def __init__(self):
super(I2, self).__init__()
iodine1= mb.Particle(pos=[0.0, 0.0, 0.0], name='I')
iodine2= mb.Particle(pos=[0.8, 0.0, 0.0], name='I')
self.add([iodine2,iodine1])
self.add_bond((iodine2,iodine1))
def __init__(self):
super(OH, self).__init__()
self.add(mb.Particle(name='O', pos=[0.0, 0.0, 0.0]), label='O')
self.add(mb.Particle(name='H', pos=[0.0, 0.1, 0.0]), label='H')
self.add_bond((self['O'], self['H']))
# add the port to the oxygen atom along the [0,-1, 0] direction
self.add(mb.Port(anchor=self['O'], orientation=[0, -1, 0], separation=0.075), label='down')
def __init__(self, chain_length):
super(AlkylSilane, self).__init__()
self.add(mb.Particle(name='H'))
self.add(mb.Port(anchor=self[0]), 'oH')
self['oH'].spin(np.pi, [0, 0, 1])
self['oH'].translate(np.array([0, 0.097 / 2, 0]))
self.add(mb.Particle(name='O'))
self.add(mb.Port(anchor=self[1]), label='Oh')
self['Oh'].spin(np.pi, [0, 0, 1])
self['Oh'].translate(np.array([0, 0.097 / 2, 0]))
mb.force_overlap(self[0], self['oH'], self['Oh'])
self.add(mb.Port(anchor=self[1]), label='alcohol')
self['alcohol'].spin(np.pi, [0, 0, 1])
self['alcohol'].translate(np.array([0, -0.097 / 2, 0]))
CH2 = mb.lib.moieties.CH2()
alkane = Polymer(CH2, chain_length, port_labels=['up', 'down'])
silane = Silane()
mb.force_overlap(silane, silane['down'], self['alcohol'])
self.add(silane, 'silane')
mb.force_overlap(alkane, alkane['down'], silane['up'])
self.add(alkane, 'alkane')
# Hoist silane port to AlkylSilane level.
#self.add(silane['down'], 'down', containment=False)
#remove a hydrogen to add a port for the second functionalgroup
self.remove(self['alkane'][3 * chain_length - 1])
self.add(self.all_ports()[0], 'secondary', containment=False)
self.add(self.all_ports()[1], 'primary', containment=False)
def __init__(self):
super(Cl2, self).__init__()
chlorine1= mb.Particle(pos=[0.0, 0.0, 0.0], name='Cl')
chlorine2= mb.Particle(pos=[0.2, 0.0, 0.0], name='Cl')
self.add([chlorine2,chlorine1])
self.add_bond((chlorine2,chlorine1))
def __init__(self, n=65, radius=1, port_distance_from_surface=.07):
"""Initialize a Sphere object.
Args:
n (int): Number of points used to construct the Sphere.
radius (float): Radius of the Sphere.
port_distance_from_surface (float): Distance of Ports from Sphere.
"""
super(Sphere, self).__init__()
particle = mb.Particle(name='np')
particle.add(mb.Port(anchor=particle), label='out')
# Generate 65 points on the surface of a unit sphere.
pattern = mb.SpherePattern(n)
# Magnify the unit sphere by the provided radius.
pattern.scale(radius)
particles = pattern.apply(particle, orientation='normal', compound_port='out')
self.add(particles, label='np_[$]')
# Create particles and Ports at pattern positions.
for i, pos in enumerate(pattern.points):
particle = mb.Particle(name="np", pos=pos)
self.add(particle, "np_{}".format(i))
port = mb.Port(anchor=particle)
self.add(port, "port_{}".format(i))
# Make the top of the port point toward the positive x axis.
port.spin(-pi/2, [0, 0, 1])
# Raise up (or down) the top of the port in the z direction.
port.spin(-arcsin(pos[2]/radius), [0, 1, 0])
# Rotate the Port along the z axis.
port.spin(arctan2(pos[1], pos[0]), [0, 0, 1])
