def test_no_atom_masses(self, universe):
#if no masses are present
u = mda.Universe.empty(6,
2,
atom_resindex=[0, 0, 0, 1, 1, 1],
trajectory=True)
with pytest.warns(SelectionWarning):
align.get_matching_atoms(u.atoms, u.atoms)
def test_one_universe_has_masses(self, universe):
u = mda.Universe.empty(6,
2,
atom_resindex=[0, 0, 0, 1, 1, 1],
trajectory=True)
ref = mda.Universe.empty(6,
2,
atom_resindex=[0, 0, 0, 1, 1, 1],
trajectory=True)
ref.add_TopologyAttr('masses')
with pytest.warns(SelectionWarning):
align.get_matching_atoms(u.atoms, ref.atoms)
def test_nomatch_atoms_raise(self, universe, reference,
strict, selection="protein and backbone"):
# one atom less but same residues; with strict=False should try
# to get selections (but current code fails, so we also raise SelectionError)
ref = reference.select_atoms(selection).atoms[1:]
mobile = universe.select_atoms(selection)
if strict:
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
else:
with pytest.warns(SelectionWarning):
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
def test_nomatch_atoms_raise(self, universe, reference,
strict, selection="protein and backbone"):
# one atom less but same residues; with strict=False should try
# to get selections (but current code fails, so we also raise SelectionError)
ref = reference.select_atoms(selection).atoms[1:]
mobile = universe.select_atoms(selection)
if strict:
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
else:
with pytest.warns(SelectionWarning):
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
def test_nomatch_residues_raise_empty(self, universe, reference_small,
strict, selection="protein and backbone"):
# one atom less and all residues different: will currently create
# empty selections with strict=False, see also
# https://gist.github.com/orbeckst/2686badcd15031e6c946baf9164a683d
ref = reference_small.select_atoms(selection)
mobile = universe.select_atoms(selection)
if strict:
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
else:
with pytest.warns(SelectionWarning):
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
def test_nomatch_residues_raise_empty(self, universe, reference_small,
strict, selection="protein and backbone"):
# one atom less and all residues different: will currently create
# empty selections with strict=False, see also
# https://gist.github.com/orbeckst/2686badcd15031e6c946baf9164a683d
ref = reference_small.select_atoms(selection)
mobile = universe.select_atoms(selection)
if strict:
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
else:
with pytest.warns(SelectionWarning):
with pytest.raises(SelectionError):
groups = align.get_matching_atoms(ref, mobile, strict=strict)
def test_match(self,
universe,
reference,
strict,
selection="protein and backbone"):
ref = reference.select_atoms(selection)
mobile = universe.select_atoms(selection)
groups = align.get_matching_atoms(ref, mobile, strict=strict)
assert_equal(groups[0].names, groups[1].names)
def test_match(self, universe, reference, strict,
selection="protein and backbone"):
ref = reference.select_atoms(selection)
mobile = universe.select_atoms(selection)
groups = align.get_matching_atoms(ref, mobile, strict=strict)
assert_equal(groups[0].names, groups[1].names)
