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_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_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_add_connection_non_member(self):
site1, site2, site3 = (Site(), Site(), Site())
bond1, bond2, bond3 = (Bond([site1, site2]), Bond([site2, site3]),
Bond([site1, site3]))
assert site1.n_connections == site2.n_connections == site3.n_connections == 2
with pytest.raises(GMSOError):
site3.add_connection(bond1)
site2.add_connection(bond3)
site1.add_connection(bond2)
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_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_add_connection_redundant(self):
site1, site2, site3 = (Site(), Site(), Site())
bond1, bond2, bond3 = (Bond([site1, site2]), Bond([site2, site3]),
Bond([site1, site3]))
assert site1.n_connections == site2.n_connections == site3.n_connections == 2
site1.add_connection(bond1)
site1.add_connection(bond3)
site2.add_connection(bond1)
site2.add_connection(bond2)
site3.add_connection(bond3)
site3.add_connection(bond2)
assert site1.n_connections == site2.n_connections == site3.n_connections == 2
def test_bond_eq(self):
site1 = Site(name='site1', position=[0, 0, 0])
site2 = Site(name='site2', position=[1, 1, 1])
ref_connection = Bond(connection_members=[site1, site2], )
same_connection = Bond(connection_members=[site1, site2], )
diff_connection = Bond(connection_members=[site1, site2], )
assert ref_connection != same_connection
assert ref_connection != diff_connection
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 from_networkx(graph):
"""Convert a networkx.Graph to a gmso.Topology
Creates a topology from the graph where each node is a site and each
edge becomes a connection.
Parameters
----------
graph : networkX.Graph
networkx.Graph instance that need to be converted
Returns
-------
top : gmso.Topology
Notes
-----
- While a lot of information is lost from converting to a graph object
(e.g. metadata, mixing rules, etc.), the graph representation is a
useful way to manipulate and extract connectivity information from
Topology objects.
- The edge has a `connection` attribute, which stores the Bond
object it was created from
"""
if not isinstance(graph, nx.Graph):
raise TypeError(
"Type mismatch, graph object is expected to be "
"an instance of networkx.Graph, was provided: {}".format(
type(graph)))
top = Topology()
node_mapping = dict()
for node in graph.nodes:
if not isinstance(node, Site):
raise TypeError("Nodes must be instances of gmso.abc.Site")
else:
top.add_site(node)
for edge in graph.edges:
try:
conn = graph.get_edge_data(*edge)["connection"]
if (isinstance(conn, Connection)
and set(edge).issubset(set(conn.connection_members))):
top.add_connection(conn)
except KeyError:
conn = Bond(connection_members=edge)
top.add_connection(conn)
warnings.simplefilter('once', UserWarning)
for node in graph.nodes:
try:
graph.nodes[node]['angles'] or graph.nodes[node]['dihedrals']
warnings.warn("Angle and Dihedral information is not converted.")
except KeyError:
pass
return top
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 ethane(self):
mytop = Topology()
c1 = Atom(name='C1')
h11 = Atom(name='H11')
h12 = Atom(name='H12')
h13 = Atom(name='H13')
c2 = Atom(name='C2')
h21 = Atom(name='H21')
h22 = Atom(name='H22')
h23 = Atom(name='H23')
c1h11 = Bond(connection_members=[c1, h11])
c1h12 = Bond(connection_members=[c1, h12])
c1h13 = Bond(connection_members=[c1, h13])
c2h21 = Bond(connection_members=[c2, h21])
c2h22 = Bond(connection_members=[c2, h22])
c2h23 = Bond(connection_members=[c2, h23])
c1c2 = Bond(connection_members=[c1, c2])
mytop.add_connection(c1h11, update_types=False)
mytop.add_connection(c1h12, update_types=False)
mytop.add_connection(c1h13, update_types=False)
mytop.add_connection(c2h21, update_types=False)
mytop.add_connection(c2h22, update_types=False)
mytop.add_connection(c2h23, update_types=False)
mytop.add_connection(c1c2, update_types=False)
mytop.update_topology()
return mytop
def test_bond_to_json_loop(self, typed_ethane, are_equivalent_atoms):
for bond in typed_ethane.bonds:
bond_json = bond.json()
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_add_connection(self):
top = Topology()
site1 = Site(name='site1')
site2 = Site(name='site2')
connect = Bond(connection_members=[site1, site2])
top.add_connection(connect)
top.add_site(site1)
top.add_site(site2)
assert len(top.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_nonparametrized(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