# Move the Port a bit away from the surface of the Sphere.
port.translate(pos/radius * port_distance_from_surface)
def __init__(self):
super(O2, self).__init__()
oxygen1= mb.Particle(pos=[0.0, 0.0, 0.0], name='O')
oxygen2= mb.Particle(pos=[0.15, 0.0, 0.0], name='O')
self.add([oxygen2,oxygen1])
self.add_bond((oxygen2,oxygen1))
def __init__(self):
super(FCl, self).__init__()
fluorine1 = mb.Particle(pos=[0.0, 0.0, 0.0], name='F')
chlorine2 = mb.Particle(pos=[0.2, 0.0, 0.0], name='Cl')
self.add([fluorine1, chlorine2])
self.add_bond((fluorine1, chlorine2))
def __init__(self):
super(N2, self).__init__()
nitrogen1 = mb.Particle(pos=[0.0, 0.0, 0.0], name='N')
nitrogen2 = mb.Particle(pos=[0.2, 0.0, 0.0], name='N')
self.add([nitrogen2, nitrogen1])
self.add_bond((nitrogen2, nitrogen1))
def __init__(self):
super(H2O, self).__init__()
self.add(mb.Particle(name="O", pos=[1.0203, 0.7604, 1.2673]))
self.add(mb.Particle(name="H", pos=[0.9626, 0.8420, 1.2673]))
self.add(mb.Particle(name="H", pos=[0.9626, 0.6787, 1.2673]))
self.add_bond((self[0], self[1]))
self.add_bond((self[0], self[2]))
def __init__(self):
super(CHF, self).__init__()
carbon = mb.Particle(name='C', pos=[0.0, 0.0, 0.0])
hydrogen = mb.Particle(name='H', pos=[0.0, -0.15, 0.0])
fluorine = mb.Particle(name='F', pos=[0.0, 0.15, 0.0])
self.add([carbon, hydrogen, fluorine])
self.add_bond((carbon, hydrogen))
self.add_bond((carbon, fluorine))
def test_parmed_element_guess(self):
compound = mb.Particle(name='foobar')
with pytest.warns(UserWarning):
_ = compound.to_parmed()
compound = mb.Particle(name='XXXXXX')
with pytest.warns(UserWarning):
_ = compound.to_parmed()
def __init__(self):
super(Hydroxyl, self).__init__()
#self.add(mb.Particle(name='_OH'))
oxygen = mb.Particle(name='O', pos=[0.0, 0.0, 0.0])
hydrogen = mb.Particle(name='H', pos=[0.0945, 0.0, 0.0])
self.add((oxygen, hydrogen))
self.add_bond((oxygen, hydrogen))
self.add(mb.Port(anchor=oxygen,
orientation=[-1, 0, 0],
separation=0.075),
label='up')
def sixpoints(self):
molecule = mb.Compound()
molecule.add(mb.Particle(name="C", pos=[5, 5, 5]), label="middle")
molecule.add(mb.Particle(name="C", pos=[6, 5, 5]), label="right")
molecule.add(mb.Particle(name="C", pos=[4, 5, 5]), label="left")
molecule.add(mb.Port(anchor=molecule[0]), label="up")
molecule["up"].translate([0, 1, 0])
molecule.add(mb.Port(anchor=molecule[0]), label="down")
molecule["down"].translate([0, -1, 0])
molecule.add(mb.Particle(name="C", pos=[5, 5, 6]), label="front")
molecule.add(mb.Particle(name="C", pos=[5, 5, 4]), label="back")
molecule.generate_bonds("C", "C", 0.9, 1.1)
return molecule
def sixpoints(self):
molecule = mb.Compound()
molecule.add(mb.Particle(name='C', pos=[5, 5, 5]), label='middle')
molecule.add(mb.Particle(name='C', pos=[6, 5, 5]), label='right')
molecule.add(mb.Particle(name='C', pos=[4, 5, 5]), label='left')
molecule.add(mb.Port(anchor=molecule[0]), label='up')
molecule['up'].translate([0, 1, 0])
molecule.add(mb.Port(anchor=molecule[0]), label='down')
molecule['down'].translate([0, -1, 0])
molecule.add(mb.Particle(name='C', pos=[5, 5, 6]), label='front')
molecule.add(mb.Particle(name='C', pos=[5, 5, 4]), label='back')
