_atoms("resid 1-3") + u.select_atoms(
"resid 5-7"
)
errmsg = "Additional torsions not found."
with pytest.raises(ValueError, match=errmsg):
R = BAT(selected_residues)
def test_bat_multifragments_atomgroup(self):
u = mda.Universe(TPR, XTC)
errmsg = "AtomGroup has more than one molecule"
with pytest.raises(ValueError, match=errmsg):
BAT(u.select_atoms("resname SOL"))
def test_bat_incorrect_dims(self, bat_npz):
u = mda.Universe(PSF, DCD)
selected_residues = u.select_atoms("resid 1-3")
errmsg = "Dimensions of array in loaded file"
with pytest.raises(ValueError, match=errmsg):
R = BAT(selected_residues, filename=bat_npz)
def test_Cartesian_does_not_modify_input(self, selected_residues, bat):
R = BAT(selected_residues)
pre_transformation = copy.deepcopy(bat[0])
R.Cartesian(bat[0])
assert_allclose(
pre_transformation,
bat[0],
rtol=0,
atol=1.5e-7,
err_msg="BAT.Cartesian modified input data",
)
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