def test_no_container(self, ref):
with tempdir.in_tempdir():
if ref.container_format:
ref.writer('foo')
else:
with pytest.raises(TypeError):
ref.writer('foo')
def test_no_container(self, ref):
with tempdir.in_tempdir():
if ref.container_format:
ref.writer('foo')
else:
with pytest.raises(TypeError):
ref.writer('foo')
def test_write_no_args(self):
with tempdir.in_tempdir():
self.u.atoms.write()
files = glob('*')
assert_equal(len(files), 1)
name = path.splitext(path.basename(DCD))[0]
assert_equal(files[0], "{}_0.pdb".format(name))
def test_AlignTraj_outfile_default(self, universe, reference):
with tempdir.in_tempdir():
reference.trajectory[-1]
x = align.AlignTraj(universe, reference)
try:
assert os.path.basename(x.filename) == 'rmsfit_adk_dims.dcd'
finally:
x._writer.close()
def test_xtc_striding():
"""testing MDAnalysis.analysis.helanal xtc striding: Check for resolution of Issue #188."""
u = MDAnalysis.Universe(GRO, XTC)
u.trajectory[1]
with tempdir.in_tempdir():
assert_raises(FinishTimeException,
MDAnalysis.analysis.helanal.helanal_trajectory,
u, selection="name CA", finish=5)
def test_save(self, universe):
with tempdir.in_tempdir():
ca = self._run_Contacts(universe)
ca.save('testfile.npy')
saved = np.genfromtxt('testfile.npy')
assert_array_almost_equal(ca.timeseries, saved)
# check the header was written correctly
with open('testfile.npy', 'r') as fin:
assert fin.readline().strip() == '# q1 analysis'
def test_xtc_striding():
"""testing MDAnalysis.analysis.helanal xtc striding: Check for resolution of Issue #188."""
u = MDAnalysis.Universe(GRO, XTC)
u.trajectory[1]
with tempdir.in_tempdir():
assert_raises(FinishTimeException,
MDAnalysis.analysis.helanal.helanal_trajectory,
u, selection="name CA", finish=5)
def test_save(self, universe):
with tempdir.in_tempdir():
ca = self._run_Contacts(universe)
ca.save('testfile.npy')
saved = np.genfromtxt('testfile.npy')
assert_array_almost_equal(ca.timeseries, saved)
# check the header was written correctly
with open('testfile.npy', 'r') as fin:
assert fin.readline().strip() == '# q1 analysis'
def test_get_writer(self, universe):
with tempdir.in_tempdir():
self.outfile = 'test-trz-writer.trz'
W = universe.trajectory.Writer(self.outfile)
assert_equal(isinstance(W, mda.coordinates.TRZ.TRZWriter), True)
assert_equal(W.n_atoms, universe.trajectory.n_atoms)
try:
os.unlink(self.outfile)
except OSError:
pass
def test_get_writer_2(self):
with tempdir.in_tempdir():
self.outfile = 'test-trz-writer-1.trz'
W = self.trz.Writer(self.outfile, n_atoms=100)
assert_equal(isinstance(W, mda.coordinates.TRZ.TRZWriter), True)
assert_equal(W.n_atoms, 100)
try:
os.unlink(self.outfile)
except OSError:
pass
def test_get_writer_2(self):
with tempdir.in_tempdir():
self.outfile = 'test-trz-writer-1.trz'
W = self.trz.Writer(self.outfile, n_atoms=100)
assert_equal(isinstance(W, mda.coordinates.TRZ.TRZWriter), True)
assert_equal(W.n_atoms, 100)
try:
os.unlink(self.outfile)
except OSError:
pass
def test_AlignTraj_outfile_default(self, universe, reference):
# NOTE: Remove the line os.remove() with release 1.0,
# when the default behavior of AlignTraj changes.
with tempdir.in_tempdir():
reference.trajectory[-1]
x = align.AlignTraj(universe, reference)
try:
assert os.path.basename(x.filename) == 'rmsfit_adk_dims.dcd'
finally:
x._writer.close()
os.remove(x.filename)
def test_AlignTraj_outfile_default(self, universe, reference):
