def test_topology_get_index(self):
top = Topology()
conn_members = [Site(), Site(), Site(), Site()]
for i in range(5):
top.add_site(Site())
top.add_connection(Bond(
connection_members=[conn_members[0], conn_members[1]]))
top.add_connection(Angle(
connection_members=[conn_members[0], conn_members[1], conn_members[2]]))
top.add_connection(Dihedral(
connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]]))
top.add_connection(Improper(
connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]]))
a_bond = Bond(connection_members=[conn_members[0], conn_members[1]])
an_angle = Angle(connection_members=[conn_members[0], conn_members[1], conn_members[2]])
a_site = Site()
a_dihedral = Dihedral(connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]])
an_improper = Improper(connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]])
top.add_site(a_site)
top.add_connection(a_bond)
top.add_connection(an_angle)
top.add_connection(a_dihedral)
top.add_connection(an_improper)
assert top.get_index(a_site) == 9
assert top.get_index(a_bond) == 5
assert top.get_index(an_angle) == 5
assert top.get_index(a_dihedral) == 5
assert top.get_index(an_improper) == 5
def test_topology_get_index(self):
top = Topology()
conn_members = [Atom() for _ in range(10)]
for atom in conn_members:
top.add_site(atom)
for i in range(5):
top.add_connection(
Bond(connection_members=[conn_members[i], conn_members[i +
1]]))
top.add_connection(
Angle(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2]
]))
top.add_connection(
Dihedral(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2],
conn_members[i + 3]
]))
top.add_connection(
Improper(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2],
conn_members[i + 3]
]))
a_atom = Atom()
a_bond = Bond(connection_members=[conn_members[6], conn_members[7]])
an_angle = Angle(connection_members=[
conn_members[6], conn_members[7], conn_members[8]
])
a_dihedral = Dihedral(connection_members=[
conn_members[6], conn_members[7], conn_members[8], conn_members[9]
])
an_improper = Improper(connection_members=[
conn_members[6], conn_members[7], conn_members[8], conn_members[9]
])
top.add_site(a_atom)
top.add_connection(a_bond)
top.add_connection(an_angle)
top.add_connection(a_dihedral)
top.add_connection(an_improper)
assert top.get_index(a_atom) == 10
assert top.get_index(a_bond) == 5
assert top.get_index(an_angle) == 5
assert top.get_index(a_dihedral) == 5
assert top.get_index(an_improper) == 5
def test_improper_fake(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
with pytest.raises(GMSOError):
Improper(connection_members=['fakesite1', 'fakesite2', 4.2])
def test_improper_fake(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Improper(connection_members=["fakeatom1", "fakeatom2", 4.2])
def test_improper_fake(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Improper(connection_members=['fakeatom1', 'fakeatom2', 4.2])
def test_improper_constituent_types(self):
atom1 = Atom(name="atom1",
position=[0, 0, 0],
atom_type=AtomType(name="A"))
atom2 = Atom(name="atom2",
position=[1, 0, 0],
atom_type=AtomType(name="B"))
atom3 = Atom(name="atom3",
position=[1, 1, 0],
atom_type=AtomType(name="C"))
atom4 = Atom(name="atom4",
position=[1, 1, 4],
atom_type=AtomType(name="D"))
imptype = ImproperType(member_types=[
atom1.atom_type.name,
atom2.atom_type.name,
atom3.atom_type.name,
atom4.atom_type.name,
])
imp = Improper(connection_members=[atom1, atom2, atom3, atom4], )
imp.improper_type = imp.connection_type = imptype
assert "A" in imp.connection_type.member_types
assert "B" in imp.connection_type.member_types
assert "C" in imp.connection_type.member_types
assert "D" in imp.connection_type.member_types
def test_improper_to_json_loop(self, typed_ethane, are_equivalent_atoms):
for improper in typed_ethane.impropers:
improper_json = improper.json()
