def test_dihedral_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"))
dihtype = DihedralType(member_types=[
atom1.atom_type.name,
atom2.atom_type.name,
atom3.atom_type.name,
atom4.atom_type.name,
])
dih = Dihedral(connection_members=[atom1, atom2, atom3, atom4], )
dih.dihedral_type = dihtype
assert "A" in dih.connection_type.member_types
assert "B" in dih.connection_type.member_types
assert "C" in dih.connection_type.member_types
assert "D" in dih.connection_type.member_types
def test_square(self):
mytop = Topology()
s1 = Atom(name="1")
s2 = Atom(name="2")
s3 = Atom(name="3")
s4 = Atom(name="4")
c12 = Bond(connection_members=[s1, s2])
c23 = Bond(connection_members=[s2, s3])
c34 = Bond(connection_members=[s3, s4])
c41 = Bond(connection_members=[s4, s1])
for site in [s1, s2, s3, s4]:
mytop.add_site(site, update_types=False)
for conn in [c12, c23, c34, c41]:
mytop.add_connection(conn, update_types=False)
assert mytop.n_bonds == 4
assert mytop.n_angles == 0
assert mytop.n_dihedrals == 0
assert mytop.n_impropers == 0
mytop.identify_connections()
assert mytop.n_bonds == 4
assert mytop.n_angles == 4
assert mytop.n_dihedrals == 4
assert mytop.n_impropers == 0
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_angle_fake_angletype(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
with pytest.raises(ValidationError):
Angle(connection_members=[atom1, atom2, atom3],
angle_type='Fake angletype')
def test_dihedral_fake(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Dihedral(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_angle_nonparametrized(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
connect = Angle(connection_members=[atom1, atom2, atom3])
assert connect.angle_type is None
def test_dihedral_fake(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Dihedral(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_bond_nonparametrized(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
connect = Bond(connection_members=[atom1, atom2])
assert connect.bond_type is None
def test_square_with_bridge(self):
mytop = Topology()
s1 = Atom(name="1")
s2 = Atom(name="2")
s3 = Atom(name="3")
s4 = Atom(name="4")
c12 = Bond(connection_members=[s1, s2])
c23 = Bond(connection_members=[s2, s3])
c34 = Bond(connection_members=[s3, s4])
c41 = Bond(connection_members=[s4, s1])
c24 = Bond(connection_members=[s2, s4])
mytop.add_site(s1, update_types=False)
mytop.add_site(s2, update_types=False)
mytop.add_site(s3, update_types=False)
mytop.add_site(s4, update_types=False)
mytop.add_connection(c12, update_types=False)
mytop.add_connection(c23, update_types=False)
mytop.add_connection(c34, update_types=False)
mytop.add_connection(c41, update_types=False)
mytop.add_connection(c24, update_types=False)
assert mytop.n_bonds == 5
assert mytop.n_angles == 0
assert mytop.n_dihedrals == 0
assert mytop.n_impropers == 0
mytop.identify_connections()
assert mytop.n_bonds == 5
assert mytop.n_angles == 8
assert mytop.n_dihedrals == 6
assert mytop.n_impropers == 2
def test_dihedral_fake_dihedraltype(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Dihedral(connection_members=[atom1, atom2, atom3, atom4],
dihedral_type='Fake dihedraltype')
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_dihedral_nonparametrized(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom1")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
connect = Dihedral(connection_members=[atom1, atom2, atom3, atom4])
assert connect.connection_type is None
def test_equivalent_members_set(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
bond = Bond(connection_members=[atom1, atom2])
bond_eq = Bond(connection_members=[atom2, atom1])
assert (tuple(bond_eq.connection_members) in bond.equivalent_members())
assert (tuple(bond.connection_members) in bond_eq.equivalent_members())
def test_equivalence(self):
ref = Atom(name="atom", position=u.nm * np.zeros(3))
same_atom = Atom(name="atom", position=u.nm * np.zeros(3))
other_pos = Atom(name="atom", position=u.nm * np.ones(3))
other_name = Atom(name="atom", position=u.nm * np.ones(3))
