def test_average_structure_in_memory(self, universe):
avg = align.AverageStructure(universe, in_memory=True).run()
reference_coordinates = universe.trajectory.timeseries().mean(axis=1)
assert_almost_equal(avg.universe.atoms.positions,
reference_coordinates,
decimal=4)
assert avg.filename is None
def test_average_structure_mass_weighted(self, universe, reference):
ref, rmsd = _get_aligned_average_positions(self.ref_files,
reference,
weights='mass')
avg = align.AverageStructure(universe, reference, weights='mass').run()
assert_almost_equal(avg.universe.atoms.positions, ref, decimal=4)
assert_almost_equal(avg.rmsd, rmsd)
def test_average_structure_select(self, universe, reference):
select = 'protein and name CA and resid 3-5'
ref, rmsd = _get_aligned_average_positions(self.ref_files,
reference,
select=select)
avg = align.AverageStructure(universe, reference, select=select).run()
assert_almost_equal(avg.universe.atoms.positions, ref, decimal=4)
assert_almost_equal(avg.rmsd, rmsd)
def test_average_structure_ref_frame(self, universe):
ref_frame = 3
u = mda.Merge(universe.atoms)
# change to ref_frame
universe.trajectory[ref_frame]
u.load_new(universe.atoms.positions)
# back to start
universe.trajectory[0]
ref, rmsd = _get_aligned_average_positions(self.ref_files, u)
avg = align.AverageStructure(universe, ref_frame=ref_frame).run()
assert_almost_equal(avg.universe.atoms.positions, ref, decimal=4)
assert_almost_equal(avg.rmsd, rmsd)
def test_rmsf_xtc(run):
"""Align multiple times + RMSF"""
u = mda.Universe(TPR, XTC)
u2 = u.copy()
average = align.AverageStructure(u2, u2, select='protein and name CA',
ref_frame=0).run()
ref = average.universe
aligner = align.AlignTraj(u2, ref,
select='protein and name CA',
in_memory=True).run()
c_alphas = u2.select_atoms('protein and name CA')
R = rms.RMSF(c_alphas).run()
assert 1 == 1
def RMSF(u, PU_directory_output):
# calcule le RMSF de la PU
print("Processing RMSF...")
average = align.AverageStructure(u,
u,
select='protein and name CA',
ref_frame=0).run()
ref = average.universe
aligner = align.AlignTraj(u,
ref,
select='protein and name CA',
in_memory=True).run()
c_alphas = u.select_atoms('protein and name CA')
R = rms.RMSF(c_alphas).run()
plt.figure()
ax3 = plt.subplot(111)
ax3.plot(c_alphas.resids, R.rmsf, 'b-', label="RMSF")
ax3.legend(loc="best")
ax3.set_title("RMSF")
ax3.set_xlabel("Residue")
ax3.set_ylabel(r"RMSF ($\AA$)")
ax3.figure.savefig(PU_directory_output + "RMSF.png")
print("Done!")
def test_mismatch_atoms(self, universe):
u = mda.Merge(universe.atoms[:10])
with pytest.raises(SelectionError):
align.AverageStructure(universe, u)
def test_average_structure_no_msf(self, universe):
avg = align.AverageStructure(universe).run()
assert not hasattr(avg, 'msf')
def test_average_structure_no_ref(self, universe):
ref, rmsd = _get_aligned_average_positions(self.ref_files, universe)
avg = align.AverageStructure(universe).run()
assert_almost_equal(avg.universe.atoms.positions, ref, decimal=4)
assert_almost_equal(avg.rmsd, rmsd)
