class TestCustomReaders(object):
"""
Can pass a reader as kwarg on Universe creation
"""
@dec.skipif(parser_not_found('TRZ'),
'TRZ parser not available. Are you using python 3?')
def test_custom_reader(self):
# check that reader passing works
u = mda.Universe(TRZ_psf,
TRZ,
format=MDAnalysis.coordinates.TRZ.TRZReader)
assert_equal(len(u.atoms), 8184)
def test_custom_reader_singleframe(self):
T = MDAnalysis.topology.GROParser.GROParser
R = MDAnalysis.coordinates.GRO.GROReader
u = mda.Universe(two_water_gro,
two_water_gro,
topology_format=T,
format=R)
assert_equal(len(u.atoms), 6)
def test_custom_reader_singleframe_2(self):
# Same as before, but only one argument to Universe
T = MDAnalysis.topology.GROParser.GROParser
R = MDAnalysis.coordinates.GRO.GROReader
u = mda.Universe(two_water_gro, topology_format=T, format=R)
assert_equal(len(u.atoms), 6)
@dec.skipif(parser_not_found('TRZ'),
'TRZ parser not available. Are you using python 3?')
def test_custom_parser(self):
# topology reader passing works
u = mda.Universe(
TRZ_psf,
TRZ,
topology_format=MDAnalysis.topology.PSFParser.PSFParser)
assert_equal(len(u.atoms), 8184)
@dec.skipif(parser_not_found('TRZ'),
'TRZ parser not available. Are you using python 3?')
def test_custom_both(self):
# use custom for both
u = mda.Universe(
TRZ_psf,
TRZ,
format=MDAnalysis.coordinates.TRZ.TRZReader,
topology_format=MDAnalysis.topology.PSFParser.PSFParser)
assert_equal(len(u.atoms), 8184)
class TestSelectionErrors(object):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.u = mda.Universe(PSF, DCD)
def tearDown(self):
del self.u
def selection_fail(self, selstr):
assert_raises(SelectionError, self.u.select_atoms, selstr)
def test_expected_errors(self):
for selstr in [
'name and H', # string selection
'name )',
'resid abcd', # range selection
'resid 1-',
'prop chicken == tasty',
'prop chicken <= 7.4',
'prop mass ^^ 12.0',
'same this as resid 1', # same selection
'same resid resname mass 5.0', # same / expect
'name H and', # check all tokens used
'naem H', # unkonwn (misplet) opertaor
'resid and name C', # rangesel not finding vals
'resnum ',
'bynum or protein',
'prop mass < 4.0 hello', # unused token
'prop mass > 10. and group this', # missing group
'prop mass > 10. and fullgroup this', # missing fullgroup
]:
yield self.selection_fail, selstr
class _SelectionWriter(TestCase):
filename = None
max_number = 357 # to keep fixtures smallish, only select CAs up to number 357
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.universe = MDAnalysis.Universe(PSF, DCD)
stream = StringIO()
self.namedfile = NamedStream(stream, self.filename)
def tearDown(self):
del self.universe
del self.namedfile
def _selection(self):
return self.universe.select_atoms(
"protein and name CA and bynum 1-{0}".format(self.max_number))
def _write(self, **kwargs):
g = self._selection()
g.write(self.namedfile, **kwargs)
return g
def _write_selection(self, **kwargs):
g = self._selection()
g.write_selection(self.namedfile, **kwargs)
return g
class TestAtomGroupTimestep(object):
"""Tests the AtomGroup.ts attribute (partial timestep)"""
@dec.skipif(parser_not_found('TRZ'),
'TRZ parser not available. Are you using python 3?')
def setUp(self):
self.universe = mda.Universe(TRZ_psf, TRZ)
self.prec = 6
def tearDown(self):
del self.universe
del self.prec
def test_partial_timestep(self):
ag = self.universe.select_atoms('name Ca')
idx = ag.indices
assert_equal(len(ag.ts._pos), len(ag))
for ts in self.universe.trajectory[0:20:5]:
assert_array_almost_equal(
ts.positions[idx],
ag.ts.positions,
self.prec,
err_msg="Partial timestep coordinates wrong")
assert_array_almost_equal(
ts.velocities[idx],
ag.ts.velocities,
self.prec,
err_msg="Partial timestep coordinates wrong")
class TestOrthogonalDistanceSelections(BaseDistanceSelection):
@dec.skipif(parser_not_found('TRZ'),
'TRZ parser not available. Are you using python 3?')
def setUp(self):
self.u = mda.Universe(TRZ_psf, TRZ)
def tearDown(self):
del self.u
def _check_cyzone(self, meth, periodic):
sel = Parser.parse('cyzone 5 4 -4 resid 2', self.u.atoms)
sel.periodic = periodic
result = sel.apply(self.u.atoms)
other = self.u.select_atoms('resid 2')
pos = other.center_of_geometry()
vecs = self.u.atoms.positions - pos
if periodic:
box = self.u.dimensions[:3]
vecs -= box * np.rint(vecs / box)
mask = (vecs[:, 2] > -4) & (vecs[:, 2] < 4)
radii = vecs[:, 0]**2 + vecs[:, 1]**2
mask &= radii < 5**2
ref = set(self.u.atoms[mask].indices)
assert_(ref == set(result.indices))
def test_cyzone(self):
for meth, periodic in self.methods[1:]:
yield self._check_cyzone, meth, periodic
class TestLAMMPSDCD(BaseTimestepInterfaceTest):
@dec.skipif(parser_not_found('LAMMPS'),
'LAMMPS parser not available. Are you using python 3?')
def setUp(self):
u = self.u = mda.Universe(LAMMPSdata2, LAMMPSdcd2,
format='LAMMPS', topology_format='DATA',
timeunit='fs')
self.ts = u.trajectory.ts
class _TestSelfDistanceArrayDCD(TestCase):
backend = None
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.universe = MDAnalysis.Universe(PSF, DCD)
self.trajectory = self.universe.trajectory
self.ca = self.universe.select_atoms('name CA')
# see comments above on precision
self.prec = 5
def tearDown(self):
del self.universe
del self.trajectory
del self.ca
def test_simple(self):
U = self.universe
self.trajectory.rewind()
x0 = U.atoms.coordinates(copy=True)
d = MDAnalysis.lib.distances.self_distance_array(x0, backend=self.backend)
N = 3341 * (3341 - 1) / 2
assert_equal(d.shape, (N,), "wrong shape (should be (Natoms*(Natoms-1)/2,))")
assert_almost_equal(d.min(), 0.92905562402529318, self.prec,
err_msg="wrong minimum distance value")
assert_almost_equal(d.max(), 52.4702570624190590, self.prec,
err_msg="wrong maximum distance value")
def test_outarray(self):
U = self.universe
self.trajectory.rewind()
x0 = U.atoms.coordinates(copy=True)
natoms = len(U.atoms)
N = natoms * (natoms - 1) / 2
d = np.zeros((N,), np.float64)
MDAnalysis.lib.distances.self_distance_array(x0, result=d, backend=self.backend)
assert_equal(d.shape, (N,), "wrong shape (should be (Natoms*(Natoms-1)/2,))")
assert_almost_equal(d.min(), 0.92905562402529318, self.prec,
err_msg="wrong minimum distance value")
assert_almost_equal(d.max(), 52.4702570624190590, self.prec,
err_msg="wrong maximum distance value")
def test_periodic(self):
# boring with the current dcd as that has no PBC
U = self.universe
self.trajectory.rewind()
x0 = U.atoms.coordinates(copy=True)
natoms = len(U.atoms)
N = natoms * (natoms - 1) / 2
d = MDAnalysis.lib.distances.self_distance_array(x0, box=U.coord.dimensions,
backend=self.backend)
assert_equal(d.shape, (N,), "wrong shape (should be (Natoms*(Natoms-1)/2,))")
assert_almost_equal(d.min(), 0.92905562402529318, self.prec,
err_msg="wrong minimum distance value with PBC")
assert_almost_equal(d.max(), 52.4702570624190590, self.prec,
err_msg="wrong maximum distance value with PBC")
class TestWaterdynamics(TestCase):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.universe = MDAnalysis.Universe(waterPSF, waterDCD)
self.selection1 = "byres name OH2"
self.selection2 = self.selection1
self.selection3 = "byres name P1"
def test_HydrogenBondLifetimes(self):
