def test_subtop_add_site(self):
subtop = SubTopology()
site = Atom()
subtop.add_site(site)
assert subtop.n_sites == 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_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 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 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