def test_protor_radii_invalid():
with pytest.raises(ValueError):
# Expect raised exception for hydrogen atoms
strucinfo.vdw_radius_protor("FOO", "H1")
with pytest.raises(KeyError):
# Expect raised exception when a residue does not contain an atom
strucinfo.vdw_radius_protor("ALA", "K")
# For all other unknown radii expect None
assert strucinfo.vdw_radius_protor("HOH", "O") == None
def test_protOr_radii():
"""
Assert that ProtOr VdW radii (except hydrogen) can be calculated for
all atoms in the given structure, since the structure (1GYA)
does only contain standard amino acids after the removal of
glycosylation.
This means, that none of the resulting radii should be the None.
"""
array = load_structure(join(data_dir("structure"), "1gya.mmtf"))
array = array[..., array.element != "H"]
array = array[..., struc.filter_amino_acids(array)]
for res_name, atom_name in zip(array.res_name, array.atom_name):
radius = strucinfo.vdw_radius_protor(res_name, atom_name)
assert isinstance(radius, float)
assert radius != None