hbl = MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes(
self.universe, self.selection1, self.selection2, 0, 5, 3)
hbl.run(verbose=False)
assert_equal(round(hbl.timeseries[2][1], 5), 0.75)
def test_WaterOrientationalRelaxation(self):
wor = MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation(
self.universe, self.selection1, 0, 5, 2)
wor.run(verbose=False)
assert_equal(round(wor.timeseries[1][2], 5), 0.35887)
def test_WaterOrientationalRelaxation_zeroMolecules(self):
wor_zero = MDAnalysis.analysis.waterdynamics.WaterOrientationalRelaxation(
self.universe, self.selection3, 0, 5, 2)
wor_zero.run(verbose=False)
assert_equal(wor_zero.timeseries[1], (0.0, 0.0, 0.0))
def test_AngularDistribution(self):
ad = MDAnalysis.analysis.waterdynamics.AngularDistribution(
self.universe, self.selection1, 40)
ad.run(verbose=False)
assert_equal(str(ad.graph[0][39]), str("0.951172947884 0.48313682125"))
def test_MeanSquareDisplacement(self):
msd = MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement(
self.universe, self.selection1, 0, 10, 2)
msd.run(verbose=False)
assert_equal(round(msd.timeseries[1], 5), 0.03984)
def test_MeanSquareDisplacement_zeroMolecules(self):
msd_zero = MDAnalysis.analysis.waterdynamics.MeanSquareDisplacement(
self.universe, self.selection3, 0, 10, 2)
msd_zero.run(verbose=False)
assert_equal(msd_zero.timeseries[1], 0.0)
def test_SurvivalProbability(self):
sp = MDAnalysis.analysis.waterdynamics.SurvivalProbability(
self.universe, self.selection1, 0, 6, 3)
sp.run(verbose=False)
assert_equal(round(sp.timeseries[1], 5), 1.0)
def test_SurvivalProbability_zeroMolecules(self):
sp_zero = MDAnalysis.analysis.waterdynamics.SurvivalProbability(
self.universe, self.selection3, 0, 6, 3)
sp_zero.run(verbose=False)
assert_equal(sp_zero.timeseries[1], 0.0)
class _Test_apply_PBC(TestCase):
backend = None
def setUp(self):
self.prec = 6
def tearDown(self):
del self.prec
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def test_ortho_PBC(self):
from MDAnalysis.lib.distances import apply_PBC
U = MDAnalysis.Universe(PSF, DCD)
atoms = U.atoms.coordinates()
box1 = np.array([2.5, 2.5, 3.5], dtype=np.float32)
box2 = np.array([2.5, 2.5, 3.5, 90., 90., 90.], dtype=np.float32)
cyth1 = apply_PBC(atoms, box1, backend=self.backend)
cyth2 = apply_PBC(atoms, box2, backend=self.backend)
reference = atoms - np.floor(atoms / box1) * box1
assert_almost_equal(cyth1, reference, self.prec,
err_msg="Ortho apply_PBC #1 failed comparison with np")
assert_almost_equal(cyth2, reference, self.prec,
err_msg="Ortho apply_PBC #2 failed comparison with np")
def test_tric_PBC(self):
from MDAnalysis.lib.distances import apply_PBC
U = MDAnalysis.Universe(TRIC)
atoms = U.atoms.coordinates()
box1 = U.dimensions
box2 = MDAnalysis.coordinates.core.triclinic_vectors(box1)
#print box2
#print box2.shape
def numpy_PBC(coords, box):
coords -= np.array([box[2] * val for val in np.floor(coords[:, 2] / box[2][2])])
coords -= np.array([box[1] * val for val in np.floor(coords[:, 1] / box[1][1])])
coords -= np.array([box[0] * val for val in np.floor(coords[:, 0] / box[0][0])])
return coords
cyth1 = apply_PBC(atoms, box1, backend=self.backend)
cyth2 = apply_PBC(atoms, box2, backend=self.backend)
reference = numpy_PBC(atoms, box2)
assert_almost_equal(cyth1, reference, self.prec,
err_msg="Triclinic apply_PBC failed comparison with np")
assert_almost_equal(cyth2, reference, self.prec,
err_msg="Trlclinic apply_PBC failed comparison with np")
class TestSegmentGroup(object):
# Legacy tests from before 363
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
"""Set up the standard AdK system in implicit solvent."""
self.universe = mda.Universe(PSF, DCD)
self.g = self.universe.atoms.segments
def test_newSegmentGroup(self):
"""test that slicing a SegmentGroup returns a new SegmentGroup (Issue 135)"""
g = self.universe.atoms.segments
newg = g[:]
assert_(isinstance(newg, mda.core.groups.SegmentGroup))
assert_equal(len(newg), len(g))
def test_n_atoms(self):
assert_equal(self.g.n_atoms, 3341)
def test_n_residues(self):
assert_equal(self.g.n_residues, 214)
def test_resids_dim(self):
assert_equal(len(self.g.resids), len(self.g))
for seg, resids in zip(self.g, self.g.resids):
assert_(len(resids) == len(seg.residues))
assert_equal(seg.residues.resids, resids)
def test_resnums_dim(self):
assert_equal(len(self.g.resnums), len(self.g))
for seg, resnums in zip(self.g, self.g.resnums):
assert_(len(resnums) == len(seg.residues))
assert_equal(seg.residues.resnums, resnums)
def test_segids_dim(self):
assert_equal(len(self.g.segids), len(self.g))
def test_set_segids(self):
s = self.universe.select_atoms('all').segments
s.segids = 'ADK'
assert_equal(self.universe.segments.segids, ['ADK'],
err_msg="failed to set_segid on segments")
def test_set_segid_updates_self(self):
g = self.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_atom_order(self):
assert_equal(self.universe.segments.atoms.indices,
sorted(self.universe.segments.atoms.indices))
class TestMergeTopology(object):
"""Test that Merge correct does topology"""
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.u = MDAnalysis.Universe(PSF, DCD)
self.u2 = MDAnalysis.Universe(merge_protein)
def tearDown(self):
del self.u
del self.u2
def test_merge_with_topology(self):
ag1 = self.u.atoms[:20]
ag2 = self.u.atoms[100:110]
u2 = MDAnalysis.Merge(ag1, ag2)
assert_(len(u2.atoms) == 30)
assert_(len(u2.atoms.bonds) == 28)
assert_(len(u2.atoms.angles) == 47)
assert_(len(u2.atoms.dihedrals) == 53)
assert_(len(u2.atoms.impropers) == 1)
# All these bonds are in the merged Universe
assert_(len(ag1[0].bonds) == len(u2.atoms[0].bonds))
# One of these bonds isn't in the merged Universe
assert_(len(ag2[0].bonds) -1 == len(u2.atoms[20].bonds))
def test_merge_with_topology_from_different_universes(self):
u3 = MDAnalysis.Merge(self.u.atoms[:110], self.u2.atoms)
# merge_protein doesn't contain bond topology, so merged universe
# shouldn't have one either
print(u3.atoms.bonds)
# PDB reader yields empty Bonds group, which means bonds from
# PSF/DCD survive the merge
#assert_(not hasattr(u3.atoms, 'bonds') or len(u3.atoms.bonds) == 0)
assert_(not hasattr(u3.atoms, 'angles') or len(u3.atoms.bonds) == 0)
assert_(not hasattr(u3.atoms, 'dihedrals') or len(u3.atoms.bonds) == 0)
assert_(not hasattr(u3.atoms, 'impropers') or len(u3.atoms.bonds) == 0)
def test_merge_without_topology(self):
# This shouldn't have topology as we merged single atoms
u2 = MDAnalysis.Merge(self.u.atoms[0:1], self.u.atoms[10:11])
assert_(len(u2.atoms) == 2)
assert_(len(u2.atoms.bonds) == 0)
assert_(len(u2.atoms.angles) == 0)
assert_(len(u2.atoms.dihedrals) == 0)
assert_(len(u2.atoms.impropers) == 0)
class _SelectionWriter(TestCase):
filename = None
max_number = 357 # to keep fixtures smallish, only select CAs up to number 357
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.universe = MDAnalysis.Universe(PSF, DCD)
stream = StringIO()
self.namedfile = NamedStream(stream, self.filename)
def tearDown(self):
del self.universe
del self.namedfile
def _selection(self):
return self.universe.select_atoms(
"protein and name CA and bynum 1-{0}".format(self.max_number))
