def test_nonprotein_residues(tmpdir):
"""Test for Issue #24 - remove once PDBWriter is fixed"""
u = mda.Universe(GRO, XTC)
with tmpdir.as_cwd():
wmsg = "Non protein atoms passed"
with pytest.warns(UserWarning, match=wmsg):
pkas = propkatraj.get_propka(u, sel="not protein", stop=1)
def run_propkatraj(self,
topology=None,
trajectory=None,
sel='protein',
start=None,
stop=None,
step=None,
session=None):
"""
Run propkatraj
Runs Propka3.1 on a MD trajectory in a format that can be handled by
the MDanalysis package
:param kwargs: PROPKA options
:type kwargs: :py:dict
:param session: WAMP session object
:type session: :py:dict
:return: PROPKA results
:rtype: :py:dict
"""
# Load trajectory
universe = mda.Universe(topology, trajectory)
# Run propkatraj
pkatrajdf = get_propka(universe,
sel=sel,
start=start,
stop=stop,
step=step)
return {'session': session}
def test_mmtf_nofilename(tmpdir):
"""See issue #23"""
# Everyone's favourite BRD4 model
u = mda.fetch_mmtf('4LYI')
with tmpdir.as_cwd():
pkas = propkatraj.get_propka(u)
assert os.path.isfile('current.pka')
def test_skipframe_pass(tmpdir, caplog, top, traj, framenum):
"""Test for Issue #10 - passes, logging raise"""
u = mda.Universe(top, traj)
with tmpdir.as_cwd():
pkas = propkatraj.get_propka(u, skip_failure=True)
perc = 1 / u.trajectory.n_frames * 100
wmsg = [
'failing frame {0}'.format(framenum),
'number of failed frames = 1',
'percent failure = {0:.3f}%'.format(perc),
'failed frames: {0}'.format([framenum])
]
for msg, rec in zip(wmsg, caplog.records):
assert msg in rec.message
def test_start_stop_step(tmpdir, u, start, stop, step):
"""Basic test to make sure the dataframe gets populated with the right
dimensions"""
with tmpdir.as_cwd():
pkas = propkatraj.get_propka(u, start=start, stop=stop, step=step)
start, stop, step = u.trajectory.check_slice_indices(start, stop, step)
nframes = len(range(start, stop, step))
# There should be nframes rows and 75 columns
assert len(pkas) == nframes
assert len(pkas.columns) == 75
# index should be time
assert pkas.index.name == 'time'
times = np.array(range(start, stop, step), dtype=np.float32) + 1
assert_almost_equal(pkas.index.values, times, decimal=5)
def test_multi_frame_regression(tmpdir, u, glu_ref):
"""Multiframe propkatraj call basic regression test
Note: slow test
"""
with tmpdir.as_cwd():
pkas = propkatraj.get_propka(u, step=10)
# load reference data for resnum and last frame pka
ref_resnums, ref_pkas = pka_from_file(PSF_FRAME_NINETY_PKA)
# test residue numbers
resnums = pkas.columns.to_numpy()
assert_equal(resnums, ref_resnums)
# test final frame pka values
assert_almost_equal(pkas.values[-1], ref_pkas, decimal=2)
# test one data series: glu 162
assert_almost_equal(pkas[162].values, glu_ref, decimal=2)
def test_single_frame_regression(tmpdir, u, selection):
"""Single frame propkatraj call compared against same frame written by
MDA
"""
with tmpdir.as_cwd():
if selection == 'array':
selection = u.select_atoms('protein').ix
elif selection == 'list':
selection = u.select_atoms('protein').ix.tolist()
pkas = propkatraj.get_propka(u, sel=selection, stop=1)
# load reference data
ref_resnums, ref_pkas = pka_from_file(PSF_FRAME_ZERO_PKA)
# test residue numbers
resnums = pkas.columns.to_numpy()
assert_equal(resnums, ref_resnums)
# test pka values
assert_almost_equal(pkas.values[0], ref_pkas, decimal=2)
def test_skipframe_error(tmpdir, u_badframe):
"""Test for Issue #10 - Error raised"""
with tmpdir.as_cwd():
with pytest.raises(RuntimeError, match="failing frame"):
pkas = propkatraj.get_propka(u_badframe)
def test_deprecate_get_propka(tmpdir, u):
"""Checks that get_propka is now deprecated"""
wmsg = "will be removed in release 2.0.0"
with tmpdir.as_cwd():
with pytest.warns(DeprecationWarning, match=wmsg):
pkas = propkatraj.get_propka(u, stop=1)