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(Site())
top.name = None
compound = to_mbuild(top)
assert compound.name == 'Compound'
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_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_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_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_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_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_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_with_1000_atom_types(self):
top = Topology()
for i in range(1000):
site = Site()
atom_type = AtomType()
site.atom_type = atom_type
top.add_site(site, update_types=False)
top.update_topology()
assert len(top.atom_types) == 1
assert top.n_sites == 1000
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_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_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_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_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_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_topology_atom_type_changes(self):
top = Topology()
for i in range(100):
site = Site(name='site{}'.format(i))
atom_type = AtomType(name='atom_type{}'.format(i % 10))
site.atom_type = atom_type
top.add_site(site, update_types=False)
top.update_topology()
assert len(top.atom_types) == 10
top.sites[0].atom_type.name = 'atom_type_changed'
assert id(top.sites[0].atom_type) == id(top.sites[10].atom_type)
assert top.sites[10].atom_type.name == 'atom_type_changed'
assert top.is_typed()
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 _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_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_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_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_add_site_parent(self):
top = Topology()
subtop = SubTopology()
site1 = Atom(position=u.nm * np.zeros(3))
site2 = Atom(position=u.nm * np.ones(3))
top.add_subtopology(subtop)
assert top.n_sites == 0
assert subtop.n_sites == 0
subtop.add_site(site1)
assert top.n_sites == 1
assert subtop.n_sites == 1
top.add_site(site2)
assert top.n_sites == 2
assert subtop.n_sites == 1
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 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_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_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
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 read_xyz(filename):
"""Reader for xyz file format.
Read in an xyz file at the given path and return a Topology object.
Parameters
----------
filename : str
Path to .xyz file that need to be read.
Return
------
top : topology.Topology
Topology object
"""
top = Topology()
with open(filename, "r") as xyz_file:
n_atoms = int(xyz_file.readline())
xyz_file.readline()
coords = np.zeros(shape=(n_atoms, 3)) * u.nanometer
for row, _ in enumerate(coords):
line = xyz_file.readline().split()
if not line:
msg = (
"Incorrect number of lines in input file. Based on the "
"number in the first line of the file, {} rows of atoms "
"were expected, but at least one fewer was found."
)
raise ValueError(msg.format(n_atoms))
tmp = np.array(line[1:4], dtype=np.float) * u.angstrom
coords[row] = tmp.in_units(u.nanometer)
site = Atom(name=line[0], position=coords[row])
top.add_site(site)
top.update_topology()
# Verify we have read the last line by ensuring the next line in blank
line = xyz_file.readline().split()
if line:
msg = (
"Incorrect number of lines in input file. Based on the "
"number in the first line of the file, {} rows of atoms "
"were expected, but at least one more was found."
)
raise ValueError(msg.format(n_atoms))
return top
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