def _write(self, **kwargs):
g = self._selection()
g.write(self.namedfile, **kwargs)
return g
def _write_selection(self, **kwargs):
g = self._selection()
g.write(self.namedfile, **kwargs)
return g
def _write_with(self, **kwargs):
g = self._selection()
with self.writer(self.namedfile, **kwargs) as outfile:
outfile.write(g)
return g
def test_write_bad_mode(self):
with self.assertRaises(ValueError):
self._write(name=self.ref_name, mode='a+')
def test_write(self):
self._write(name=self.ref_name)
self._assert_selectionstring()
def test_writeselection(self):
self._write_selection(name=self.ref_name)
self._assert_selectionstring()
def test_write_with(self):
self._write_with(name=self.ref_name)
self._assert_selectionstring()
class TestAnalysisBase(object):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
# has 98 frames
self.u = mda.Universe(PSF, DCD)
def tearDown(self):
del self.u
def test_default(self):
an = FrameAnalysis(self.u.trajectory).run()
assert_equal(an.n_frames, len(self.u.trajectory))
assert_equal(an.frames, list(range(len(self.u.trajectory))))
def test_start(self):
an = FrameAnalysis(self.u.trajectory, start=20).run()
assert_equal(an.n_frames, len(self.u.trajectory) - 20)
assert_equal(an.frames, list(range(20, len(self.u.trajectory))))
def test_stop(self):
an = FrameAnalysis(self.u.trajectory, stop=20).run()
assert_equal(an.n_frames, 20)
assert_equal(an.frames, list(range(20)))
def test_step(self):
an = FrameAnalysis(self.u.trajectory, step=20).run()
assert_equal(an.n_frames, 5)
assert_equal(an.frames, list(range(98))[::20])
def test_verbose(self):
a = FrameAnalysis(self.u.trajectory, verbose=True)
assert_(a._verbose)
assert_(not a._quiet)
@raises(NotImplementedError)
def test_incomplete_defined_analysis(self):
IncompleteAnalysis(self.u.trajectory).run()
def test_old_api(self):
OldAPIAnalysis(self.u.trajectory).run()
def test_start_stop_step_conversion(self):
an = FrameAnalysis(self.u.trajectory)
assert_equal(an.start, 0)
assert_equal(an.stop, self.u.trajectory.n_frames)
assert_equal(an.step, 1)
class TestPSAnalysis(TestCase):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.tmpdir = tempdir.TempDir()
self.iu1 = np.triu_indices(3, k=1)
self.universe1 = MDAnalysis.Universe(PSF, DCD)
self.universe2 = MDAnalysis.Universe(PSF, DCD2)
self.universe_rev = MDAnalysis.Universe(PSF, DCD)
self.universes = [self.universe1, self.universe2, self.universe_rev]
self.psa = MDAnalysis.analysis.psa.PSAnalysis(self.universes, \
path_select='name CA', \
targetdir=self.tmpdir.name)
self.psa.generate_paths(align=True)
self.psa.paths[-1] = self.psa.paths[-1][::
-1, :, :] # reverse third path
self._run()
def _run(self):
self.psa.run(metric='hausdorff')
self.hausd_matrix = self.psa.get_pairwise_distances()
self.psa.run(metric='discrete_frechet')
self.frech_matrix = self.psa.get_pairwise_distances()
self.hausd_dists = self.hausd_matrix[self.iu1]
self.frech_dists = self.frech_matrix[self.iu1]
def tearDown(self):
del self.universe1
del self.universe2
del self.universe_rev
del self.psa
del self.tmpdir
def test_hausdorff_bound(self):
err_msg = "Some Frechet distances are smaller than corresponding " \
+ "Hausdorff distances"
assert_array_less(self.hausd_dists, self.frech_dists, err_msg)
def test_reversal_hausdorff(self):
err_msg = "Hausdorff distances changed after path reversal"
assert_array_almost_equal(self.hausd_matrix[1,2], \
self.hausd_matrix[0,1], \
decimal=3, err_msg=err_msg)
def test_reversal_frechet(self):
err_msg = "Frechet distances did not increase after path reversal"
assert_(self.frech_matrix[1, 2] >= self.frech_matrix[0, 1], err_msg)
class MemoryReference(BaseReference):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def __init__(self):
super(MemoryReference, self).__init__()
self.topology = PSF
self.trajectory = DCD
self.universe = mda.Universe(PSF, DCD)
self.n_atoms = self.universe.trajectory.n_atoms
self.n_frames = self.universe.trajectory.n_frames
self.dt = self.universe.trajectory.ts.dt
self.dimensions = self.universe.trajectory.ts.dimensions
self.totaltime = self.universe.trajectory.totaltime
self.volume = self.universe.trajectory.ts.volume
self.first_frame = Timestep(self.n_atoms)
self.first_frame.positions = np.array(self.universe.trajectory[0])
self.first_frame.frame = 0
self.first_frame.time = self.first_frame.frame * self.dt
self.second_frame = Timestep(self.n_atoms)
self.second_frame.positions = np.array(self.universe.trajectory[1])
self.second_frame.frame = 1
self.second_frame.time = self.second_frame.frame * self.dt
self.last_frame = Timestep(self.n_atoms)
self.last_frame.positions = \
np.array(self.universe.trajectory[self.n_frames - 1])
self.last_frame.frame = self.n_frames - 1
self.last_frame.time = self.last_frame.frame * self.dt
self.jump_to_frame = self.first_frame.copy()
self.jump_to_frame.positions = np.array(self.universe.trajectory[3])
self.jump_to_frame.frame = 3
self.jump_to_frame.time = self.jump_to_frame.frame * self.dt
def reader(self, trajectory):
return mda.Universe(self.topology, trajectory,
in_memory=True).trajectory
def iter_ts(self, i):
ts = self.universe.trajectory[i]
return ts
class TestContactAnalysis1(TestCase):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.universe = MDAnalysis.Universe(PSF, DCD)
self.trajectory = self.universe.trajectory
def tearDown(self):
del self.universe
del self.trajectory
def _run_ContactAnalysis1(self, **runkwargs):
sel_basic = "(resname ARG or resname LYS) and (name NH* or name NZ)"
sel_acidic = "(resname ASP or resname GLU) and (name OE* or name OD*)"
acidic = self.universe.select_atoms(sel_acidic)
basic = self.universe.select_atoms(sel_basic)
outfile = 'qsalt.dat'
CA1 = MDAnalysis.analysis.contacts.ContactAnalysis1(
self.universe,
selection=(sel_acidic, sel_basic), refgroup=(acidic, basic),
radius=6.0, outfile=outfile)
kwargs = runkwargs.copy()
kwargs['force'] = True
CA1.run(**kwargs)
return CA1
def test_startframe(self):
"""test_startframe: TestContactAnalysis1: start frame set to 0 (resolution of Issue #624)"""
with tempdir.in_tempdir():
CA1 = self._run_ContactAnalysis1()
self.assertEqual(CA1.timeseries.shape[1], self.universe.trajectory.n_frames)
def test_end_zero(self):
"""test_end_zero: TestContactAnalysis1: stop frame 0 is not ignored"""
with tempdir.in_tempdir():
CA1 = self._run_ContactAnalysis1(stop=0)
self.assertEqual(len(CA1.timeseries), 0)
def test_slicing(self):
start, stop, step = 10, 30, 5
with tempdir.in_tempdir():
CA1 = self._run_ContactAnalysis1(start=start, stop=stop, step=step)
frames = np.arange(self.universe.trajectory.n_frames)[start:stop:step]
self.assertEqual(CA1.timeseries.shape[1], len(frames))
class TestBondedSelection(object):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.u = mda.Universe(PSF, DCD)
def tearDown(self):
del self.u
def test_bonded_1(self):
ag = self.u.select_atoms('type 2 and bonded name N')
assert_(len(ag) == 3)
def test_nobonds_warns(self):
self.u.bonds = TopologyGroup([])
assert_warns(UserWarning, self.u.select_atoms,
'type 2 and bonded name N')
class TestChainReaderFormats(TestCase):
"""Test of ChainReader with explicit formats (Issue 76)."""
