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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.datafiles import PSF, DCD
# Legacy tests from before 363
@pytest.fixture()
def universe():
return mda.Universe(PSF, DCD)
@pytest.fixture()
def g(universe):
return universe.atoms.segments
def test_newSegmentGroup(universe):
"""test that slicing a SegmentGroup returns a new SegmentGroup (Issue 135)"""
g = universe.atoms.segments
newg = g[:]
assert isinstance(newg, mda.core.groups.SegmentGroup)
assert_equal(len(newg), len(g))
def test_n_atoms(g):
assert_equal(g.n_atoms, 3341)
def test_n_residues(g):
assert_equal(g.n_residues, 214)
def test_resids_dim(g):
assert_equal(len(g.resids), len(g))
for seg, resids in zip(g, g.resids):
assert len(resids) == len(seg.residues)
assert_equal(seg.residues.resids, resids)
def test_resnums_dim(g):
assert_equal(len(g.resnums), len(g))
for seg, resnums in zip(g, g.resnums):
assert len(resnums) == len(seg.residues)
assert_equal(seg.residues.resnums, resnums)
def test_segids_dim(g):
assert_equal(len(g.segids), len(g))
def test_set_segids(universe):
s = universe.select_atoms("all").segments
s.segids = "ADK"
assert_equal(
universe.segments.segids,
["ADK"],
err_msg="failed to set_segid on segments",
)
def test_set_segid_updates_(universe):
g = universe.select_atoms("resid 10:18").segments
g.segids = "ADK"
assert_equal(
g.segids,
["ADK"],
err_msg="old selection was not changed in place after set_segid",
)
def test_set_segids_many():
u = mda.Universe.empty(
n_atoms=6,
n_residues=2,
n_segments=2,
atom_resindex=[0, 0, 0, 1, 1, 1],
residue_segindex=[0, 1],
)
u.add_TopologyAttr("segids", ["A", "B"])
# universe with 2 segments, A and B
u.segments.segids = ["X", "Y"]
assert u.segments[0].segid == "X"
assert u.segments[1].segid == "Y"
assert len(u.select_atoms("segid A")) == 0
assert len(u.select_atoms("segid B")) == 0
assert len(u.select_atoms("segid X")) == 3
assert len(u.select_atoms("segid Y")) == 3
def test_atom_order(universe):
assert_equal(
universe.segments.atoms.indices,
sorted(universe.segments.atoms.indices),
)
def test_segmentgroup_pickle():
u = mda.Universe.empty(10)
u.add_Segment(segid="X")
u.add_Segment(segid="Y")
u.add_Segment(segid="Z")
segids = ["A", "X", "Y", "Z"]
u.add_TopologyAttr("segids", values=["A", "X", "Y", "Z"])
seg_group = mda.SegmentGroup((1, 3), u)
seg = pickle.loads(pickle.dumps(seg_group))
assert_equal(seg.universe.segments.segids, segids)
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