def test_nonprotein_residues_analysisbase(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):
pkatraj = propkatraj.PropkaTraj(u, select="not protein")
def test_single_frame_regression_analysisbase(tmpdir, u, selection):
"""Single frame PropkaTraj regression test"""
with tmpdir.as_cwd():
if selection == 'ag':
pkatraj = propkatraj.PropkaTraj(u.select_atoms('protein'),
select=None)
elif selection == 'array':
selection = u.select_atoms('protein').ix
pkatraj = propkatraj.PropkaTraj(u, select=selection)
else:
pkatraj = propkatraj.PropkaTraj(u)
pkatraj.run(stop=1)
# load reference data
ref_resnums, ref_pkas = pka_from_file(PSF_FRAME_ZERO_PKA)
# test residue numbers
resnums = pkatraj.pkas.columns.to_numpy()
assert_equal(resnums, ref_resnums)
# test pka values
assert_almost_equal(pkatraj.pkas.values[0], ref_pkas, decimal=2)
def test_skipframe_pass_analysisbase(tmpdir, caplog, top, traj, framenum):
"""Test for Issue #10 - passes, logging raise"""
u = mda.Universe(top, traj)
with tmpdir.as_cwd():
wmsg = "failure on frame: {0}".format(framenum)
with pytest.warns(UserWarning, match=wmsg):
pkatraj = propkatraj.PropkaTraj(u, skip_failure=True)
pkatraj.run()
perc = 1 / u.trajectory.n_frames * 100
msg = ("number of failed frames = 1\n"
"percentage failure = {0}\n"
"failed frames: {1}".format(perc, [framenum]))
assert msg in caplog.records[0].message
# times should have been modified in-place
assert len(pkatraj.times) == (len(u.trajectory) - 1)
assert u.trajectory[framenum].time not in pkatraj.times
def test_start_stop_step_analysisbase(tmpdir, u, start, stop, step):
"""Basic test to make sure the dataframe gets populated with the right
dimensions"""
with tmpdir.as_cwd():
pkatraj = propkatraj.PropkaTraj(u)
pkatraj.run(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(pkatraj.pkas) == nframes
assert len(pkatraj.pkas.columns) == 75
# index should be time
assert pkatraj.pkas.index.name == 'time'
times = np.array(range(start, stop, step), dtype=np.float32) + 1
assert_almost_equal(pkatraj.pkas.index.values, times, decimal=5)
def test_multi_frame_regression_analysisbase(tmpdir, u, glu_ref):
"""Multiframe propkatraj call basic regression test
Note: slow test
"""
with tmpdir.as_cwd():
pkatraj = propkatraj.PropkaTraj(u)
pkatraj.run(step=10)
# load reference data for resnum and the last frame pka
ref_resnums, ref_pkas = pka_from_file(PSF_FRAME_NINETY_PKA)
# test residue numbers
resnums = pkatraj.pkas.columns.to_numpy()
assert_equal(resnums, ref_resnums)
# test final frame pka values
assert_almost_equal(pkatraj.pkas.values[-1], ref_pkas, decimal=2)
# test one data series: glu 162
assert_almost_equal(pkatraj.pkas[162].values, glu_ref, decimal=2)
#write file with python propka_run.py xxx.pdb xxx.xtc
import MDAnalysis as mda
import sys
from MDAnalysisTests.datafiles import PDB, XTC
u = mda.Universe(sys.argv[1], sys.argv[2]) #import file here
import propkatraj #import module
protein = u.select_atoms('protein') #defining your protein
pkatraj = propkatraj.PropkaTraj(protein)
pkatraj.run(verbose=True)
pkatraj.pkas
pkatraj.pkas.describe()
data = pkatraj.pkas
data.to_csv("pka-trajctory-full.csv") #save file
data2 = pkatraj.pkas.describe()
data2.to_csv("pka-trajctory-summary.csv")
def test_skipframe_error_analysisbase(tmpdir, u_badframe):
"""Test for Issue #10 - Error raised"""
with tmpdir.as_cwd():
with pytest.raises(RuntimeError, match="failure on frame"):
pkatraj = propkatraj.PropkaTraj(u_badframe)
pkatraj.run()