@attr('issue')
def test_set_all_format_tuples(self):
universe = mda.Universe(GRO, [(PDB, 'pdb'), (XTC, 'xtc'),
(TRR, 'trr')])
assert_equal(universe.trajectory.n_frames, 21)
@attr('issue')
@dec.skipif(parser_not_found('DCD'),
'DCD parset not available. Are you using python 3?')
def test_set_one_format_tuple(self):
universe = mda.Universe(PSF, [(PDB_small, 'pdb'), DCD])
assert_equal(universe.trajectory.n_frames, 99)
@attr('issue')
def test_set_all_formats(self):
universe = mda.Universe(PSF, [PDB_small, PDB_closed], format='pdb')
assert_equal(universe.trajectory.n_frames, 2)
class TestChainReaderCommonDt(TestCase):
@dec.skipif(parser_not_found('DCD'),
'DCD parset not available. Are you using python 3?')
def setUp(self):
self.common_dt = 100.0
self.universe = mda.Universe(PSF,
[DCD, CRD, DCD, CRD, DCD, CRD, CRD],
dt=self.common_dt)
self.trajectory = self.universe.trajectory
self.prec = 3
def test_time(self):
# We test this for the beginning, middle and end of the trajectory.
for frame_n in (0, self.trajectory.n_frames // 2, -1):
self.trajectory[frame_n]
assert_almost_equal(self.trajectory.time,
self.trajectory.frame*self.common_dt,
5,
err_msg="Wrong time for frame {0:d}".format(frame_n) )
class TestBaseTimestep(BaseTimestepTest):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def test_other_timestep(self):
# use a subclass to base.Timestep to check it works
ts1 = mda.coordinates.base.Timestep(10)
ts1.positions = self._get_pos()
# can't do TRR Timestep here as it always has vels and forces
# so isn't actually equal to a position only timestep
for otherTS in [mda.coordinates.DCD.Timestep,
mda.coordinates.TRJ.Timestep,
mda.coordinates.DMS.Timestep,
mda.coordinates.GRO.Timestep,
mda.coordinates.TRZ.Timestep,
]:
ts2 = otherTS(10)
ts2.positions = self._get_pos()
yield (self._check_ts_equal, ts1, ts2,
"Failed on {0}".format(otherTS))
class TestResidue(object):
# Legacy tests from before 363
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.universe = mda.Universe(PSF, DCD)
self.res = self.universe.residues[100]
def test_type(self):
assert_(isinstance(self.res, mda.core.groups.Residue))
assert_equal(self.res.resname, "ILE")
assert_equal(self.res.resid, 101)
def test_index(self):
atom = self.res.atoms[2]
assert_(isinstance(atom, mda.core.groups.Atom))
assert_equal(atom.name, "CA")
assert_equal(atom.index, 1522)
assert_equal(atom.resid, 101)
def test_atom_order(self):
assert_equal(self.res.atoms.indices, sorted(self.res.atoms.indices))
class TestMergeTopology(object):
"""Test that Merge correct does topology"""
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.u = MDAnalysis.Universe(PSF, DCD)
def tearDown(self):
del self.u
def test_merge_with_topology(self):
ag1 = self.u.atoms[:20]
ag2 = self.u.atoms[100:110]
u2 = MDAnalysis.Merge(ag1, ag2)
assert_(len(u2.atoms) == 30)
assert_(len(u2.bonds) == 28)
assert_(len(u2.angles) == 47)
assert_(len(u2.dihedrals) == 53)
assert_(len(u2.impropers) == 1)
# All these bonds are in the merged Universe
assert_(len(ag1[0].bonds) == len(u2.atoms[0].bonds))
# One of these bonds isn't in the merged Universe
assert_(len(ag2[0].bonds) -1 == len(u2.atoms[20].bonds))
def test_merge_without_topology(self):
# This shouldn't have topology as we merged single atoms
ag1 = AtomGroup([self.u.atoms[1]])
ag2 = AtomGroup([self.u.atoms[10]])
u2 = MDAnalysis.Merge(ag1, ag2)
assert_(len(u2.atoms) == 2)
assert_(len(u2.bonds) == 0)
assert_(len(u2.angles) == 0)
assert_(len(u2.dihedrals) == 0)
assert_(len(u2.impropers) == 0)
class TestBondedSelection(object):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.u = mda.Universe(PSF, DCD)
def tearDown(self):
del self.u
def test_bonded_1(self):
ag = self.u.select_atoms('type 2 and bonded name N')
assert_(len(ag) == 3)
@staticmethod
def test_nobonds_warns():
u = make_Universe(('names', ))
# empty bond topology attr
batt = mda.core.topologyattrs.Bonds([])
u.add_TopologyAttr(batt)
assert_warns(UserWarning, u.select_atoms, 'bonded name AAA')
class TestAnalysisBase(object):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
# has 98 frames
self.u = mda.Universe(PSF, DCD)
def tearDown(self):
del self.u
def test_default(self):
an = FrameAnalysis(self.u.trajectory)
assert_(an.nframes == len(self.u.trajectory))
an.run()
assert_(an.frames == list(range(len(self.u.trajectory))))
def test_start(self):
an = FrameAnalysis(self.u.trajectory, start=20)
assert_(an.nframes == len(self.u.trajectory) - 20)
an.run()
assert_(an.frames == list(range(20, len(self.u.trajectory))))
def test_stop(self):
an = FrameAnalysis(self.u.trajectory, stop=20)
assert_(an.nframes == 20)
an.run()
assert_(an.frames == list(range(20)))
def test_step(self):
an = FrameAnalysis(self.u.trajectory, step=20)
assert_(an.nframes == 5)
an.run()
assert_(an.frames == list(range(98))[::20])
class TestWrap(object):
@dec.skipif(parser_not_found('TRZ'),
'TRZ parser not available. Are you using python 3?')
def setUp(self):
self.u = mda.Universe(TRZ_psf, TRZ)
self.ag = self.u.atoms[:100]
def tearDown(self):
del self.u
del self.ag
def test_wrap_comp_fail(self):
assert_raises(ValueError, self.ag.wrap, compound='strawberries')
def test_wrap_cent_fail(self):
assert_raises(ValueError,
self.ag.wrap,
compound='residues',
center='avacado')
def test_wrap_box_fail(self):
assert_raises(ValueError, self.ag.wrap, box=np.array([0, 1]))
def _in_box(self, coords):
"""Check that a set of coordinates are 0.0 <= r <= box"""
box = self.u.dimensions[:3]
return (coords >= 0.0).all() and (coords <= box).all()
def test_wrap_atoms(self):
ag = self.u.atoms[100:200]
ag.wrap(compound='atoms')
assert_equal(self._in_box(ag.positions), True)
def test_wrap_group(self):
ag = self.u.atoms[:100]
ag.wrap(compound='group')
cen = ag.center_of_mass()
assert_equal(self._in_box(cen), True)
def test_wrap_residues(self):
ag = self.u.atoms[300:400]
ag.wrap(compound='residues')
cen = np.vstack([r.atoms.center_of_mass() for r in ag.residues])
assert_equal(self._in_box(cen), True)
def test_wrap_segments(self):
ag = self.u.atoms[1000:1200]
ag.wrap(compound='segments')
cen = np.vstack([s.atoms.center_of_mass() for s in ag.segments])
assert_equal(self._in_box(cen), True)
def test_wrap_fragments(self):
ag = self.u.atoms[:250]
ag.wrap(compound='fragments')
cen = np.vstack([f.center_of_mass() for f in ag.fragments])
assert_equal(self._in_box(cen), True)
def test_contact_matrix():
d = np.arange(5)
radius = np.ones(5) * 2.5
out = contacts.contact_matrix(d, radius)
assert_array_equal(out, [True, True, True, False, False])
# check in-place update
out = np.empty(out.shape)
contacts.contact_matrix(d, radius, out=out)
assert_array_equal(out, [True, True, True, False, False])
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def test_new_selection():
u = mda.Universe(PSF, DCD)
selections = ('all', )
sel = contacts._new_selections(u, selections, -1)[0]
u.trajectory[-1]
assert_array_equal(sel.positions, u.atoms.positions)
def soft_cut(ref, u, selA, selB, radius=4.5, beta=5.0, lambda_constant=1.8):
"""
Reference implementation for testing
"""
# reference groups A and B from selection strings
refA, refB = ref.select_atoms(selA), ref.select_atoms(selB)
class TestSelectionsCHARMM(object):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
"""Set up the standard AdK system in implicit solvent.