# NOTE: Remove the line os.remove() with release 1.0,
# when the default behavior of AlignTraj changes.
with tempdir.in_tempdir():
reference.trajectory[-1]
x = align.AlignTraj(universe, reference)
try:
assert os.path.basename(x.filename) == 'rmsfit_adk_dims.dcd'
finally:
x._writer.close()
os.remove(x.filename)
def test_writer_trz_from_other(self, u):
with tempdir.in_tempdir():
outfile = 'trz-writer-2.trz'
W = mda.coordinates.TRZ.TRZWriter(outfile, n_atoms=len(u.atoms))
W.write(u.trajectory.ts)
W.close()
u2 = mda.Universe(two_water_gro, outfile)
assert_almost_equal(u.atoms.positions, u2.atoms.positions, 3)
def setUpClass(cls):
cls.universe = MDAnalysis.Universe(cls.filename)
if not executable_not_found("hole"):
with tempdir.in_tempdir():
H = HOLEtraj(cls.universe, start=cls.start,
stop=cls.stop, raseed=31415)
H.run()
cls.H = H
else:
cls.H = None
cls.frames = [ts.frame
for ts in cls.universe.trajectory[cls.start:cls.stop]]
def test_writer_trz_from_other(self):
with tempdir.in_tempdir():
outfile = 'trz-writer-2.trz'
W = mda.coordinates.TRZ.TRZWriter(outfile,
n_atoms=len(self.u.atoms))
W.write(self.u.trajectory.ts)
W.close()
u2 = mda.Universe(two_water_gro, outfile)
assert_array_almost_equal(self.u.atoms.positions,
u2.atoms.positions, 3)
def test_File_write(self):
with tempdir.in_tempdir():
outfile = "lookingglas.txt"
with open(outfile, "w") as obj:
with util.NamedStream(obj, outfile, close=True) as ns:
assert_equal(ns.name, outfile)
assert_equal(str(ns), outfile)
ns.writelines(self.text)
with open(outfile) as fh:
text = fh.readlines()
assert_equal(len(text), len(self.text))
assert_equal("".join(text), "".join(self.text))
def test_conect_bonds_all(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'pdb-connect-bonds.pdb'
self.conect.atoms.write(outfile, bonds="all")
u2 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u2.atoms), 1890)
assert_equal(len([b for b in u2.bonds if not b.is_guessed]), 1922)
def test_hole_module_fd_closure(self):
"""test open file descriptors are closed (MDAnalysisTests.analysis.test_hole.TestHoleModule): Issue 129"""
# If Issue 129 isn't resolved, this function will produce an OSError on
# the system, and cause many other tests to fail as well.
#
# Successful test takes ~10 s, failure ~2 s.
# Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
import resource
# ----- temporary hack -----
# on Mac OS X (on Travis) we run out of open file descriptors
# before even starting this test (see
# https://github.com/MDAnalysis/mdanalysis/pull/901#issuecomment-231938093);
# if this issue is solved by #363 then revert the following
# hack:
#
import platform
if platform.platform() == "Darwin":
max_open_files = 512
else:
max_open_files = 64
#
# --------------------------
resource.setrlimit(resource.RLIMIT_NOFILE,
(max_open_files, self.hard_max_open_files))
with tempdir.in_tempdir():
try:
H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
finally:
self._restore_rlimits()
# pretty unlikely that the code will get through 2 rounds if the MDA
# issue 129 isn't fixed, although this depends on the file descriptor
# open limit for the machine in question
try:
for i in range(2):
# will typically get an OSError for too many files being open after
# about 2 seconds if issue 129 isn't resolved
H.run()
except OSError as err:
if err.errno == errno.EMFILE:
raise AssertionError(
"HOLEtraj does not close file descriptors (Issue 129)")
raise
finally:
# make sure to restore open file limit !!
self._restore_rlimits()
def test_conect_bonds_conect(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'test-pdb-hbonds.pdb'
self.conect.atoms.write(outfile, bonds="conect")
u1 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u1.atoms), 1890)
assert_equal(len(u1.bonds), 1922)
def test_rms_fit_trj_defaultfilename(self):
filename = 'rmsfit_' + os.path.basename(self.universe.trajectory.filename)
with tempdir.in_tempdir():
# Need to pretend to have the universe trajectory INSIDE the tempdir because
# filename=None uses the full path
self.universe.trajectory.filename = os.path.abspath(
os.path.join(
os.curdir,
os.path.basename(self.universe.trajectory.filename)))
#test filename=none and different selection
align.rms_fit_trj(self.universe, self.reference, select="name CA",
filename=None, verbose=False)
assert_(os.path.exists(filename),
"rms_fit_trj did not write to {}".format(filename))
def test_helanal_trajectory(reference=HELANAL_BENDING_MATRIX,
outfile="helanal_bending_matrix.dat"):
u = mda.Universe(PSF, DCD)
with tempdir.in_tempdir():
# Helix 8: 161 - 187 http://www.rcsb.org/pdb/explore.do?structureId=4AKE
MDAnalysis.analysis.helanal.helanal_trajectory(u,
selection="name CA and resnum 161-187")
bendingmatrix = read_bending_matrix(outfile)
ref = read_bending_matrix(reference)
assert_equal(sorted(bendingmatrix.keys()), sorted(ref.keys()),
err_msg="different contents in bending matrix data file")
for label in ref.keys():
assert_array_almost_equal(bendingmatrix[label], ref[label],
err_msg="bending matrix stats for {0} mismatch".format(label))
def test_File_write(self):
with tempdir.in_tempdir():
outfile = "lookingglas.txt"
with open(outfile, "w") as obj:
with util.NamedStream(obj, outfile, close=True) as ns:
assert_equal(ns.name, outfile)
assert_equal(str(ns), outfile)
ns.writelines(self.text)
with open(outfile) as fh:
text = fh.readlines()
assert_equal(len(text), len(self.text))
assert_equal("".join(text), "".join(self.text))
def test_conect_bonds_all(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'pdb-connect-bonds.pdb'
self.conect.atoms.write(outfile, bonds="all")
u2 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u2.atoms), 1890)
assert_equal(len([b for b in u2.bonds if not b.is_guessed]), 1922)
def test_conect_bonds_conect(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'test-pdb-hbonds.pdb'
self.conect.atoms.write(outfile, bonds="conect")
u1 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u1.atoms), 1890)
assert_equal(len(u1.bonds), 1922)
def test_helanal_trajectory(reference=HELANAL_BENDING_MATRIX,
outfile="helanal_bending_matrix.dat"):
u = mda.Universe(PSF, DCD)
with tempdir.in_tempdir():
# Helix 8: 161 - 187 http://www.rcsb.org/pdb/explore.do?structureId=4AKE
MDAnalysis.analysis.helanal.helanal_trajectory(u,
selection="name CA and resnum 161-187")
bendingmatrix = read_bending_matrix(outfile)
ref = read_bending_matrix(reference)
assert_equal(sorted(bendingmatrix.keys()), sorted(ref.keys()),
err_msg="different contents in bending matrix data file")
for label in ref.keys():
assert_array_almost_equal(bendingmatrix[label], ref[label],
err_msg="bending matrix stats for {0} mismatch".format(label))
def test_hole_module_fd_closure(self):
"""test open file descriptors are closed (MDAnalysisTests.analysis.test_hole.TestHoleModule): Issue 129"""
# If Issue 129 isn't resolved, this function will produce an OSError on
# the system, and cause many other tests to fail as well.
#
# Successful test takes ~10 s, failure ~2 s.
# Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
import resource
# ----- temporary hack -----
# on Mac OS X (on Travis) we run out of open file descriptors
# before even starting this test (see
# https://github.com/MDAnalysis/mdanalysis/pull/901#issuecomment-231938093);
# if this issue is solved by #363 then revert the following
# hack:
#
import platform
if platform.platform() == "Darwin":
max_open_files = 512
else:
max_open_files = 64
#
# --------------------------
resource.setrlimit(resource.RLIMIT_NOFILE,
(max_open_files, self.hard_max_open_files))
with tempdir.in_tempdir():
try:
H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
finally:
self._restore_rlimits()
# pretty unlikely that the code will get through 2 rounds if the MDA
# issue 129 isn't fixed, although this depends on the file descriptor
# open limit for the machine in question
try:
for i in range(2):
# will typically get an OSError for too many files being open after
# about 2 seconds if issue 129 isn't resolved
H.run()
except OSError as err:
if err.errno == errno.EMFILE:
raise AssertionError("HOLEtraj does not close file descriptors (Issue 129)")
raise
finally:
# make sure to restore open file limit !!
self._restore_rlimits()
def check_density_from_Universe(self, atomselection,
ref_meandensity, **kwargs):
import MDAnalysis.analysis.density
with tempdir.in_tempdir():
D = MDAnalysis.analysis.density.density_from_Universe(
self.universe, atomselection=atomselection,
delta=self.delta, **kwargs)
assert_almost_equal(D.grid.mean(), ref_meandensity,
err_msg="mean density does not match")
D.export(self.outfile)
D2 = MDAnalysis.analysis.density.Density(self.outfile)
assert_almost_equal(D.grid, D2.grid, decimal=self.precision,
err_msg="DX export failed: different grid sizes")
def check_density_from_Universe(self, atomselection,
ref_meandensity, **kwargs):
import MDAnalysis.analysis.density
with tempdir.in_tempdir():
D = MDAnalysis.analysis.density.density_from_Universe(
self.universe, atomselection=atomselection,
delta=self.delta, **kwargs)
assert_almost_equal(D.grid.mean(), ref_meandensity,
err_msg="mean density does not match")
D.export(self.outfile)
D2 = MDAnalysis.analysis.density.Density(self.outfile)
assert_almost_equal(D.grid, D2.grid, decimal=self.precision,
err_msg="DX export failed: different grid sizes")
def setUpClass(cls):
cls.universe = MDAnalysis.Universe(cls.filename)
if not executable_not_found("hole"):
with tempdir.in_tempdir():
H = HOLEtraj(cls.universe,
start=cls.start,
stop=cls.stop,
raseed=31415)
H.run()
cls.H = H
else:
cls.H = None
cls.frames = [
ts.frame for ts in cls.universe.trajectory[cls.start:cls.stop]
]
def test_save(self):
hbond = HBAC(self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
with tempdir.in_tempdir():
hbond.save_results('hbondout.npz')
loaded = np.load('hbondout.npz')
assert_('time' in loaded)
assert_('results' in loaded)
def test_save(self, u, hydrogens, oxygens, nitrogens):
hbond = HBAC(
u,
hydrogens=hydrogens,
acceptors=oxygens,
donors=nitrogens,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
with tempdir.in_tempdir():
hbond.save_results('hbondout.npz')
loaded = np.load('hbondout.npz')
assert 'time' in loaded
assert 'results' in loaded
def test_File_write(self):
with tempdir.in_tempdir():
outfile = "lookingglas.txt"
try:
obj = open(outfile, "w")
ns = util.NamedStream(obj, outfile, close=True)
ns.writelines(self.text)
ns.close()
text = open(outfile).readlines()
assert_equal(ns.name, outfile)
assert_equal(str(ns), outfile)
assert_equal(len(text), len(self.text))
assert_equal("".join(text), "".join(self.text))
finally:
ns.close()
obj.close()
def test_File_write(self):
with tempdir.in_tempdir():
outfile = "lookingglas.txt"
try:
obj = open(outfile, "w")
ns = util.NamedStream(obj, outfile, close=True)
ns.writelines(self.text)
ns.close()
text = open(outfile).readlines()
assert_equal(ns.name, outfile)
assert_equal(str(ns), outfile)
assert_equal(len(text), len(self.text))
assert_equal("".join(text), "".join(self.text))
finally:
ns.close()
obj.close()
def test_save(self):
hbond = HBAC(
self.u,
hydrogens=self.H,
acceptors=self.O,
donors=self.N,
bond_type='continuous',
sample_time=0.06,
)
hbond.run()
with tempdir.in_tempdir():
hbond.save_results('hbondout.npz')
loaded = np.load('hbondout.npz')
assert_('time' in loaded)
assert_('results' in loaded)
def test_rms_fit_trj_defaultfilename(self):
filename = 'rmsfit_' + os.path.basename(
self.universe.trajectory.filename)
with tempdir.in_tempdir():
# Need to pretend to have the universe trajectory INSIDE the tempdir because
# filename=None uses the full path
self.universe.trajectory.filename = os.path.abspath(
os.path.join(
os.curdir,
os.path.basename(self.universe.trajectory.filename)))
#test filename=none and different selection
align.rms_fit_trj(self.universe,
self.reference,
select="name CA",
filename=None,
verbose=False)
assert_(os.path.exists(filename),
"rms_fit_trj did not write to {}".format(filename))
def test_AlignTraj_outfile_default_exists(self, universe, reference,
tmpdir):
reference.trajectory[-1]
outfile = str(tmpdir.join('align_test.dcd'))
align.AlignTraj(universe, reference, filename=outfile).run()
fitted = mda.Universe(PSF, outfile)
# ensure default file exists
with mda.Writer(str(tmpdir.join("rmsfit_align_test.dcd")),
n_atoms=fitted.atoms.n_atoms) as w:
w.write(fitted.atoms)
with tempdir.in_tempdir():
align.AlignTraj(fitted, reference)
# we are careful now. The default does nothing
with pytest.raises(IOError):
align.AlignTraj(fitted, reference, force=False)
def test_hole_module_fd_closure(self):
"""MDAnalysis.analysis.hole: Issue 129: ensure low level file descriptors to PDB files used by Hole program are properly closed"""
# If Issue 129 isn't resolved, this function will produce an OSError on
# the system, and cause many other tests to fail as well.
#
# Successful test takes ~10 s, failure ~2 s.
try:
# Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
import resource
resource.setrlimit(resource.RLIMIT_NOFILE,
(64, self.hard_max_open_files))
except ImportError:
raise NotImplementedError(
"Test cannot be run without the resource module.")