assert site1.n_connections == 0
assert site2.n_connections == 0
connect = Bond(connection_members=[site1, site2])
assert site1.n_connections == 1
assert site2.n_connections == 1
assert connect.connection_type is None
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_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_bond_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'))
bondtype = BondType(
member_types=[site1.atom_type.name, site2.atom_type.name])
bond = Bond(connection_members=[site1, site2],
connection_type=bondtype)
assert 'A' in bond.connection_type.member_types
assert 'B' in bond.connection_type.member_types
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 methane(self):
mytop = Topology()
c = Atom(name='c')
h1 = Atom(name='h1')
h2 = Atom(name='h2')
h3 = Atom(name='h3')
h4 = Atom(name='h4')
ch1 = Bond(connection_members=[c, h1])
ch2 = Bond(connection_members=[c, h2])
ch3 = Bond(connection_members=[c, h3])
ch4 = Bond(connection_members=[c, h4])
mytop.add_site(c, update_types=False)
mytop.add_site(h1, update_types=False)
mytop.add_site(h2, update_types=False)
mytop.add_site(h3, update_types=False)
mytop.add_site(h4, update_types=False)
mytop.add_connection(ch1, update_types=False)
mytop.add_connection(ch2, update_types=False)
mytop.add_connection(ch3, update_types=False)
mytop.add_connection(ch4, update_types=False)
mytop.update_topology()
return mytop
def test_add_untyped_bond_update(self):
site1 = Site(atom_type=None)
site2 = Site(atom_type=None)
bond = Bond(connection_members=[site1, site2], connection_type=None)
top = Topology()
assert len(top.bond_types) == 0
top.add_connection(bond, update_types=False)
assert len(top.bond_types) == 0
top = Topology()
assert len(top.bond_types) == 0
top.add_connection(bond, update_types=True)
assert len(top.bond_types) == 0
def test_top_update(self):
top = Topology()
top.update_topology()
assert top.n_sites == 0
assert len(top.atom_types) == 0
assert len(top.atom_type_expressions) == 0
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
atomtype = AtomType()
site1 = Site(name='site1', atom_type=atomtype)
top.add_site(site1)
site2 = Site(name='site2', atom_type=atomtype)
top.add_site(site2)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
ctype = BondType()
connection_12 = Bond(connection_members=[site1, site2],
connection_type=ctype)
top.add_connection(connection_12)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
site1.atom_type = AtomType(expression='sigma*epsilon')
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
top.update_atom_types()
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
def test_add_typed_bond_update(self):
atom1 = Atom(atom_type=None)
atom2 = Atom(atom_type=None)
bond = Bond(connection_members=[atom1, atom2], bond_type=BondType())
top = Topology()
top.add_site(atom1)
top.add_site(atom2)
top.add_connection(bond, update_types=False)
assert len(top.connection_types) == 0
top = Topology()
top.add_connection(bond, update_types=True)
assert len(top.bond_types) == 1
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_top_update(self):
top = Topology()
top.update_topology()
assert top.n_sites == 0
assert len(top.atom_types) == 0
assert len(top.atom_type_expressions) == 0
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
atomtype = AtomType()
atom1 = Atom(name='atom1', atom_type=atomtype)
top.add_site(atom1)
atom2 = Atom(name='atom2', atom_type=atomtype)
top.add_site(atom2)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
ctype = BondType()
connection_12 = Bond(connection_members=[atom1, atom2],
bond_type=ctype)
top.add_connection(connection_12)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
atom1.atom_type = AtomType(expression='sigma*epsilon*r')
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
top.update_atom_types()
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
def test_bond_bondtype_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)
btype = BondType()
bond = Bond(connection_members=[site1, site2], connection_type=btype)
top.add_site(site1)
top.add_site(site2)
top.add_connection(bond)
assert top.n_bonds == 1
assert len(top.bond_types) == 1
assert len(top.bond_type_expressions) == 1
def test_bond_bondtype_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)
btype = BondType()
bond = Bond(connection_members=[atom1, atom2], bond_type=btype)
top.add_site(atom1)
top.add_site(atom2)
top.add_connection(bond)
assert top.n_bonds == 1
assert len(top.bond_types) == 1
assert len(top.bond_type_expressions) == 1