Geometry here is orthogonal
"""
self.universe = MDAnalysis.Universe(PSF, DCD)
def tearDown(self):
self.universe.trajectory.close()
del self.universe
def test_segid(self):
sel = self.universe.select_atoms('segid 4AKE')
assert_equal(sel.n_atoms, 3341, "failed to select segment 4AKE")
assert_array_equal(
sorted(sel.indices), sorted(self.universe.s4AKE.atoms.indices),
"selected segment 4AKE is not the same as auto-generated segment s4AKE"
)
def test_protein(self):
sel = self.universe.select_atoms('protein')
assert_equal(sel.n_atoms, 3341, "failed to select protein")
assert_array_equal(
sorted(sel.indices), sorted(self.universe.s4AKE.atoms.indices),
"selected protein is not the same as auto-generated protein segment s4AKE"
)
def test_backbone(self):
sel = self.universe.select_atoms('backbone')
assert_equal(sel.n_atoms, 855)
def test_resid_single(self):
sel = self.universe.select_atoms('resid 100')
assert_equal(sel.n_atoms, 7)
assert_equal(sel.residues.resnames, ['GLY'])
def test_resid_range(self):
sel = self.universe.select_atoms('resid 100:105')
assert_equal(sel.n_atoms, 89)
assert_equal(sel.residues.resnames,
['GLY', 'ILE', 'ASN', 'VAL', 'ASP', 'TYR'])
def test_selgroup(self):
sel = self.universe.select_atoms('not resid 100')
sel2 = self.universe.select_atoms('not group notr100', notr100=sel)
assert_equal(sel2.n_atoms, 7)
assert_equal(sel2.residues.resnames, ['GLY'])
def test_fullselgroup(self):
sel1 = self.universe.select_atoms('resid 101')
sel2 = self.universe.select_atoms('resid 100')
sel3 = sel1.select_atoms('fullgroup r100', r100=sel2)
assert_equal(sel2.n_atoms, 7)
assert_equal(sel2.residues.resnames, ['GLY'])
# resnum selections are boring here because we haven't really a mechanism yet
# to assign the canonical PDB resnums
def test_resnum_single(self):
sel = self.universe.select_atoms('resnum 100')
assert_equal(sel.n_atoms, 7)
assert_equal(sel.residues.resids, [100])
assert_equal(sel.residues.resnames, ['GLY'])
def test_resnum_range(self):
sel = self.universe.select_atoms('resnum 100:105')
assert_equal(sel.n_atoms, 89)
assert_equal(sel.residues.resids, range(100, 106))
assert_equal(sel.residues.resnames,
['GLY', 'ILE', 'ASN', 'VAL', 'ASP', 'TYR'])
def test_resname(self):
sel = self.universe.select_atoms('resname LEU')
assert_equal(sel.n_atoms, 304,
"Failed to find all 'resname LEU' atoms.")
assert_equal(sel.n_residues, 16,
"Failed to find all 'resname LEU' residues.")
assert_array_equal(
sorted(sel.indices), sorted(self.universe.s4AKE.LEU.atoms.indices),
"selected 'resname LEU' atoms are not the same as auto-generated s4AKE.LEU"
)
def test_name(self):
sel = self.universe.select_atoms('name CA')
assert_equal(sel.n_atoms, 214)
def test_atom(self):
sel = self.universe.select_atoms('atom 4AKE 100 CA')
assert_equal(len(sel), 1)
assert_equal(sel.resnames, ['GLY'])
assert_array_almost_equal(
sel.positions,
np.array([[20.38685226, -3.44224262, -5.92158318]],
dtype=np.float32))
def test_atom_empty(self):
sel = self.universe.select_atoms('atom 4AKE 100 XX') # Does not exist
assert_equal(len(sel), 0)
def test_type(self):
sel = self.universe.select_atoms("type 1")
assert_equal(len(sel), 253)
def test_and(self):
sel = self.universe.select_atoms('resname GLY and resid 100')
assert_equal(len(sel), 7)
def test_or(self):
sel = self.universe.select_atoms('resname LYS or resname ARG')
assert_equal(sel.n_residues, 31)
def test_not(self):
sel = self.universe.select_atoms('not backbone')
assert_equal(len(sel), 2486)
def test_around(self):
sel = self.universe.select_atoms('around 4.0 bynum 1943')
assert_equal(len(sel), 32)
def test_sphlayer(self):
sel = self.universe.select_atoms('sphlayer 4.0 6.0 bynum 1281')
assert_equal(len(sel), 66)
def test_sphzone(self):
sel = self.universe.select_atoms('sphzone 6.0 bynum 1281')
assert_equal(len(sel), 86)
def test_cylayer(self):
sel = self.universe.select_atoms('cylayer 4.0 6.0 10 -10 bynum 1281')
assert_equal(len(sel), 88)
def test_cyzone(self):
sel = self.universe.select_atoms('cyzone 6.0 10 -10 bynum 1281')
assert_equal(len(sel), 166)
def test_point(self):
ag = self.universe.select_atoms('point 5.0 5.0 5.0 3.5')
d = distance_array(np.array([[5.0, 5.0, 5.0]], dtype=np.float32),
self.universe.atoms.positions,
box=self.universe.dimensions)
idx = np.where(d < 3.5)[1]
assert_equal(set(ag.indices), set(idx))
def test_prop(self):
sel = self.universe.select_atoms('prop y <= 16')
sel2 = self.universe.select_atoms('prop abs z < 8')
assert_equal(len(sel), 3194)
assert_equal(len(sel2), 2001)
def test_bynum(self):
"Tests the bynum selection, also from AtomGroup instances (Issue 275)"
sel = self.universe.select_atoms('bynum 5')
assert_equal(sel[0].index, 4)
sel = self.universe.select_atoms('bynum 1:10')
assert_equal(len(sel), 10)
assert_equal(sel[0].index, 0)
assert_equal(sel[-1].index, 9)
subsel = sel.select_atoms('bynum 5')
assert_equal(subsel[0].index, 4)
subsel = sel.select_atoms('bynum 2:5')
assert_equal(len(subsel), 4)
assert_equal(subsel[0].index, 1)
assert_equal(subsel[-1].index, 4)
def test_byres(self):
sel = self.universe.select_atoms('byres bynum 0:5')
assert_equal(len(sel), len(self.universe.residues[0].atoms))
def test_same_resname(self):
"""Test the 'same ... as' construct (Issue 217)"""
sel = self.universe.select_atoms(
"same resname as resid 10 or resid 11")
assert_equal(len(sel), 331,
("Found a wrong number of atoms with same resname as "
"resids 10 or 11"))
target_resids = np.array([
7, 8, 10, 11, 12, 14, 17, 25, 32, 37, 38, 42, 46, 49, 55, 56, 66,
73, 80, 85, 93, 95, 99, 100, 122, 127, 130, 144, 150, 176, 180,
186, 188, 189, 194, 198, 203, 207, 214
])
assert_array_equal(sel.residues.resids, target_resids,
("Found wrong residues with same resname as "
"resids 10 or 11"))
def test_same_segment(self):
"""Test the 'same ... as' construct (Issue 217)"""
SNew_A = self.universe.add_Segment(segid='A')
SNew_B = self.universe.add_Segment(segid='B')
SNew_C = self.universe.add_Segment(segid='C')
self.universe.residues[:100].segments = SNew_A
self.universe.residues[100:150].segments = SNew_B
self.universe.residues[150:].segments = SNew_C
target_resids = np.arange(100) + 1
sel = self.universe.select_atoms("same segment as resid 10")
assert_equal(
len(sel), 1520,
"Found a wrong number of atoms in the same segment of resid 10")
assert_array_equal(
sel.residues.resids, target_resids,
"Found wrong residues in the same segment of resid 10")
target_resids = np.arange(100, 150) + 1
sel = self.universe.select_atoms("same segment as resid 110")
assert_equal(
len(sel), 797,
"Found a wrong number of atoms in the same segment of resid 110")
assert_array_equal(
sel.residues.resids, target_resids,
"Found wrong residues in the same segment of resid 110")
target_resids = np.arange(150, self.universe.atoms.n_residues) + 1
sel = self.universe.select_atoms("same segment as resid 160")
assert_equal(
len(sel), 1024,
"Found a wrong number of atoms in the same segment of resid 160")
assert_array_equal(
sel.residues.resids, target_resids,
"Found wrong residues in the same segment of resid 160")
def test_empty_same(self):
ag = self.universe.select_atoms('resname MET')
# No GLY, so 'as resname GLY' is empty
ag2 = ag.select_atoms('same mass as resname GLY')
assert_(len(ag2) == 0)
def test_empty_selection(self):
"""Test that empty selection can be processed (see Issue 12)"""
# no Trp in AdK
assert_equal(len(self.universe.select_atoms('resname TRP')), 0)
def test_parenthesized_expression(self):
sel = self.universe.select_atoms(
'( name CA or name CB ) and resname LEU')
assert_equal(len(sel), 32)
def test_no_space_around_parentheses(self):
"""Test that no space is needed around parentheses (Issue 43)."""
# note: will currently be ERROR because it throws a ParseError
sel = self.universe.select_atoms(
'(name CA or name CB) and resname LEU')
assert_equal(len(sel), 32)
# TODO:
# test for checking ordering and multiple comma-separated selections
def test_concatenated_selection(self):
E151 = self.universe.s4AKE.atoms.select_atoms('resid 151')
# note that this is not quite phi... HN should be C of prec. residue
phi151 = E151.atoms.select_atoms('name HN', 'name N', 'name CA',
'name CB')
assert_equal(len(phi151), 4)
assert_equal(phi151[0].name, 'HN',
"wrong ordering in selection, should be HN-N-CA-CB")
def test_global(self):
"""Test the `global` modifier keyword (Issue 268)"""
ag = self.universe.select_atoms("resname LYS and name NZ")
# Lys amines within 4 angstrom of the backbone.
ag1 = self.universe.select_atoms(
"resname LYS and name NZ and around 4 backbone")
ag2 = ag.select_atoms("around 4 global backbone")
assert_array_equal(ag2.indices, ag1.indices)
class TestAtomGroup(object):
"""Tests of AtomGroup; selections are tested separately.