improper_copy = Improper.parse_raw(improper_json)
for member1, member2 in zip(improper_copy.connection_members,
improper.connection_members):
assert are_equivalent_atoms(member1, member2)
assert improper_copy.improper_type == improper.improper_type
def test_add_equivalent_connections(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
atom3 = Atom(name="AtomC")
atom4 = Atom(name="AtomD")
improper = Improper(connection_members=[atom1, atom2, atom3, atom4])
improper_eq = Improper(connection_members=[atom1, atom3, atom2, atom4])
improper_not_eq = Improper(
connection_members=[atom2, atom3, atom1, atom4])
top = Topology()
top.add_connection(improper)
top.add_connection(improper_eq)
assert top.n_impropers == 1
top.add_connection(improper_not_eq)
assert top.n_impropers == 2
def test_improper_fake_impropertype(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
with pytest.raises(GMSOError):
Improper(connection_members=[site1, site2, site3, site4],
connection_type='Fake impropertype')
def test_improper_fake_impropertype(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Improper(connection_members=[atom1, atom2, atom3, atom4],
connection_type='Fake impropertype')
def test_improper_eq(self):
atom1 = Atom(name="atom1", position=[0, 0, 0])
atom2 = Atom(name="atom2", position=[1, 0, 0])
atom3 = Atom(name="atom3", position=[1, 1, 0])
atom4 = Atom(name="atom4", position=[1, 1, 1])
ref_improper = Improper(
connection_members=[atom1, atom2, atom3, atom4], )
same_improper = Improper(
connection_members=[atom1, atom2, atom3, atom4], )
diff_improper = Improper(
connection_members=[atom1, atom2, atom3, atom4], )
assert ref_improper != same_improper
assert ref_improper != diff_improper
def test_improper_nonparametrized(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
connect = Improper(connection_members=[atom1, atom2, atom3, atom4])
assert connect.connection_type is None
def test_improper_fake_impropertype(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Improper(
connection_members=[atom1, atom2, atom3, atom4],
connection_type="Fake impropertype",
)
def test_improper_eq(self):
site1 = Site(name='site1', position=[0, 0, 0])
site2 = Site(name='site2', position=[1, 0, 0])
site3 = Site(name='site3', position=[1, 1, 0])
site4 = Site(name='site4', position=[1, 1, 1])
ref_improper = Improper(
connection_members=[site1, site2, site3, site4],
)
same_improper = Improper(
connection_members=[site1, site2, site3, site4],
)
diff_improper = Improper(
connection_members=[site1, site2, site3, site4],
)
assert ref_improper != same_improper
assert ref_improper != diff_improper
def test_equivalent_members_set(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
atom3 = Atom(name="AtomC")
atom4 = Atom(name="AtomD")
improper = Improper(connection_members=[atom1, atom2, atom3, atom4])
improper_eq = Improper(connection_members=[atom1, atom3, atom2, atom4])
improper_not_eq = Improper(
connection_members=[atom2, atom3, atom1, atom4])
assert (tuple(improper_eq.connection_members)
in improper.equivalent_members())
assert (tuple(improper.connection_members)
in improper_eq.equivalent_members())
assert not (tuple(improper.connection_members)
in improper_not_eq.equivalent_members())
def test_improper_constituent_types(self):
site1 = Site(name='site1', position=[0,0,0], atom_type=AtomType(name='A'))
site2 = Site(name='site2', position=[1,0,0], atom_type=AtomType(name='B'))
site3 = Site(name='site3', position=[1,1,0], atom_type=AtomType(name='C'))
site4 = Site(name='site4', position=[1,1,4], atom_type=AtomType(name='D'))
imptype = ImproperType(member_types=[site1.atom_type.name,
site2.atom_type.name,
site3.atom_type.name,
site4.atom_type.name])
imp = Improper(connection_members=[site1, site2, site3, site4],
connection_type=imptype)