with tempdir.in_tempdir():
try:
# will need to have the 'hole' command available in the path
H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
except OSError as err:
if err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
self._restore_rlimits()
# pretty unlikely that the code will get through 2 rounds if the MDA
# issue 129 isn't fixed, although this depends on the file descriptor
# open limit for the machine in question
try:
for i in range(2):
# will typically get an OSError for too many files being open after
# about 2 seconds if issue 129 isn't resolved
H.run()
except OSError as err:
if err.errno == errno.EMFILE:
raise AssertionError(
"HOLEtraj does not close file descriptors (Issue 129)")
elif err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
# make sure to restore open file limit !!
self._restore_rlimits()
def test_hole_module_fd_closure(self):
"""MDAnalysis.analysis.hole: Issue 129: ensure low level file descriptors to PDB files used by Hole program are properly closed"""
# If Issue 129 isn't resolved, this function will produce an OSError on
# the system, and cause many other tests to fail as well.
#
# Successful test takes ~10 s, failure ~2 s.
try:
# Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
import resource
resource.setrlimit(resource.RLIMIT_NOFILE, (64, self.hard_max_open_files))
except ImportError:
raise NotImplementedError("Test cannot be run without the resource module.")
with tempdir.in_tempdir():
try:
# will need to have the 'hole' command available in the path
H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
except OSError as err:
if err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
self._restore_rlimits()
# pretty unlikely that the code will get through 2 rounds if the MDA
# issue 129 isn't fixed, although this depends on the file descriptor
# open limit for the machine in question
try:
for i in range(2):
# will typically get an OSError for too many files being open after
# about 2 seconds if issue 129 isn't resolved
H.run()
except OSError as err:
if err.errno == errno.EMFILE:
raise AssertionError("HOLEtraj does not close file descriptors (Issue 129)")
elif err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
# make sure to restore open file limit !!
self._restore_rlimits()
def test_get_writer_1(self, ref, reader):
with tempdir.in_tempdir():
outfile = 'test-writer' + ref.ext
with reader.Writer(outfile) as W:
assert_equal(isinstance(W, ref.writer), True)
assert_equal(W.n_atoms, reader.n_atoms)
def test_save(self):
with tempdir.in_tempdir():
ca = self._run_Contacts()
ca.save('testfile.npy')
saved = np.genfromtxt('testfile.npy')
assert_array_almost_equal(ca.timeseries, saved)
def test_save(self):
with tempdir.in_tempdir():
ca = self._run_Contacts()
ca.save('testfile.npy')
saved = np.genfromtxt('testfile.npy')
assert_array_almost_equal(ca.timeseries, saved)
def test_get_writer_1(self, ref, reader):
with tempdir.in_tempdir():
outfile = 'test-writer' + ref.ext
with reader.Writer(outfile) as W:
assert_equal(isinstance(W, ref.writer), True)
assert_equal(W.n_atoms, reader.n_atoms)
def test_bogus_kwarg_pdb(self):
# test for resolution of Issue 877
with tempdir.in_tempdir():
with assert_raises(TypeError):
self.u.atoms.write('dummy.pdb', bogus="what?")
def test_write_selection(self):
with tempdir.in_tempdir():
self.u.atoms.write("test.vmd")
def test_write_coordinates(self):
with tempdir.in_tempdir():
self.u.atoms.write("test.xtc")
def test_raises(self):
with tempdir.in_tempdir():
self.u.atoms.write('useless.format123')
def test_no_container(self):
with tempdir.in_tempdir():
if self.ref.container_format:
self.ref.writer('foo')
else:
assert_raises(TypeError, self.ref.writer, 'foo')
def test_get_writer_2(self):
with tempdir.in_tempdir():
self.outfile = 'test-writer' + self.ref.ext
with self.reader.Writer(self.outfile, n_atoms=100) as W:
assert_equal(isinstance(W, self.ref.writer), True)
assert_equal(W.n_atoms, 100)
def test_get_writer_2(self):
with tempdir.in_tempdir():
self.outfile = 'test-writer' + self.ref.ext
with self.reader.Writer(self.outfile, n_atoms=100) as W:
assert_equal(isinstance(W, self.ref.writer), True)
assert_equal(W.n_atoms, 100)
def test_no_container(self):
with tempdir.in_tempdir():
if self.ref.container_format:
self.ref.writer('foo')
else:
assert_raises(TypeError, self.ref.writer, 'foo')