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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 numpy.testing import (
assert_equal,
)
import pytest
import pickle
import MDAnalysis as mda
from MDAnalysisTests import make_Universe
from MDAnalysis.tests.datafiles import PSF, DCD
class TestSegment(object):
@pytest.fixture()
def universe(self):
return make_Universe(("segids",))
@pytest.fixture()
def sB(self, universe):
return universe.segments[1]
def test_type(self, sB):
assert isinstance(sB, mda.core.groups.Segment)
assert_equal(sB.segid, "SegB")
def test_index(self, sB):
s = sB
res = s.residues[3]
assert isinstance(res, mda.core.groups.Residue)
def test_slicing(self, sB):
res = sB.residues[:3]
assert_equal(len(res), 3)
assert isinstance(res, mda.core.groups.ResidueGroup)
def test_advanced_slicing(self, sB):
res = sB.residues[[2, 1, 0, 2]]
assert_equal(len(res), 4)
assert isinstance(res, mda.core.groups.ResidueGroup)
def test_atom_order(self, universe):
assert_equal(
universe.segments[0].atoms.indices,
sorted(universe.segments[0].atoms.indices),
)
@pytest.mark.parametrize("ix", (1, -1))
def test_residue_pickle(self, universe, ix):
seg_out = universe.segments[ix]
seg_in = pickle.loads(pickle.dumps(seg_out))
assert seg_in == seg_out
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