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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 --- http://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 numpy as np
from numpy.testing import assert_equal
import pytest
from MDAnalysisTests.datafiles import PSF, DCD, PDB_small
import MDAnalysis as mda
from MDAnalysis.core import topology
from MDAnalysis.core import topologyattrs as ta
@pytest.fixture()
def refTT():
ref = topology.TransTable(
9,
6,
3,
atom_resindex=np.array([0, 0, 1, 1, 2, 2, 3, 4, 5]),
residue_segindex=np.array([0, 1, 2, 0, 1, 1]),
)
return ref
class TestTransTableCopy(object):
def test_size(self, refTT):
new = refTT.copy()
assert new.n_atoms == refTT.n_atoms
assert new.n_residues == refTT.n_residues
assert new.n_segments == refTT.n_segments
def test_size_independent(self, refTT):
# check changing
new = refTT.copy()
old = refTT.n_atoms
refTT.n_atoms = -10
assert new.n_atoms == old
@pytest.mark.parametrize("attr", ["_AR", "RA", "_RS", "SR"])
def test_AR(self, refTT, attr):
new = refTT.copy()
ref = getattr(refTT, attr)
other = getattr(new, attr)
# arrays are dtype='object'
for a, b in zip(ref, other):
assert_equal(a, b)
@pytest.mark.parametrize("attr", ["_AR", "RA", "_RS", "SR"])
def test_AR_independent(self, refTT, attr):
new = refTT.copy()
ref = getattr(refTT, attr)
other = getattr(new, attr)
# check that arrays don't share memory instead maybe?
assert ref is not other
def test_move_atom(self, refTT):
new = refTT.copy()
# move atom 0 to residue 3
refTT.move_atom(0, 3)
assert refTT.atoms2residues(0) == 3
assert new.atoms2residues(0) == 0
def test_move_residue(self, refTT):
new = refTT.copy()
refTT.move_residue(1, 2)
assert refTT.residues2segments(1) == 2
assert new.residues2segments(1) == 1
TA_FILLER = {
object: np.array(["dave", "steve", "hugo"], dtype=object),
int: np.array([5, 4, 6]),
float: np.array([15.4, 5.7, 22.2]),
"record": np.array(["ATOM", "ATOM", "HETATM"], dtype="object"),
"bond": [(0, 1), (1, 2), (5, 6)],
"angles": [(0, 1, 2), (1, 2, 3), (4, 5, 6)],
"dihe": [(0, 1, 2, 3), (1, 2, 3, 4), (5, 6, 7, 8)],
}
@pytest.fixture(
params=[
(ta.Atomids, int),
(ta.Atomnames, object),
(ta.Atomtypes, object),
(ta.Elements, object),
(ta.Radii, float),
(ta.RecordTypes, "record"),
(ta.ChainIDs, object),
(ta.Tempfactors, float),
(ta.Masses, float),
(ta.Charges, float),
(ta.Occupancies, float),
(ta.AltLocs, object),
(ta.Resids, int),
(ta.Resnames, object),
(ta.Resnums, int),
(ta.ICodes, object),
(ta.Segids, object),
(ta.Bonds, "bond"),
(ta.Angles, "angles"),
(ta.Dihedrals, "dihe"),
(ta.Impropers, "dihe"),
]
)
def refTA(request):
cls, dt = request.param
return cls(TA_FILLER[dt])
def test_copy_attr(refTA):
new = refTA.copy()
assert_equal(new.values, refTA.values)
assert new.values is not refTA.values
@pytest.fixture()
def refTop():
return topology.Topology(
3,
2,
2,
attrs=[
ta.Atomnames(TA_FILLER[object]),
ta.Masses(TA_FILLER[float]),
ta.Resids(TA_FILLER[int]),
ta.Bonds(TA_FILLER["bond"]),
],
atom_resindex=np.array([0, 0, 1]),
residue_segindex=np.array([0, 1]),
)
def test_topology_copy_n_attrs(refTop):
new = refTop.copy()
assert len(new.attrs) == 7 # 4 + 3 indices
@pytest.mark.parametrize(
"attr",
[
"names",
"masses",
"resids",
"bonds",
"tt",
],
)
def test_topology_copy_unique_attrs(refTop, attr):
new = refTop.copy()
assert getattr(refTop, attr) is not getattr(new, attr)
@pytest.fixture(scope="module")
def refUniverse():
return mda.Universe(PSF, DCD)
class TestCopyUniverse(object):
def test_universe_copy(self, refUniverse):
new = refUniverse.copy()
assert new is not refUniverse
assert len(new.atoms) == len(refUniverse.atoms)
def test_positions(self, refUniverse):
new = refUniverse.copy()
assert_equal(new.atoms.positions, refUniverse.atoms.positions)
def test_change_positions(self, refUniverse):
# check that coordinates act independently
new = refUniverse.copy()
previous = new.atoms[0].position.copy()
refUniverse.atoms[0].position = 1, 2, 3
assert_equal(new.atoms[0].position, previous)
assert_equal(refUniverse.atoms[0].position, [1, 2, 3])
def test_topology(self, refUniverse):
new = refUniverse.copy()
assert_equal(new.atoms.names, refUniverse.atoms.names)
def test_change_topology(self, refUniverse):
new = refUniverse.copy()
previous = new.atoms[0].name
refUniverse.atoms[0].name = "newname"
assert new.atoms[0].name == previous
assert refUniverse.atoms[0].name == "newname"
def test_pdb_copy():
u = mda.Universe(PDB_small)
u2 = u.copy()
assert_equal(u.atoms.record_types, u2.atoms.record_types)
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