def test_write_refs_multiple(self, requests_mock):
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path="works/10.1021/ja9621760/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
text=RESPONSE_BIB_ETHANE_JA962170,
)
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path="works/10.1021/jp0484579/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
text=RESPONSE_BIB_ETHANE_JP0484579,
)
mol2 = mb.load(get_fn("ethane.mol2"))
oplsaa = Forcefield(forcefield_files=get_fn("refs-multi.xml"),
strict=False)
ethane = oplsaa.apply(
mol2,
references_file="ethane-multi.bib",
assert_improper_params=False,
)
assert os.path.isfile("ethane-multi.bib")
with open(get_fn("ethane-multi.bib")) as file1:
with open("ethane-multi.bib") as file2:
diff = list(
difflib.unified_diff(file1.readlines(),
file2.readlines(),
n=0))
assert not diff
def test_missing_topo_params(self, ff_filename, kwargs):
"""Test that the user is notified if not all topology parameters are found."""
ethane = mb.load(get_fn("ethane.mol2"))
oplsaa_with_typo = Forcefield(forcefield_files=get_fn(ff_filename),
strict=False)
with pytest.raises(Exception):
ethane = oplsaa_with_typo.apply(ethane,
assert_improper_params=False)
with pytest.warns(UserWarning):
ethane = oplsaa_with_typo.apply(ethane,
assert_improper_params=False,
**kwargs)
def test_write_bad_ref(self, requests_mock):
register_mock_request(
mocker=requests_mock,
url="http://api.crossref.org/",
path=
"works/10.1021/garbage_bad_44444444jjjj/transform/application/x-bibtex",
headers={"accept": "application/x-bibtex"},
status_code=404,
)
mol2 = mb.load(get_fn("ethane.mol2"), backend="parmed")
oplsaa = Forcefield(forcefield_files=get_fn("refs-bad.xml"),
strict=False)
with pytest.warns(UserWarning):
ethane = oplsaa.apply(mol2,
references_file="ethane.bib",
assert_improper_params=False)
def test_assert_bonds(self):
ff = Forcefield(name="trappe-ua", strict=False)
derponium = mb.Compound()
at1 = mb.Particle(name="H")
at2 = mb.Particle(name="O")
at3 = mb.Particle(name="_CH4")
derponium.add([at1, at2, at3])
derponium.add_bond((at1, at2))
derponium.add_bond((at2, at3))
with pytest.raises(Exception):
ff.apply(derponium, assert_improper_params=False)
thing = ff.apply(
derponium,
assert_bond_params=False,
assert_angle_params=False,
assert_improper_params=False,
)
assert any(b.bond_type is None for b in thing.bonds)
def test_urey_bradley(self):
system = mb.Compound()
first = mb.Particle(name="_CTL2", pos=[-1, 0, 0])
second = mb.Particle(name="_CL", pos=[0, 0, 0])
third = mb.Particle(name="_OBL", pos=[1, 0, 0])
fourth = mb.Particle(name="_OHL", pos=[0, 1, 0])
system.add([first, second, third, fourth])
system.add_bond((first, second))
system.add_bond((second, third))
system.add_bond((second, fourth))
ff = Forcefield(forcefield_files=[get_fn("charmm36_cooh.xml")],
strict=False)
struc = ff.apply(
system,
assert_angle_params=False,
assert_dihedral_params=False,
assert_improper_params=False,
)
assert len(struc.angles) == 3
assert len(struc.angle_types) == 3 # 1 harmonic, 2 Urey Bradley
def test_charmm_improper(self):
system = mb.Compound()
first = mb.Particle(name="_CTL2", pos=[-1, 0, 0])
second = mb.Particle(name="_CL", pos=[0, 0, 0])
third = mb.Particle(name="_OBL", pos=[1, 0, 0])
fourth = mb.Particle(name="_OHL", pos=[0, 1, 0])
system.add([first, second, third, fourth])
system.add_bond((first, second))
system.add_bond((second, third))
system.add_bond((second, fourth))
ff = Forcefield(forcefield_files=[get_fn("charmm36_cooh.xml")],
strict=False)
struc = ff.apply(
system,
assert_angle_params=False,
assert_dihedral_params=False,
assert_improper_params=False,
remove_untyped_connections=False,
)
assert len(struc.impropers) == 1
assert len(struc.dihedrals) == 0
def test_remove_untyped(self):
mol2 = mb.load(get_fn("ethane.mol2"), backend="parmed")
# test removal of untyped each class of connection seperately
oplsaa_bond = Forcefield(
forcefield_files=get_fn("ethane-missing_bond.xml"), strict=False)
oplsaa_angle = Forcefield(
forcefield_files=get_fn("ethane-missing_angle.xml"), strict=False)
oplsaa_dihedral = Forcefield(
forcefield_files=get_fn("ethane-missing_dihedral.xml"),
strict=False)
ethane1 = oplsaa_bond.apply(
mol2,
assert_improper_params=False,
assert_bond_params=False,
remove_untyped_connections=True,
)
ethane2 = oplsaa_angle.apply(
mol2,
assert_improper_params=False,
assert_angle_params=False,
remove_untyped_connections=True,
)
ethane3 = oplsaa_dihedral.apply(
mol2,
assert_improper_params=False,
assert_dihedral_params=False,
remove_untyped_connections=True,
)
assert ethane1.n_bonds == 1
assert ethane2.n_angles == 6
assert ethane3.n_dihedrals == 0
def test_unsupported_backend(self):
with pytest.raises(FoyerError, match=r"Backend not supported"):
FF = Forcefield(name="oplsaa", backend="void")
def test_missing_type_definitions(self):
with pytest.raises(FoyerError):
FF = Forcefield()
ethane = mb.load(get_fn("ethane.mol2"), backend="parmed")
FF.apply(ethane, assert_improper_params=False)
def test_load_gmso_xml(self):
spce_water = get_fn("gmso_spce_water.xml")
ff1 = Forcefield(forcefield_files=spce_water, strict=False)
assert len(ff1.atomTypeDesc) > 0
def test_load_files(self, ff_file):
ff1 = Forcefield(forcefield_files=ff_file, strict=False)
assert len(ff1.ff.atom_types) > 0
ff2 = Forcefield(forcefield_files=ff_file, strict=False)
assert len(ff1.ff.atom_types) == len(ff2.ff.atom_types)
def oplsaa(self):
return Forcefield(name="oplsaa", strict=False)