def test_from_pdb():
"""
Make sure we can make a protein from a pdb file.
"""
pro = Protein.from_file(file_name=get_data("capped_leu.pdb"))
assert pro.n_atoms == 31
assert pro.coordinates.shape == (pro.n_atoms, 3)
def test_protein_params(tmpdir):
"""
Load up the small protein and make sure it is parametrised with the general qube forcefield.
"""
with tmpdir.as_cwd():
pro = Protein.from_file(file_name=get_data("capped_leu.pdb"))
shutil.copy(get_data("capped_leu.pdb"), "capped_leu.pdb")
XMLProtein(protein=pro)
def test_pdb_round_trip(tmpdir):
"""
Make sure we can round trip a protein to pdb.
"""
with tmpdir.as_cwd():
pro = Protein.from_file(file_name=get_data("capped_leu.pdb"))
pro.write_pdb(name="test")
pro2 = Protein.from_file("test.pdb")
assert pro.n_atoms == pro2.n_atoms
assert pro.n_bonds == pro.n_bonds
for bond in pro.bonds:
assert bond in pro2.bonds
for angle in pro.angles:
assert angle in pro2.angles
for central_bond, torsions in pro.dihedrals.items():
for d in torsions:
assert d in pro2.dihedrals[central_bond]
def test_not_pdb():
"""
Make sure an error is raised if we try and make a protein from a non pdb file.
"""
with pytest.raises(FileTypeError):
_ = Protein.from_file(file_name=get_data("bace0.xyz"))