assert 'A' in imp.connection_type.member_types
assert 'B' in imp.connection_type.member_types
assert 'C' in imp.connection_type.member_types
assert 'D' in imp.connection_type.member_types
def test_improper_parametrized(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
improper_type = ImproperType()
connect = Improper(connection_members=[atom1, atom2, atom3, atom4],
improper_type=improper_type,
name='improper_name')
assert len(connect.connection_members) == 4
assert connect.connection_type is not None
assert connect.improper_type is not None
assert connect.name == 'improper_name'
def test_improper_nonparametrized(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
assert site1.n_connections == 0
assert site2.n_connections == 0
assert site3.n_connections == 0
assert site4.n_connections == 0
connect = Improper(connection_members=[site1, site2, site3, site4])
assert site1.n_connections == 1
assert site2.n_connections == 1
assert site3.n_connections == 1
assert site4.n_connections == 1
assert connect.connection_type is None
def test_improper_impropertype_update(self):
top = Topology()
atype1 = AtomType(expression='sigma + epsilon')
atype2 = AtomType(expression='sigma * epsilon')
site1 = Site('a', atom_type=atype1)
site2 = Site('b', atom_type=atype2)
site3 = Site('c', atom_type=atype2)
site4 = Site('d', atom_type=atype1)
atype = ImproperType()
improper = Improper(connection_members=[site1, site2, site3, site4], connection_type=atype)
top.add_site(site1)
top.add_site(site2)
top.add_site(site3)
top.add_site(site4)
top.add_connection(improper)
assert top.n_impropers == 1
assert len(top.improper_types) == 1
assert len(top.improper_type_expressions) == 1
assert len(top.atom_type_expressions) == 2
def test_improper_impropertype_update(self):
top = Topology()
atype1 = AtomType(expression='sigma + epsilon*r')
atype2 = AtomType(expression='sigma * epsilon*r')
atom1 = Atom(name='a', atom_type=atype1)
atom2 = Atom(name='b', atom_type=atype2)
atom3 = Atom(name='c', atom_type=atype2)
atom4 = Atom(name='d', atom_type=atype1)
atype = ImproperType()
improper = Improper(connection_members=[atom1, atom2, atom3, atom4],
improper_type=atype)
top.add_site(atom1)
top.add_site(atom2)
top.add_site(atom3)
top.add_site(atom4)
top.add_connection(improper)
assert top.n_impropers == 1
assert len(top.improper_types) == 1
assert len(top.improper_type_expressions) == 1
assert len(top.atom_type_expressions) == 2
def test_improper_constituent_types(self):
atom1 = Atom(name='atom1',
position=[0, 0, 0],
atom_type=AtomType(name='A'))
atom2 = Atom(name='atom2',
position=[1, 0, 0],
atom_type=AtomType(name='B'))
atom3 = Atom(name='atom3',
position=[1, 1, 0],
atom_type=AtomType(name='C'))
atom4 = Atom(name='atom4',
position=[1, 1, 4],
atom_type=AtomType(name='D'))
imptype = ImproperType(member_types=[
atom1.atom_type.name, atom2.atom_type.name, atom3.atom_type.name,
atom4.atom_type.name
])
imp = Improper(connection_members=[atom1, atom2, atom3, atom4], )
imp.improper_type = imp.connection_type = imptype
assert 'A' in imp.connection_type.member_types
assert 'B' in imp.connection_type.member_types
assert 'C' in imp.connection_type.member_types
assert 'D' in imp.connection_type.member_types
def test_improper_parametrized(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
assert site1.n_connections == 0
assert site2.n_connections == 0
assert site3.n_connections == 0
assert site4.n_connections == 0
improper_type = ImproperType()
connect = Improper(connection_members=[site1, site2, site3, site4],
connection_type=improper_type,
name='improper_name')
assert site1.n_connections == 1
assert site2.n_connections == 1
assert site3.n_connections == 1
assert site4.n_connections == 1
assert len(connect.connection_members) == 4
assert connect.connection_type is not None
assert connect.name == 'improper_name'