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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 collections import OrderedDict
import pytest
from numpy.testing import assert_equal, assert_allclose
import MDAnalysis as mda
import os
from MDAnalysisTests.datafiles import CRD
from MDAnalysisTests import make_Universe
class TestCRDWriter(object):
@pytest.fixture()
def u(self):
return mda.Universe(CRD)
@pytest.fixture()
def outfile(self, tmpdir):
return os.path.join(str(tmpdir), "test.crd")
@pytest.mark.parametrize(
"testfile", ["test.crd", "test.crd.bz2", "test.crd.gz"]
)
def test_write_atoms(self, u, testfile, tmpdir):
# Test that written file when read gives same coordinates
with tmpdir.as_cwd():
u.atoms.write(testfile)
u2 = mda.Universe(testfile)
assert_equal(u.atoms.positions, u2.atoms.positions)
def test_roundtrip(self, u, outfile):
# Write out a copy of the Universe, and compare this against the original
# This is more rigorous than simply checking the coordinates as it checks
# all formatting
u.atoms.write(outfile)
def CRD_iter(fn):
with open(fn, "r") as inf:
for line in inf:
if not line.startswith("*"):
yield line
for ref, other in zip(CRD_iter(CRD), CRD_iter(outfile)):
assert ref == other
def test_write_EXT(self, u, outfile):
# Use the `extended` keyword to force the EXT format
u.atoms.write(outfile, extended=True)
with open(outfile, "r") as inf:
format_line = inf.readlines()[2]
assert "EXT" in format_line, "EXT format expected"
def test_write_EXT_read(self, u, outfile):
# Read EXT format and check atom positions
u.atoms.write(outfile, extended=True)
u2 = mda.Universe(outfile)
sel1 = u.select_atoms("all")
sel2 = u2.select_atoms("all")
cog1 = sel1.center_of_geometry()
cog2 = sel2.center_of_geometry()
assert_equal(
len(u.atoms), len(u2.atoms)
), "Equal number of " "atoms expected in both CRD formats"
assert_equal(
len(u.atoms.residues), len(u2.atoms.residues)
), "Equal number of residues expected in" "both CRD formats"
assert_equal(
len(u.atoms.segments), len(u2.atoms.segments)
), "Equal number of segments expected in" "both CRD formats"
assert_allclose(
cog1, cog2, rtol=1e-6, atol=0
), "Same centroid expected for both CRD formats"
class TestCRDWriterMissingAttrs(object):
# All required attributes with the default value
req_attrs = OrderedDict(
[
("resnames", "UNK"),
("resids", 1),
("names", "X"),
("tempfactors", 0.0),
]
)
@pytest.mark.parametrize("missing_attr", req_attrs)
def test_warns(self, missing_attr, tmpdir):
attrs = list(self.req_attrs.keys())
attrs.remove(missing_attr)
u = make_Universe(attrs, trajectory=True)
outfile = str(tmpdir) + "/out.crd"
with pytest.warns(UserWarning):
u.atoms.write(outfile)
@pytest.mark.parametrize("missing_attr", req_attrs)
def test_write(self, missing_attr, tmpdir):
attrs = list(self.req_attrs.keys())
attrs.remove(missing_attr)
u = make_Universe(attrs, trajectory=True)
outfile = str(tmpdir) + "/out.crd"
u.atoms.write(outfile)
u2 = mda.Universe(outfile)
# Check all other attrs aren't disturbed
for attr in attrs:
assert_equal(getattr(u.atoms, attr), getattr(u2.atoms, attr))
# Check missing attr is as expected
assert_equal(
getattr(u2.atoms, missing_attr), self.req_attrs[missing_attr]
)
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