def test_nested_compound(self):
num_chidren = 100
num_grand_children = 100
num_ports = 2
ancestor = mb.Compound(name="Ancestor")
for i in range(num_chidren):
this_child = mb.Compound(name="Child{}".format(i + 1))
ancestor.add(this_child, label="Ancestor'sChild{}".format(i + 1))
for j in range(num_ports):
port1 = mb.Port(anchor=this_child)
this_child.add(port1, label="port{}".format(j + 1))
for k in range(num_grand_children):
this_grand_child = mb.Compound(name="GrandChild{}".format(k +
1))
this_child.add(
this_grand_child,
label="Child{0}GrandChild{1}".format(i + 1, k + 1),
)
compound_to_json(ancestor, "large_compound.json", include_ports=True)
ancestor_copy = compound_from_json("large_compound.json")
assert ancestor.n_particles == ancestor_copy.n_particles
assert ancestor.n_bonds == ancestor_copy.n_bonds
assert len(ancestor.children) == len(ancestor_copy.children)
assert len(ancestor.all_ports()) == len(ancestor_copy.all_ports())
assert ancestor.labels.keys() == ancestor_copy.labels.keys()
def test_loop_with_ports(self):
from mbuild.lib.moieties import CH3
ethane_without_overlap = mb.Compound()
methyl1 = CH3()
methyl2 = CH3()
ethane_without_overlap.add(methyl1, label="methyl1")
ethane_without_overlap.add(methyl2, label="methyl2")
compound_to_json(
ethane_without_overlap,
"ethane_without_overlap.json",
include_ports=True,
)
ethane_copy = compound_from_json("ethane_without_overlap.json")
assert ethane_copy.n_particles == ethane_without_overlap.n_particles
assert ethane_copy.n_bonds == ethane_without_overlap.n_bonds
assert len(ethane_copy.children) == len(ethane_without_overlap.children)
assert len(ethane_copy.all_ports()) == len(
ethane_without_overlap.all_ports()
)
assert ethane_copy.labels.keys() == ethane_without_overlap.labels.keys()
assert (
ethane_without_overlap["methyl2"].labels.keys()
== ethane_copy["methyl2"].labels.keys()
)
def test_loop_for_propyl(self, hexane):
compound_to_json(hexane, 'hexane.json', include_ports=True)
hexane_copy = compound_from_json('hexane.json')
assert hexane.n_particles == hexane_copy.n_particles
assert hexane.n_bonds == hexane_copy.n_bonds
assert len(hexane.children) == len(hexane_copy.children)
assert len(hexane.all_ports()) == len(hexane_copy.all_ports())
assert hexane.labels.keys() == hexane_copy.labels.keys()
def test_loop(self, ethane):
for part in ethane:
part.element = part.name
compound_to_json(ethane, "ethane.json")
ethane_copy = compound_from_json("ethane.json")
for part_orig, part_copy in zip(ethane, ethane_copy):
assert part_orig.element.symbol == part_copy.element.symbol
assert ethane.n_particles == ethane_copy.n_particles
assert ethane.n_bonds == ethane_copy.n_bonds
assert len(ethane.children) == len(ethane_copy.children)
def test_label_consistency(self):
from mbuild.lib.moieties import CH2, CH3
parent = mb.Compound(name='Hierarchy1')
for i in range(10):
parent.add(CH2())
parent.add(CH3())
compound_to_json(parent, 'parent.json', include_ports=True)
parent_copy = compound_from_json('parent.json')
assert len(parent_copy['CH2']) == len(parent['CH2'])
assert parent_copy.labels.keys() == parent.labels.keys()
for child, child_copy in zip(parent.successors(), parent_copy.successors()):
assert child.labels.keys() == child_copy.labels.keys()
assert parent_copy.available_ports() == parent.available_ports()
def test_loop(self, ethane):
compound_to_json(ethane, 'ethane.json')
ethane_copy = compound_from_json('ethane.json')
assert ethane.n_particles == ethane_copy.n_particles
assert ethane.n_bonds == ethane_copy.n_bonds
assert len(ethane.children) == len(ethane_copy.children)
def test_float_64_position(self):
ethane = mb.lib.molecules.Ethane()
ethane.xyz = np.asarray(ethane.xyz, dtype=np.float64)
compound_to_json(ethane, "ethane.json", include_ports=True)
ethane_copy = compound_from_json("ethane.json")
assert np.allclose(ethane.xyz, ethane_copy.xyz, atol=10**-6)
