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_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 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_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_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_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_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_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_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_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
def test_angle_angletype_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)
atype = AngleType()
angle = Angle(connection_members=[site1, site2, site3], connection_type=atype, name='angle_name')
top.add_site(site1)
top.add_site(site2)
top.add_site(site3)
top.add_connection(angle)
assert top.n_angles == 1
assert len(top.angle_types) == 1
assert len(top.angle_type_expressions) == 1
assert len(top.atom_type_expressions) == 2
def test_dihedral_dihedraltype_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 = DihedralType()
dihedral = Dihedral(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(dihedral)
assert top.n_dihedrals == 1
assert len(top.dihedral_types) == 1
assert len(top.dihedral_type_expressions) == 1
assert len(top.atom_type_expressions) == 2
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_angle_angletype_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)
atype = AngleType()
angle = Angle(connection_members=[atom1, atom2, atom3],
angle_type=atype,
name='angle_name')
top.add_site(atom1)
top.add_site(atom2)
top.add_site(atom3)
top.add_connection(angle)
assert top.n_angles == 1
assert len(top.angle_types) == 1
assert len(top.angle_type_expressions) == 1
assert len(top.atom_type_expressions) == 2
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_dihedraltype_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 = DihedralType()
dihedral = Dihedral(connection_members=[atom1, atom2, atom3, atom4],
dihedral_type=atype)
top.add_site(atom1)
top.add_site(atom2)
top.add_site(atom3)
top.add_site(atom4)
top.add_connection(dihedral)
assert top.n_dihedrals == 1
assert len(top.dihedral_types) == 1
assert len(top.dihedral_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 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_equivalent_connections(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])
top = Topology()
top.add_connection(angle)
top.add_connection(angle_eq)
assert top.n_angles == 1
top.add_connection(angle_not_eq)
assert top.n_angles == 2
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_add_equivalent_connections(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
atom3 = Atom(name="AtomC")
atom4 = Atom(name="AtomD")
dihedral = Dihedral(connection_members=[atom1, atom2, atom3, atom4])
dihedral_eq = Dihedral(connection_members=[atom4, atom3, atom2, atom1])
dihedral_not_eq = Dihedral(
connection_members=[atom4, atom2, atom3, atom1])
top = Topology()
top.add_connection(dihedral)
top.add_connection(dihedral_eq)
assert top.n_dihedrals == 1
top.add_connection(dihedral_not_eq)
assert top.n_dihedrals == 2
def from_mbuild(compound, box=None, search_method=element_by_symbol):
"""Convert an mbuild.Compound to a gmso.Topology
This conversion makes the following assumptions about the inputted
`Compound`:
* All positional and box dimension values in compound are in nanometers
* If the `Compound` has 4 or more levels of hierarchy, these are\
compressed to 3 levels of hierarchy in the resulting `Topology`. The\
top level `Compound` becomes the `Topology`, the second level\
Compounds become `SubTopologies`, and each particle becomes a `Site`,\
which are added to their corresponding `SubTopologies`.\
* Furthermore, `Sites` that do not belong to a sub-`Compound` are\
added to a single-`Site` `SubTopology`.
* The box dimension are extracted from `compound.periodicity`. If the\
`compound.periodicity` is `None`, the box lengths are the lengths of\
the bounding box + a 0.5 nm buffer.
* Only `Bonds` are added for each bond in the `Compound`. If `Angles`\
and `Dihedrals` are desired in the resulting `Topology`, they must be\
added separately from this function.
Parameters
----------
compound : mbuild.Compound
mbuild.Compound instance that need to be converted
box : mbuild.Box, optional, default=None
Box information to be loaded to a gmso.Topology
search_method : function, optional, default=element_by_symbol
Searching method used to assign element from periodic table to
particle site.
The information specified in the `search_method` argument is extracted
from each `Particle`'s `name` attribute.
Valid functions are element_by_symbol, element_by_name,
element_by_atomic_number, and element_by_mass, which can be imported
from `gmso.core.element'
Returns
-------
top : gmso.Topology
"""
msg = ("Argument compound is not an mbuild.Compound")
assert isinstance(compound, mb.Compound), msg
top = Topology()
top.typed = False
# Keep the name if it is not the default mBuild Compound name
if compound.name != mb.Compound().name:
top.name = compound.name
site_map = dict()
for child in compound.children:
if len(child.children) == 0:
continue
else:
subtop = SubTopology(name=child.name)
top.add_subtopology(subtop)
for particle in child.particles():
pos = particle.xyz[0] * u.nanometer
ele = search_method(particle.name)
site = Site(name=particle.name, position=pos, element=ele)
site_map[particle] = site
subtop.add_site(site)
top.update_topology()
for particle in compound.particles():
already_added_site = site_map.get(particle, None)
if already_added_site:
continue
pos = particle.xyz[0] * u.nanometer
ele = search_method(particle.name)
site = Site(name=particle.name, position=pos, element=ele)
site_map[particle] = site
# If the top has subtopologies, then place this particle into
# a single-site subtopology -- ensures that all sites are in the
# same level of hierarchy.
if len(top.subtops) > 0:
subtop = SubTopology(name=particle.name)
top.add_subtopology(subtop)
subtop.add_site(site)
else:
top.add_site(site)
for b1, b2 in compound.bonds():
new_bond = Bond(connection_members=[site_map[b1], site_map[b2]],
connection_type=None)
top.add_connection(new_bond)
top.update_topology()
if box:
top.box = from_mbuild_box(box)
# Assumes 2-D systems are not supported in mBuild
# if compound.periodicity is None and not box:
else:
if np.allclose(compound.periodicity, np.zeros(3)):
box = from_mbuild_box(compound.boundingbox)
if box:
box.lengths += [0.5, 0.5, 0.5] * u.nm
top.box = box
else:
top.box = Box(lengths=compound.periodicity)
return 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_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
