def psa(self, tmpdir):
universe1 = mda.Universe(PSF, DCD)
universe2 = mda.Universe(PSF, DCD2)
universe_rev = mda.Universe(PSF, DCD)
psa = PSA.PSAnalysis([universe1, universe2, universe_rev],
path_select='name CA',
targetdir=str(tmpdir))
psa.generate_paths(align=True)
psa.paths[-1] = psa.paths[-1][::-1, :, :] # reverse third path
return psa
def test_save_nopaths(self, tmpdir):
"""Test case were save_paths is called without calcualted paths"""
match_exp = "Paths have not been calculated yet"
with pytest.raises(NoDataError, match=match_exp):
universe1 = mda.Universe(PSF, DCD)
universe2 = mda.Universe(PSF, DCD2)
universe_rev = mda.Universe(PSF, DCD)
psa = PSA.PSAnalysis([universe1, universe2, universe_rev],
path_select='name CA',
targetdir=str(tmpdir))
psa.save_paths()
def test_load(self, stored, tmpdir):
"""Test that the automatically saved files can be loaded"""
# To allow for testing the store keyword, ignore fixture
universe1 = mda.Universe(PSF, DCD)
universe2 = mda.Universe(PSF, DCD2)
universe_rev = mda.Universe(PSF, DCD)
psa = PSA.PSAnalysis([universe1, universe2, universe_rev],
path_select='name CA',
targetdir=str(tmpdir))
psa2 = PSA.PSAnalysis([universe1, universe2, universe_rev],
path_select='name CA',
targetdir=str(tmpdir))
psa.generate_paths(align=True, store=stored)
# Make copies to the existing data
# Note: path names are set after save_paths has been called
expected_paths = [p.copy() for p in psa.paths]
if not stored:
psa.save_paths()
expected_path_names = psa.path_names[:]
# Load data in the empty PSAnalysis object
psa2.load()
assert psa2.path_names == expected_path_names
assert len(psa2.paths) == len(expected_paths)
for ipath, (observed, expected) in enumerate(zip(psa2.paths,
expected_paths)):
assert_almost_equal(observed, expected, decimal=6,
err_msg=("loaded path {} does not agree with "
"input").format(ipath))
def setUp(self):
self.tmpdir = tempdir.TempDir()
self.iu1 = np.triu_indices(3, k=1)
self.universe1 = mda.Universe(PSF, DCD)
self.universe2 = mda.Universe(PSF, DCD2)
self.universe_rev = mda.Universe(PSF, DCD)
self.universes = [self.universe1, self.universe2, self.universe_rev]
self.psa = 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()
self._plot()
def pairwise_rmsds_traj(universes: List[mda.Universe], labels: List[str]):
"""Calculate pairwise RMSD for multiple trajectories using Hausdorff distance."""
# Align trajectories because there seems to be a bug
# in PSAnalysis.
for k in universes[1:]:
align.AlignTraj(k,
universes[0],
select=STANDARD_SELECTION,
in_memory=True)
ps = psa.PSAnalysis(universes,
labels=labels,
reference=universes[0],
ref_frame=0,
select=STANDARD_SELECTION,
path_select=STANDARD_SELECTION)
ps.generate_paths(align=False, save=False, weights='mass')
ps.run(metric='hausdorff')
return ps.D