# Two sites are never equivalent
assert ref != same_atom
assert ref != other_pos
assert ref != other_name
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_angle_fake_angletype(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
with pytest.raises(ValidationError):
Angle(
connection_members=[atom1, atom2, atom3],
angle_type="Fake angletype",
)
def test_dihedral_fake_dihedraltype(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Dihedral(
connection_members=[atom1, atom2, atom3, atom4],
dihedral_type="Fake dihedraltype",
)
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_add_equivalent_connections(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
bond = Bond(connection_members=[atom1, atom2])
bond_eq = Bond(connection_members=[atom2, atom1])
top = Topology()
top.add_connection(bond)
top.add_connection(bond_eq)
assert top.n_bonds == 1
def test_add_duplicate_connected_atom(self):
top = Topology()
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
bond = Bond(connection_members=[atom1, atom2])
bond_eq = Bond(connection_members=[atom1, atom2])
top.add_connection(bond)
top.add_connection(bond_eq)
top.update_topology()
assert top.n_connections == 1
def test_add_connection(self):
top = Topology()
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
connect = Bond(connection_members=[atom1, atom2])
top.add_connection(connect)
top.add_site(atom1)
top.add_site(atom2)
assert len(top.connections) == 1
def test_bond_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'))
bondtype = BondType(
member_types=[atom1.atom_type.name, atom2.atom_type.name])
bond = Bond(connection_members=[atom1, atom2], bond_type=bondtype)
assert 'A' in bond.connection_type.member_types
assert 'B' in bond.connection_type.member_types
def test_bond_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"))
bondtype = BondType(
member_types=[atom1.atom_type.name, atom2.atom_type.name])
bond = Bond(connection_members=[atom1, atom2], bond_type=bondtype)
assert "A" in bond.connection_type.member_types
assert "B" in bond.connection_type.member_types
def test_bond_eq(self):
atom1 = Atom(name='atom1', position=[0, 0, 0])
atom2 = Atom(name='atom2', position=[1, 1, 1])
ref_connection = Bond(connection_members=[atom1, atom2], )
same_connection = Bond(connection_members=[atom1, atom2], )
diff_connection = Bond(connection_members=[atom1, atom2], )
assert ref_connection != same_connection
assert ref_connection != diff_connection
def test_bond_parametrized(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
bond_type = BondType()
connect = Bond(connection_members=[atom1, atom2],
bond_type=bond_type,
name='bond_name')
assert len(connect.connection_members) == 2
assert connect.connection_type is not None
assert connect.name == 'bond_name'
def test_atom_type_with_topology_and_site_change_properties(self):
site1 = Atom()
site2 = Atom()
top = Topology()
atom_type1 = AtomType()
atom_type2 = AtomType()
site1.atom_type = atom_type1
site2.atom_type = atom_type2
top.add_site(site1)
top.add_site(site2)
site1.atom_type.mass = 250
assert site2.atom_type.mass == 250
assert top.atom_types[0].mass == 250
def test_angle_eq(self):
atom1 = Atom(name='atom1', position=[0, 0, 0])
atom2 = Atom(name='atom2', position=[1, 1, 1])
atom3 = Atom(name='atom3', position=[1, 1, 1])
ref_angle = Angle(connection_members=[atom1, atom2, atom3], )
same_angle = Angle(connection_members=[atom1, atom2, atom3], )
diff_angle = Angle(connection_members=[atom3, atom2, atom1], )
assert ref_angle != same_angle
assert ref_angle != diff_angle
def test_equivalent_members_set(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
atom3 = Atom(name="AtomC")
angle = Angle(connection_members=[atom1, atom2, atom3])
angle_eq = Angle(connection_members=[atom3, atom2, atom1])
angle_not_eq = Angle(connection_members=[atom1, atom3, atom2])
assert tuple(angle_eq.connection_members) in angle.equivalent_members()
assert tuple(angle.connection_members) in angle_eq.equivalent_members()
assert not (tuple(angle.connection_members)
in angle_not_eq.equivalent_members())
