def test_AnalysisFromFunction():
u = mda.Universe(PSF, DCD)
step = 2
ana1 = base.AnalysisFromFunction(
simple_function, mobile=u.atoms).run(step=step)
ana2 = base.AnalysisFromFunction(simple_function, u.atoms).run(step=step)
ana3 = base.AnalysisFromFunction(
simple_function, u.trajectory, u.atoms).run(step=step)
results = []
for ts in u.trajectory[::step]:
results.append(simple_function(u.atoms))
results = np.asarray(results)
for ana in (ana1, ana2, ana3):
assert_equal(results, ana.results)
def test_AnalysisFromFunction_args_content(u):
protein = u.select_atoms('protein')
masses = protein.masses.reshape(-1, 1)
another = mda.Universe(TPR, XTC).select_atoms("protein")
ans = base.AnalysisFromFunction(mass_xyz, protein, another, masses)
assert len(ans.args) == 3
result = np.sum(ans.run().results)
assert_almost_equal(result, -317054.67757345125, decimal=6)
assert (ans.args[0] is protein) and (ans.args[1] is another)
assert ans._trajectory is protein.universe.trajectory
def test_AnalysisFromFunction(u, start, stop, step, nframes):
ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms)
ana1.run(start=start, stop=stop, step=step)
ana2 = base.AnalysisFromFunction(simple_function, u.atoms)
ana2.run(start=start, stop=stop, step=step)
ana3 = base.AnalysisFromFunction(simple_function, u.trajectory, u.atoms)
ana3.run(start=start, stop=stop, step=step)
results = []
for ts in u.trajectory[start:stop:step]:
results.append(simple_function(u.atoms))
results = np.asarray(results)
assert np.size(results, 0) == nframes
for ana in (ana1, ana2, ana3):
assert_equal(results, ana.results)
def test_AnalysisFromFunction_warning(u):
func = base.AnalysisFromFunction(simple_function, mobile=u.atoms)
msg = ("The structure of the `results` array will change in MDAnalysis "
"version 2.0.")
with pytest.warns(DeprecationWarning, match=msg):
func.run()