def test_element_by_symbol(self):
for symbol in ["N", "n", " N7"]:
nitrogen = element.element_by_symbol(symbol)
assert nitrogen.name == element.Nitrogen.name
assert nitrogen.symbol == element.Nitrogen.symbol
assert nitrogen.mass == element.Nitrogen.mass
def test_element_by_symbol(self):
for symbol in ['N', 'n', ' N7']:
nitrogen = element.element_by_symbol(symbol)
assert nitrogen.name == element.Nitrogen.name
assert nitrogen.symbol == element.Nitrogen.symbol
assert nitrogen.mass == element.Nitrogen.mass
def test_bond_every_field_set(self, full_atom_type, are_equivalent_atoms):
atom1 = Atom(
name="test_atom1",
label="test_label1",
position=[0.0, 0.0, 0.0],
charge=1.5,
mass=2.0,
element=element_by_symbol("C"),
atom_type=full_atom_type,
)
atom2 = Atom(
name="test_atom1",
label="test_label1",
position=[0.1, 0.4, 0.5],
charge=5,
mass=2.6,
element=element_by_symbol("H"),
atom_type=full_atom_type,
)
bond = Bond(name="test_bond1", connection_members=(atom1, atom2))
bond_type = BondType(
name="test_bond_type",
expression="a*b+c**2",
parameters={
"a": 10 * u.nm,
"b": 20 * u.angstrom
},
independent_variables={"c"},
)
bond_copy = Bond.parse_raw(bond.json())
assert bond_copy.name == bond.name
for member1, member2 in zip(bond.connection_members,
bond_copy.connection_members):
assert are_equivalent_atoms(member1, member2)
assert bond_copy.bond_type == bond.bond_type
def test_atom_every_field_set(self, full_atom_type, are_equivalent_atoms):
atom = Atom(
name="test_atom",
label="test_label",
position=[0.0, 0.0, 0.0],
charge=1.5,
mass=2.0,
element=element_by_symbol("C"),
atom_type=full_atom_type,
)
atom_copy = Atom.parse_raw(atom.json())
assert are_equivalent_atoms(atom, atom_copy)
def _parse_gmso(self, forcefield_files, **kwargs):
"""Parse metadata information when using GMSO as backend."""
if forcefield_files:
self.ff = gmso.ForceField(forcefield_files, **kwargs)
self._version = self.ff.version
self._name = self.ff.name
for name, atype in self.ff.atom_types.items():
self.atomTypeDefinitions[name] = atype.definition
self.atomTypeOverrides[name] = atype.overrides
self.atomTypeDesc[name] = atype.description
self.atomTypeRefs[name] = set(atype.doi.split(","))
self.atomTypeClasses[name] = atype.atomclass
if atype.tags.get("element"):
ele = atype.tags["element"]
if element.element_by_symbol(ele):
self.atomTypeElements[atype.name] = ele
else:
self.non_element_types[ele] = None
else:
# Register atomtype with missing atomtype as atomistic (empty string)
self.atomTypeElements[name] = ""
return None