These are from before the big topology rework (aka #363) but are still valid.
There is likely lots of duplication between here and other tests.
"""
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
"""Set up the standard AdK system in implicit solvent."""
self.universe = mda.Universe(PSF, DCD)
self.ag = self.universe.atoms # prototypical AtomGroup
self.dih_prec = 2
def test_getitem_int(self):
assert_equal(self.universe.atoms[0].ix, self.universe.atoms.ix[0])
def test_getitem_slice(self):
assert_array_equal(self.universe.atoms[0:4].ix,
self.universe.atoms.ix[:4])
def test_getitem_slice2(self):
assert_equal(self.universe.atoms[0:8:2].ix,
self.universe.atoms.ix[0:8:2])
def test_getitem_str(self):
ag1 = self.universe.atoms['HT1']
# select_atoms always returns an AtomGroup even if single result
ag2 = self.universe.select_atoms('name HT1')[0]
assert_equal(ag1, ag2)
def test_getitem_IE(self):
d = {'A': 1}
assert_raises(IndexError, self.universe.atoms.__getitem__, d)
def test_bad_make(self):
assert_raises(TypeError, mda.core.groups.AtomGroup,
['these', 'are', 'not', 'atoms'])
def test_n_atoms(self):
assert_equal(self.ag.n_atoms, 3341)
def test_n_residues(self):
assert_equal(self.ag.n_residues, 214)
def test_n_segments(self):
assert_equal(self.ag.n_segments, 1)
def test_resids_dim(self):
assert_equal(len(self.ag.resids), len(self.ag))
def test_resnums_dim(self):
assert_equal(len(self.ag.resnums), len(self.ag))
def test_segids_dim(self):
assert_equal(len(self.ag.segids), len(self.ag))
def test_len(self):
"""testing that len(atomgroup) == atomgroup.n_atoms"""
assert_equal(len(self.ag), self.ag.n_atoms, "len and n_atoms disagree")
def test_center_of_geometry(self):
assert_array_almost_equal(
self.ag.center_of_geometry(),
np.array([-0.04223963, 0.0141824, -0.03505163], dtype=np.float32))
def test_center_of_mass(self):
assert_array_almost_equal(
self.ag.center_of_mass(),
np.array([-0.01094035, 0.05727601, -0.12885778]))
def test_coordinates(self):
assert_array_almost_equal(
self.ag.positions[1000:2000:200],
np.array([[3.94543672, -12.4060812, -7.26820087],
[13.21632767, 5.879035, -14.67914867],
[12.07735443, -9.00604534, 4.09301519],
[11.35541916, 7.0690732, -0.32511973],
[-13.26763439, 4.90658951, 10.6880455]],
dtype=np.float32))
def test_principal_axes(self):
assert_array_almost_equal(
self.ag.principal_axes(),
np.array([
[1.53389276e-03, 4.41386224e-02, 9.99024239e-01],
[1.20986911e-02, 9.98951474e-01, -4.41539838e-02],
[-9.99925632e-01, 1.21546132e-02, 9.98264877e-04],
]))
def test_total_charge(self):
assert_almost_equal(self.ag.total_charge(), -4.0, decimal=4)
def test_total_mass(self):
assert_almost_equal(self.ag.total_mass(), 23582.043)
def test_indices_ndarray(self):
assert_equal(isinstance(self.ag.indices, np.ndarray), True)
def test_indices(self):
assert_array_equal(self.ag.indices[:5], np.array([0, 1, 2, 3, 4]))
def test_resids_ndarray(self):
assert_equal(isinstance(self.ag.resids, np.ndarray), True)
def test_resids(self):
assert_array_equal(self.ag.residues.resids, np.arange(1, 215))
def test_resnums_ndarray(self):
assert_equal(isinstance(self.ag.residues.resnums, np.ndarray), True)
def test_resnums(self):
assert_array_equal(self.ag.residues.resnums, np.arange(1, 215))
def test_resnames_ndarray(self):
assert_equal(isinstance(self.ag.residues.resnames, np.ndarray), True)
def test_resnames(self):
resnames = self.ag.residues.resnames
assert_array_equal(resnames[0:3], np.array(["MET", "ARG", "ILE"]))
def test_names_ndarray(self):
assert_equal(isinstance(self.ag.names, np.ndarray), True)
def test_names(self):
names = self.ag.names
assert_array_equal(names[0:3], np.array(["N", "HT1", "HT2"]))
def test_segids_ndarray(self):
assert_equal(isinstance(self.ag.segids, np.ndarray), True)
def test_segids(self):
segids = self.ag.segids
assert_array_equal(segids[0], np.array(["4AKE"]))
def test_masses_ndarray(self):
assert_equal(isinstance(self.ag.masses, np.ndarray), True)
def test_masses(self):
masses = self.ag.masses
assert_array_equal(masses[0:3], np.array([14.007, 1.008, 1.008]))
def test_charges_ndarray(self):
assert_equal(isinstance(self.ag.charges, np.ndarray), True)
def test_charges(self):
assert_array_almost_equal(self.ag.charges[1000:2000:200],
np.array([-0.09, 0.09, -0.47, 0.51, 0.09]))
def test_bad_add_AG(self):
def bad_add():
return self.ag + [1, 2, 3]
assert_raises(TypeError, bad_add)
def test_bool_false(self):
# Issue #304
ag = self.universe.atoms[[]]
assert_equal(bool(ag), False)
def test_bool_true(self):
# Issue #304
ag = self.universe.atoms[:3]
assert_equal(bool(ag), True)
def test_repr(self):
# Should make sure that the user facing info stays as expected
assert_equal(repr(self.ag), "<AtomGroup with 3341 atoms>")
def test_set_resnum_single(self):
ag = self.universe.atoms[:3]
ag.residues.resnums = 5
for at in ag:
assert_equal(at.resnum, 5)
assert_equal(all(ag.resnums == 5), True)
def test_set_resname_single(self):
ag = self.universe.atoms[:3]
new = 'abc'
ag.residues.resnames = new
for at in ag:
assert_equal(at.resname, new)
assert_equal(all(ag.resnames == new), True)
def test_packintobox_badshape(self):
ag = self.universe.atoms[:10]
box = np.zeros(9, dtype=np.float32).reshape(3, 3)
assert_raises(ValueError, ag.pack_into_box, box=box)
def test_packintobox_noshape(self):
ag = self.universe.atoms[:10]
assert_raises(ValueError, ag.pack_into_box)
def test_packintobox(self):
"""test AtomGroup.pack_into_box(): Tests application of periodic boundary
conditions on coordinates
Reference system doesn't have dimensions, so an arbitrary box is
imposed on the system
"""
u = self.universe
u.trajectory.rewind() # just to make sure...
ag = u.atoms[1000:2000:200]
# Provide arbitrary box
ag.pack_into_box(box=np.array([5., 5., 5.], dtype=np.float32))
assert_array_almost_equal(
ag.positions,
np.array([[3.94543672, 2.5939188, 2.73179913],
[3.21632767, 0.879035, 0.32085133],
[2.07735443, 0.99395466, 4.09301519],
[1.35541916, 2.0690732, 4.67488003],
[1.73236561, 4.90658951, 0.6880455]],
dtype=np.float32))
def test_residues(self):
u = self.universe
assert_equal(
u.residues[100].atoms.ix,
u.select_atoms('resname ILE and resid 101').atoms.ix,
"Direct selection from residue group does not match "
"expected I101.")
def test_segments(self):
u = self.universe
assert_equal(len(u.segments.s4AKE.atoms),
len(u.select_atoms('segid 4AKE').atoms),
"Direct selection of segment 4AKE from segments failed.")
