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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 pickle
import pytest
import numpy as np
import MDAnalysis as mda
from MDAnalysis import NoDataError
from MDAnalysisTests.datafiles import (
PSF,
DCD,
XYZ_mini,
)
from numpy.testing import assert_almost_equal
class TestAtom(object):
# Legacy tests from before 363
"""Tests of Atom."""
"""Set up the standard AdK system in implicit solvent."""
@staticmethod
@pytest.fixture()
def universe():
return mda.Universe(PSF, DCD)
@staticmethod
@pytest.fixture()
def atom(universe):
# Leu67:CG
return universe.atoms[1000]
def test_attributes_names(self, atom):
a = atom
assert a.name == "CG"
assert a.resname == "LEU"
def test_setting_attribute_name(self, atom):
atom.name = "AA"
assert atom.name == "AA"
def test_setting_attribute_type(self, atom):
atom.type = "Z"
assert atom.type == "Z"
def test_setting_attribute_mass(self, atom):
atom.mass = 13
assert atom.mass == 13
def test_setting_attributes_charge(self, atom):
atom.charge = 6
assert atom.charge == 6
def test_attributes_positions(self, atom):
known_pos = np.array(
[3.94543672, -12.4060812, -7.26820087], dtype=np.float32
)
a = atom
# new position property (mutable)
assert_almost_equal(a.position, known_pos)
pos = a.position + 3.14
a.position = pos
assert_almost_equal(a.position, pos)
def test_atom_selection(self, universe, atom):
asel = universe.select_atoms("atom 4AKE 67 CG").atoms[0]
assert atom == asel
def test_hierarchy(self, universe, atom):
u = universe
a = atom
assert a.segment == u.select_atoms("segid 4AKE").segments[0]
assert a.residue == u.residues[66]
def test_bad_add(self, atom):
with pytest.raises(TypeError):
atom + 1
def test_add_AG(self, universe, atom):
ag = universe.atoms[:2]
ag2 = atom + ag
for at in [atom, ag[0], ag[1]]:
assert at in ag2
def test_no_velo(self, atom):
with pytest.raises(NoDataError):
atom.velocity
def test_bonded_atoms(self, universe):
at = universe.atoms[0]
ref = [b.partner(at) for b in at.bonds]
assert ref == list(at.bonded_atoms)
def test_undefined_occupancy(self, universe):
with pytest.raises(AttributeError):
universe.atoms[0].occupancy
@pytest.mark.parametrize("ix", (1, -1))
def test_atom_pickle(self, universe, ix):
atm_out = universe.atoms[ix]
atm_in = pickle.loads(pickle.dumps(atm_out))
assert atm_in == atm_out
def test_improper_initialisation(self, universe):
with pytest.raises(IndexError):
indices = [0, 1]
mda.core.groups.Atom(indices, universe)
class TestAtomNoForceNoVel(object):
@staticmethod
@pytest.fixture()
def a():
u = mda.Universe(XYZ_mini)
return u.atoms[0]
def test_velocity_fail(self, a):
with pytest.raises(NoDataError):
getattr(a, "velocity")
def test_force_fail(self, a):
with pytest.raises(NoDataError):
getattr(a, "force")
def test_velocity_set_fail(self, a):
with pytest.raises(NoDataError):
setattr(a, "velocity", [1.0, 1.0, 1.0])
def test_force_set_fail(self, a):
with pytest.raises(NoDataError):
setattr(a, "force", [1.0, 1.0, 1.0])
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