def test_zero_atoms(self, universe):
"""Test error if zero atoms are present after conversion."""
analysis_parameters = {"atomgroup": "name foo"}
with pytest.raises(ValueError, match="AtomGroup `-atomgroup` with "):
convert_analysis_parameters(
analysis_callable=RMSF,
analysis_parameters=analysis_parameters,
reference_universe=universe)
def test_multi_atomgroup_fail(self, universe):
"""Test error raise for empty atomgroup for multiple AtomGroups."""
analysis_parameters = {"p0": ["name foo"]}
with pytest.raises(ValueError, match="AtomGroup `-p0` with "):
convert_analysis_parameters(
analysis_callable=complete_docstring,
analysis_parameters=analysis_parameters,
reference_universe=universe)
def test_multi_atomgroup(self, universe):
"""Test conversion of a list containing multiple AtomGroups."""
selection_keywords = ["name OW", "name HW*"]
analysis_parameters = {"p0": ["name OW", "name HW*"]}
convert_analysis_parameters(analysis_callable=complete_docstring,
analysis_parameters=analysis_parameters,
reference_universe=universe)
for i, sel in enumerate(selection_keywords):
assert universe.select_atoms(sel) == analysis_parameters["p0"][i]
def test_None(self, universe):
"""Test that `None` objects are NOT converted.
Could be default arguments
"""
analysis_parameters = {"atomgroup": None}
convert_analysis_parameters(analysis_callable=RMSF,
analysis_parameters=analysis_parameters,
reference_universe=universe)
assert analysis_parameters["atomgroup"] is None
def test_multi_atomgroup_None(self, universe):
"""Test that `None` objects are NOT converted.
Could be default arguments
"""
analysis_parameters = {"p0": None}
convert_analysis_parameters(analysis_callable=complete_docstring,
analysis_parameters=analysis_parameters,
reference_universe=universe)
assert analysis_parameters["p0"] is None
def test_only_set_if_key_exists(self, universe):
"""
Test if keys exist.
The docparser does not distinguis between mandatory and positional
arguments. So we only should set the value if it is inside the dict.
"""
analysis_parameters = {}
convert_analysis_parameters(analysis_callable=RMSF,
analysis_parameters=analysis_parameters,
reference_universe=universe)
assert not analysis_parameters
def test_Atomgroup(self, universe):
"""Test AtomGroup conversion."""
analysis_parameters = {"atomgroup": "all"}
test_Universe = convert_analysis_parameters(
analysis_callable=RMSF,
analysis_parameters=analysis_parameters,
reference_universe=universe)
# `None` is returned if no Universe is created
assert test_Universe is None
assert analysis_parameters["atomgroup"] == universe.atoms
def test_Universe_creation(self, universe):
"""Test the universe creation from different parameters."""
analysis_parameters = {}
analysis_parameters["topology_u"] = TPR
analysis_parameters["topology_format_u"] = None
analysis_parameters["coordinates_u"] = XTC
analysis_parameters["trajectory_format_u"] = None
analysis_parameters["atom_style_u"] = None
analysis_parameters["dimensions_u"] = None
test_u = convert_analysis_parameters(
analysis_callable=EinsteinMSD,
analysis_parameters=analysis_parameters,
reference_universe=None)
# Extra parameters should be removed
assert len(analysis_parameters.keys()) == 1
assert analysis_parameters["u"] is test_u
# We can not test accros several universes so we just compare
# the atomic positions
assert (universe.atoms.positions == test_u.atoms.positions).all()