def test_change_comb_rule(self):
top = Topology()
assert top.combining_rule == 'lorentz'
top.combining_rule = 'geometric'
assert top.combining_rule == 'geometric'
with pytest.raises(GMSOError):
top.combining_rule = 'kong'
def test_add_site(self):
top = Topology()
site = Atom(name="site")
assert top.n_sites == 0
top.add_site(site)
assert top.n_sites == 1
def test_add_subtopology(self):
top = Topology()
subtop = SubTopology()
assert top.n_subtops == 0
top.add_subtopology(subtop)
assert top.n_subtops == 1
def test_change_comb_rule(self):
top = Topology()
assert top.combining_rule == "lorentz"
top.combining_rule = "geometric"
assert top.combining_rule == "geometric"
with pytest.raises(GMSOError):
top.combining_rule = "kong"
def test_add_site(self):
top = Topology()
site = Site(name='site')
assert top.n_sites == 0
top.add_site(site)
assert top.n_sites == 1
def test_to_mbuild_name_none(self):
top = Top()
top.add_site(Atom(position=[0.0, 0.0, 0.0]))
top.name = None
compound = to_mbuild(top)
assert compound.name == "Compound"
def test_to_mbuild_name_none(self):
top = Top()
top.add_site(Site())
top.name = None
compound = to_mbuild(top)
assert compound.name == 'Compound'
def test_add_box(self):
top = Topology()
box = Box(2 * u.nm * np.ones(3))
assert top.box is None
top.box = box
assert top.box is not None
assert allclose(top.box.lengths, u.nm * 2 * np.ones(3))
def test_parametrization_setter(self):
top = Topology()
assert top.typed == False
assert top.is_typed() == False
top.typed = True
assert top.typed == True
assert top.is_typed() == False
def test_parametrization(self):
top = Topology()
assert top.typed == False
top.add_site(Site(atom_type=AtomType()))
assert top.typed == True
assert top.is_typed() == True
assert top.typed == True
def test_add_box(self):
top = Topology()
box = Box(2 * u.nm * np.ones(3))
assert top.box is None
top.box = box
assert top.box is not None
assert_allclose_units(
top.box.lengths, u.nm * 2 * np.ones(3), rtol=1e-5, atol=1e-8
)
def test_positions_dtype(self):
top = Topology()
site1 = Site(name='site1')
top.add_site(site1)
assert set([type(site.position) for site in top.sites]) == {u.unyt_array}
assert set([site.position.units for site in top.sites]) == {u.nm}
assert top.positions.dtype == float
assert top.positions.units == u.nm
assert isinstance(top.positions, u.unyt_array)
def test_positions_dtype(self):
top = Topology()
atom1 = Atom(name='atom1', position=[0.0, 0.0, 0.0])
top.add_site(atom1)
assert set([type(site.position)
for site in top.sites]) == {u.unyt_array}
assert set([site.position.units for site in top.sites]) == {u.nm}
assert top.positions.dtype == float
assert top.positions.units == u.nm
assert isinstance(top.positions, u.unyt_array)
def test_3_layer_top(self):
top_top = Top()
mid_top = SubTop()
site = Site()
top_top.add_subtopology(mid_top)
mid_top.add_site(site)
compound = to_mbuild(top_top)
assert len(compound.children) == 1
assert compound.children[0].n_particles == 1
assert compound.n_particles == 1
def _topology(sites=1):
top = Topology()
top.box = Box(lengths=[1, 1, 1])
H = Hydrogen
site1 = Site(
name='site1',
element=H,
atom_type=AtomType(name="at1", mass=H.mass),
)
for i in range(sites):
top.add_site(site1)
return top
def test_atom_type_with_topology_and_site_change_properties(self):
site1 = Site()
site2 = Site()
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_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_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 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_atom_type_with_topology_and_site(self):
site1 = Site()
site2 = Site()
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)
assert id(site1.atom_type) == id(site2.atom_type)
assert site1.atom_type is not None
assert len(top.atom_types) == 1
assert site1.atom_type.topology == top
assert site2.atom_type.topology == top
def test_add_typed_bond_update(self):
site1 = Site(atom_type=None)
site2 = Site(atom_type=None)
bond = Bond(connection_members=[site1, site2],
connection_type=BondType())
top = Topology()
top.add_site(site1)
top.add_site(site2)
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 to_mbuild(topology):
""" Convert a gmso.Topology to mbuild.Compound
Parameters
----------
topology : gmso.Topology
topology instance that need to be converted
Returns
-------
compound : mbuild.Compound
"""
msg = ("Argument topology is not a Topology")
assert isinstance(topology, Topology), msg
compound = mb.Compound()
if topology.name is Topology().name:
compound.name = 'Compound'
else:
compound.name = topology.name
particle_map = dict()
for site in topology.sites:
particle = mb.Compound(name=site.name, pos=site.position[0])
particle_map[site] = particle
compound.add(particle)
for connect in topology.connections:
if isinstance(connect, Bond):
compound.add_bond((particle_map[connect.connection_members[0]],
particle_map[connect.connection_members[1]]))
return compound
def test_subtop_assign_parent(self):
subtop = SubTopology()
top = Topology()
subtop.parent = top
assert subtop.parent is not None
def test_atomtype_update(self):
top = Topology()
assert top.n_sites == 0
assert top.n_bonds == 0
assert top.n_connections == 0
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)
top.add_site(atom1)
top.add_site(atom2)
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
def test_atomtype_update(self):
top = Topology()
assert top.n_sites == 0
assert top.n_bonds == 0
assert top.n_connections == 0
atype1 = AtomType(expression='sigma + epsilon')
atype2 = AtomType(expression='sigma * epsilon')
site1 = Site('a', atom_type=atype1)
site2 = Site('b', atom_type=atype2)
top.add_site(site1)
top.add_site(site2)
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
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_subtop_add_site_parent(self):
top = Topology()
subtop = SubTopology(parent=top)
site = Atom()
subtop.add_site(site)
assert subtop.n_sites == 1
assert subtop.parent.n_sites == 1
assert top.n_sites == 1
def test_add_untyped_site_update(self):
untyped_site = Site(atom_type=None)
top = Topology()
assert len(top.atom_types) == 0
top.add_site(untyped_site, update_types=False)
assert len(top.atom_types) == 0
top = Topology()
assert len(top.atom_types) == 0
top.add_site(untyped_site, update_types=True)
assert len(top.atom_types) == 0
def test_add_typed_site_update(self):
typed_site = Site(atom_type=AtomType())
top = Topology()
assert len(top.atom_types) == 0
top.add_site(typed_site, update_types=False)
assert len(top.atom_types) == 0
top = Topology()
assert len(top.atom_types) == 0
top.add_site(typed_site, update_types=True)
assert len(top.atom_types) == 1
def test_subtop_setters(self):
subtop = SubTopology()
assert subtop.name == 'Sub-Topology'
assert subtop.parent is None
assert subtop.n_sites == 0
subtop.name = 'NewSubTopology'
assert subtop.name == 'NewSubTopology'
newparent = Topology()
subtop.parent = newparent
assert subtop.parent == newparent