def test_index_integer(self):
u = self.universe
a = u.atoms[100]
assert_(isinstance(a, mda.core.groups.Atom),
"integer index did not return Atom")
def test_index_slice(self):
u = self.universe
a = u.atoms[100:200:10]
assert_(isinstance(a, mda.core.groups.AtomGroup),
"slice index did not return AtomGroup")
def test_index_slice_empty(self):
u = self.universe
assert_array_equal(u.atoms[0:0], [],
"making an empty AtomGroup failed")
def test_index_advancedslice(self):
u = self.universe
aslice = [0, 10, 20, -1, 10]
ag = u.atoms[aslice]
assert_(isinstance(ag, mda.core.groups.AtomGroup),
"advanced slicing does not produce a AtomGroup")
assert_equal(ag[1], ag[-1], "advanced slicing does not preserve order")
def test_boolean_indexing(self):
# index an array with a sequence of bools
# issue #282
sel = np.array([True, False, True])
ag = self.universe.atoms[10:13]
ag2 = ag[sel]
assert_equal(len(ag2), 2)
for at in [ag[0], ag[2]]:
assert_equal(at in ag2, True)
def test_boolean_indexing_2(self):
# index an array with a sequence of bools
# issue #282
sel = [True, False, True]
ag = self.universe.atoms[10:13]
ag2 = ag[sel]
assert_equal(len(ag2), 2)
for at in [ag[0], ag[2]]:
assert_equal(at in ag2, True)
def test_bool_IE(self):
# indexing with empty list doesn't run foul of bool check
sel = []
ag = self.universe.atoms[10:30]
ag2 = ag[sel]
assert_equal(len(ag2), 0)
def test_dihedral_ValueError(self):
"""test that AtomGroup.dihedral() raises ValueError if not exactly
4 atoms given"""
nodih = self.universe.select_atoms("resid 3:10")
assert_raises(ValueError, getattr, nodih, 'dihedral')
nodih = self.universe.select_atoms("resid 3:5")
assert_raises(ValueError, getattr, nodih, 'dihedral')
def test_improper(self):
u = self.universe
u.trajectory.rewind() # just to make sure...
peptbond = u.select_atoms("atom 4AKE 20 C", "atom 4AKE 21 CA",
"atom 4AKE 21 N", "atom 4AKE 21 HN")
assert_almost_equal(
peptbond.improper.value(), 168.52952575683594, self.dih_prec,
"Peptide bond improper dihedral for M21 "
"calculated wrongly.")
def test_dihedral_equals_improper(self):
u = self.universe
u.trajectory.rewind() # just to make sure...
peptbond = u.select_atoms("atom 4AKE 20 C", "atom 4AKE 21 CA",
"atom 4AKE 21 N", "atom 4AKE 21 HN")
assert_equal(
peptbond.improper.value(), peptbond.dihedral.value(),
"improper() and proper dihedral() give different results")
def test_bond(self):
self.universe.trajectory.rewind() # just to make sure...
sel2 = self.universe.s4AKE.r98.atoms.select_atoms(
"name OE1", "name OE2")
assert_almost_equal(sel2.bond.value(), 2.1210737228393555, 3,
"distance of Glu98 OE1--OE2 wrong")
def test_bond_pbc(self):
self.universe.trajectory.rewind()
sel2 = self.universe.s4AKE.r98.atoms.select_atoms(
"name OE1", "name OE2")
assert_almost_equal(sel2.bond.value(pbc=True), 2.1210737228393555, 3,
"distance of Glu98 OE1--OE2 wrong")
def test_bond_ValueError(self):
ag = self.universe.atoms[:4]
assert_raises(ValueError, getattr, ag, 'bond')
def test_angle(self):
self.universe.trajectory.rewind() # just to make sure...
sel3 = self.universe.s4AKE.r98.atoms.select_atoms(
"name OE1", "name CD", "name OE2")
assert_almost_equal(sel3.angle.value(), 117.46187591552734, 3,
"angle of Glu98 OE1-CD-OE2 wrong")
def test_angle_ValueError(self):
ag = self.universe.atoms[:2]
assert_raises(ValueError, getattr, ag, 'angle')
def test_shape_parameter(self):
s = self.universe.s4AKE.atoms.shape_parameter()
assert_almost_equal(s, 0.00240753939086033, 6)
def test_asphericity(self):
a = self.universe.s4AKE.atoms.asphericity()
assert_almost_equal(a, 0.020227504542775828, 6)
def test_positions(self):
ag = self.universe.select_atoms("bynum 12:42")
pos = ag.positions + 3.14
ag.positions = pos
# should work
assert_almost_equal(ag.positions,
pos,
err_msg="failed to update atoms 12:42 position "
"to new position")
def set_badarr(pos=pos):
# create wrong size array
badarr = np.random.random((pos.shape[0] - 1, pos.shape[1] - 1))
ag.positions = badarr
assert_raises(ValueError, set_badarr)
def test_set_names(self):
ag = self.universe.atoms[:2]
names = ['One', 'Two']
ag.names = names
for a, b in zip(ag, names):
assert_equal(a.name, b)
@attr("issue")
def test_nonexistent_instantselector_raises_AttributeError(self):
def access_nonexistent_instantselector():
self.universe.atoms.NO_SUCH_ATOM
assert_raises(AttributeError, access_nonexistent_instantselector)
def test_atom_order(self):
assert_equal(self.universe.atoms.indices,
sorted(self.universe.atoms.indices))
class TestPBCFlag(object):
@dec.skipif(parser_not_found('TRZ'),
'TRZ parser not available. Are you using python 3?')
def setUp(self):
self.prec = 3
self.universe = mda.Universe(TRZ_psf, TRZ)
self.ref_noPBC = {
'COG':
np.array([4.23789883, 0.62429816, 2.43123484], dtype=np.float32),
'COM':
np.array([4.1673783, 0.70507009, 2.21175832]),
'ROG':
119.30368949900134,
'Shape':
0.6690026954813445,
'Asph':
0.5305456387833748,
'MOI':
np.array([[152117.06620921, 55149.54042136, -26630.46034023],
[55149.54042136, 72869.64061494, 21998.1778074],
[-26630.46034023, 21998.1778074, 162388.70002471]]),
'BBox':
np.array([[-75.74159241, -144.86634827, -94.47974396],
[95.83090973, 115.11561584, 88.09812927]],
dtype=np.float32),
'BSph': (173.40482,
np.array([4.23789883, 0.62429816, 2.43123484],
dtype=np.float32)),
'PAxes':
np.array([[-0.78787867, -0.26771575, 0.55459488],
[0.40611024, 0.45112859, 0.7947059],
[0.46294889, -0.85135849, 0.24671249]])
}
self.ref_PBC = {
'COG':
np.array([26.82960892, 31.5592289, 30.98238945], dtype=np.float32),
'COM':
np.array([26.67781143, 31.2104336, 31.19796289]),
'ROG':
27.713008969174918,
'Shape':
0.0017390512580463542,
'Asph':
0.020601215358731016,
'MOI':
np.array([[7333.79167791, -211.8997285, -721.50785456],
[-211.8997285, 7059.07470427, -91.32156884],
[-721.50785456, -91.32156884, 6509.31735029]]),
'BBox':
np.array([[1.45964116e-01, 1.85623169e-02, 4.31785583e-02],
[5.53314018e+01, 5.54227829e+01, 5.54158211e+01]],
dtype=np.float32),
'BSph': (47.923367,
np.array([26.82960892, 31.5592289, 30.98238945],
dtype=np.float32)),
'PAxes':
np.array([[-0.85911708, 0.19258726, 0.4741603],
[-0.07520116, -0.96394227, 0.25526473],
[-0.50622389, -0.18364489, -0.84262206]])
}
self.ag = self.universe.residues[0:3]
def tearDown(self):
mda.core.flags['use_pbc'] = False
del self.universe
del self.ref_noPBC
del self.ref_PBC
del self.ag
def test_flag(self):
# Test default setting of flag
assert_equal(mda.core.flags['use_pbc'], False)
def test_default(self):
# Test regular behaviour
assert_almost_equal(self.ag.center_of_geometry(),
self.ref_noPBC['COG'], self.prec)
assert_almost_equal(self.ag.center_of_mass(), self.ref_noPBC['COM'],
self.prec)
assert_almost_equal(self.ag.radius_of_gyration(),
self.ref_noPBC['ROG'], self.prec)
assert_almost_equal(self.ag.shape_parameter(), self.ref_noPBC['Shape'],
self.prec)
assert_almost_equal(self.ag.asphericity(), self.ref_noPBC['Asph'],
self.prec)
assert_almost_equal(self.ag.moment_of_inertia(), self.ref_noPBC['MOI'],
self.prec)
assert_almost_equal(self.ag.bbox(), self.ref_noPBC['BBox'], self.prec)
assert_almost_equal(self.ag.bsphere()[0], self.ref_noPBC['BSph'][0],
self.prec)
assert_almost_equal(self.ag.bsphere()[1], self.ref_noPBC['BSph'][1],
self.prec)
assert_almost_equal(self.ag.principal_axes(), self.ref_noPBC['PAxes'],
self.prec)
def test_pbcflag(self):
# Test using ag method flag
assert_almost_equal(self.ag.center_of_geometry(pbc=True),
self.ref_PBC['COG'], self.prec)
assert_almost_equal(self.ag.center_of_mass(pbc=True),
self.ref_PBC['COM'], self.prec)
assert_almost_equal(self.ag.radius_of_gyration(pbc=True),
self.ref_PBC['ROG'], self.prec)
assert_almost_equal(self.ag.shape_parameter(pbc=True),
self.ref_PBC['Shape'], self.prec)
assert_almost_equal(self.ag.asphericity(pbc=True),
self.ref_PBC['Asph'], self.prec)
assert_almost_equal(self.ag.moment_of_inertia(pbc=True),
self.ref_PBC['MOI'], self.prec)
assert_almost_equal(self.ag.bbox(pbc=True), self.ref_PBC['BBox'],
self.prec)
assert_almost_equal(
self.ag.bsphere(pbc=True)[0], self.ref_PBC['BSph'][0], self.prec)
assert_almost_equal(
self.ag.bsphere(pbc=True)[1], self.ref_PBC['BSph'][1], self.prec)
assert_almost_equal(self.ag.principal_axes(pbc=True),
self.ref_PBC['PAxes'], self.prec)
def test_usepbc_flag(self):
# Test using the core.flags flag
mda.core.flags['use_pbc'] = True
assert_almost_equal(self.ag.center_of_geometry(), self.ref_PBC['COG'],
self.prec)
assert_almost_equal(self.ag.center_of_mass(), self.ref_PBC['COM'],
self.prec)
assert_almost_equal(self.ag.radius_of_gyration(), self.ref_PBC['ROG'],
self.prec)
assert_almost_equal(self.ag.shape_parameter(), self.ref_PBC['Shape'],
self.prec)
assert_almost_equal(self.ag.asphericity(), self.ref_PBC['Asph'],
self.prec)
assert_almost_equal(self.ag.moment_of_inertia(), self.ref_PBC['MOI'],
self.prec)
assert_almost_equal(self.ag.bbox(), self.ref_PBC['BBox'], self.prec)
assert_almost_equal(self.ag.bsphere()[0], self.ref_PBC['BSph'][0],
self.prec)
assert_almost_equal(self.ag.bsphere()[1], self.ref_PBC['BSph'][1],
self.prec)
assert_almost_equal(self.ag.principal_axes(), self.ref_PBC['PAxes'],
self.prec)
mda.core.flags['use_pbc'] = False
def test_override_flag(self):
# Test using the core.flags flag, then overriding
mda.core.flags['use_pbc'] = True
assert_almost_equal(self.ag.center_of_geometry(pbc=False),
self.ref_noPBC['COG'], self.prec)
assert_almost_equal(self.ag.center_of_mass(pbc=False),
self.ref_noPBC['COM'], self.prec)
assert_almost_equal(self.ag.radius_of_gyration(pbc=False),
self.ref_noPBC['ROG'], self.prec)
assert_almost_equal(self.ag.shape_parameter(pbc=False),
self.ref_noPBC['Shape'], self.prec)
assert_almost_equal(self.ag.asphericity(pbc=False),
self.ref_noPBC['Asph'], self.prec)
assert_almost_equal(self.ag.moment_of_inertia(pbc=False),
self.ref_noPBC['MOI'], self.prec)
assert_almost_equal(self.ag.bbox(pbc=False), self.ref_noPBC['BBox'],
self.prec)
assert_almost_equal(
self.ag.bsphere(pbc=False)[0], self.ref_noPBC['BSph'][0],
self.prec)
assert_almost_equal(
self.ag.bsphere(pbc=False)[1], self.ref_noPBC['BSph'][1],
self.prec)
assert_almost_equal(self.ag.principal_axes(pbc=False),
self.ref_noPBC['PAxes'], self.prec)
mda.core.flags['use_pbc'] = False
class TestDihedralSelections(object):
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def setUp(self):
self.universe = mda.Universe(PSF, DCD)
self.dih_prec = 2
def tearDown(self):
del self.universe
del self.dih_prec
def test_phi_selection(self):
phisel = self.universe.s4AKE.r10.phi_selection()
assert_equal(phisel.names, ['C', 'N', 'CA', 'C'])
assert_equal(phisel.residues.resids, [9, 10])
assert_equal(phisel.residues.resnames, ['PRO', 'GLY'])
def test_psi_selection(self):
psisel = self.universe.s4AKE.r10.psi_selection()
assert_equal(psisel.names, ['N', 'CA', 'C', 'N'])
assert_equal(psisel.residues.resids, [10, 11])
assert_equal(psisel.residues.resnames, ['GLY', 'ALA'])
def test_omega_selection(self):
osel = self.universe.s4AKE.r8.omega_selection()
assert_equal(osel.names, ['CA', 'C', 'N', 'CA'])
assert_equal(osel.residues.resids, [8, 9])
assert_equal(osel.residues.resnames, ['ALA', 'PRO'])
def test_chi1_selection(self):
sel = self.universe.s4AKE.r13.chi1_selection() # LYS
assert_equal(sel.names, ['N', 'CA', 'CB', 'CG'])
assert_equal(sel.residues.resids, [13])
assert_equal(sel.residues.resnames, ['LYS'])
def test_phi_sel_fail(self):
sel = self.universe.residues[0].phi_selection()
assert_equal(sel, None)
def test_psi_sel_fail(self):
sel = self.universe.residues[-1].psi_selection()
assert_equal(sel, None)
def test_omega_sel_fail(self):
sel = self.universe.residues[-1].omega_selection()
assert_equal(sel, None)
def test_ch1_sel_fail(self):
sel = self.universe.s4AKE.r8.chi1_selection()
assert_equal(sel, None) # ALA
def test_dihedral_phi(self):
u = self.universe
phisel = u.s4AKE.r10.phi_selection()
assert_almost_equal(phisel.dihedral.value(), -168.57384, self.dih_prec)
def test_dihedral_psi(self):
u = self.universe
psisel = u.s4AKE.r10.psi_selection()
assert_almost_equal(psisel.dihedral.value(), -30.064838, self.dih_prec)
def test_dihedral_omega(self):
u = self.universe
osel = u.s4AKE.r8.omega_selection()
assert_almost_equal(osel.dihedral.value(), -179.93439, self.dih_prec)
def test_dihedral_chi1(self):
u = self.universe
sel = u.s4AKE.r13.chi1_selection() # LYS
assert_almost_equal(sel.dihedral.value(), -58.428127, self.dih_prec)
class TestAtomGroupProperties(object):
"""Test working with the properties of Atoms via AtomGroups
Check that:
- getting properties from AG matches the Atom values
- setting properties from AG changes the Atom
- setting the property on Atom changes AG
"""
@staticmethod
def get_new(att_type):
"""Return enough values to change the small g"""
if att_type == 'string':
return ['A', 'B', 'C', 'D', 'E', 'F']
elif att_type == 'float':
return np.array([0.001, 0.002, 0.003, 0.005, 0.012, 0.025],
dtype=np.float32)
elif att_type == 'int':
return [4, 6, 8, 1, 5, 4]
def _check_ag_matches_atom(self, att, atts, ag):
"""Checking Atomgroup property matches Atoms"""
# Check that accessing via AtomGroup is identical to doing
# a list comprehension over AG
ref = [getattr(atom, att) for atom in ag]
assert_equal(
ref,
getattr(ag, atts),
err_msg="AtomGroup doesn't match Atoms for property: {0}".format(
att))
def _change_atom_check_ag(self, att, atts, vals, ag):
"""Changing Atom, checking AtomGroup matches this"""
# Set attributes via Atoms
for atom, val in zip(ag, vals):
setattr(atom, att, val)
# Check that AtomGroup returns new values
other = getattr(ag, atts)
assert_equal(
vals,
other,
err_msg=
"Change to Atoms not reflected in AtomGroup for property: {0}".
format(att))
@dec.skipif(parser_not_found('DCD'),
'DCD parser not available. Are you using python 3?')
def test_attributes(self):
u = make_Universe(
('names', 'resids', 'segids', 'types', 'altLocs', 'charges',
'masses', 'radii', 'bfactors', 'occupancies'))
u.atoms.occupancies = 1.0
master = u.atoms
idx = [0, 1, 4, 7, 11, 14]
ag = master[idx]
for att, atts, att_type in (('name', 'names',
'string'), ('type', 'types', 'string'),
('altLoc', 'altLocs',
'string'), ('charge', 'charges', 'float'),
('mass', 'masses',
'float'), ('radius', 'radii', 'float'),
('bfactor', 'bfactors', 'float'),
('occupancy', 'occupancies', 'float')):
vals = self.get_new(att_type)
yield self._check_ag_matches_atom, att, atts, ag
yield self._change_atom_check_ag, att, atts, vals, ag