molecule.generate_bonds('C', 'C', 0.9, 1.1)
return molecule
def __init__(self, nano, n, box, seed=12345):
super(PatchyBox, self).__init__()
if type(nano) is not list:
nano = [nano]
if type(n) is not list:
n = [n]
# Define positions for nanoparticles (use points to speed
# this up)
point_rep = mb.Particle(name='point0')
d_vdw = max([
max(nano[0].xyz[:, dim]) - min(nano[0].xyz[:, dim])
for dim in range(3)
])
point_box = mb.fill_box(point_rep,
n[0],
box,
overlap=d_vdw + 0.5,
edge=d_vdw / 2 + 0.25,
seed=seed)
for i, (np_proto, np_n) in enumerate(zip(nano[1:], n[1:])):
point_rep = mb.Particle(name='point{:d}'.format(i + 1))
d_vdw = max([
max(np_proto.xyz[:, dim]) - min(np_proto.xyz[:, dim])
for dim in range(3)
])
point_box = mb.solvate(solute=point_box,
solvent=point_rep,
n_solvent=np_n,
box=box,
overlap=d_vdw + 0.5,
edge=d_vdw / 2 + 0.25,
seed=seed)
self.periodicity = box.lengths
random.seed(seed)
# Replicate the nanoparticle at the defined positions
for particle in point_box.particles():
nano_index = int(particle.name.strip('point'))
nano_clone = mb.clone(nano[nano_index])
nano_clone.spin(
random.random() * 2 * np.pi,
np.array([random.random(),
random.random(),
random.random()]) - 0.5)
#mb.translate_to(nano_clone, particle.pos)
nano_clone.translate_to(particle.pos)
self.add(nano_clone)
def __init__(self,
n_beads=10,
build='linear',
bead_name='bead',
spring_distance=1):
super(BeadSpring, self).__init__()
prev_bead = mb.Particle(pos=[0.0, 0.0, 0.0], name=bead_name)
self.add(prev_bead)
for n in range(1, n_beads):
current_bead = mb.Particle(pos=[0.0, 0.0, n * spring_distance],
name=bead_name)
self.add(current_bead)
self.add_bond((prev_bead, current_bead))
prev_bead = current_bead
def __init__(self):
super().__init__(name='mvp')
n = mb.Particle(name='N')
c1 = mb.Particle(name='C')
c2 = mb.Particle(name='C')
c3 = mb.Particle(name='C')
c4 = mb.Particle(name='C')
o41 = mb.Particle(name='O')
c5 = mb.Particle(name='C')
c6 = mb.Particle(name='C')
self.add([n, c1, c2, c3, c4, o41, c5, c6])
self.add_bond([n, c1])
self.add_bond([c1, c2])
self.add_bond([c3, c2])
self.add_bond([c3, c4])
self.add_bond([c4, o41])
self.add_bond([c4, n])
self.add_bond([n, c5])
self.add_bond([c5, c6])
self.add(mb.Port(anchor=c5), 'up')
self.add(mb.Port(anchor=c6), 'down')
def visualize_qcc_input(self, i, single=True):
"""Visualize the input for pyscf using mbuild.
Parameters
----------
i : int
Index of the single or pair input to visualize.
single : bool, default True
Whether to visualize a single or pair input.
Note
----
The visualize functions require mbuild, a visualization backend (py3Dmol
or nglview), and a jupyter notebook. They are designed only to help
troubleshoot.
"""
import mbuild as mb
if single:
qcc_input = self.chromophores[i].qcc_input
else:
qcc_input = self.qcc_pairs[i][1]
comp = mb.Compound()
for line in qcc_input.split(";")[:-1]:
atom, x, y, z = line.split()
xyz = np.array([x,y,z], dtype=float)
# Angstrom -> nm
xyz /= 10
comp.add(mb.Particle(name=atom, pos=xyz))
comp.visualize().show()
def offmol_to_compound(off_mol: "Molecule") -> "mb.Compound":
"""Covert an OpenFF Molecule into an mBuild Compound.
Examples
--------
.. code-block:: pycon
>>> from openff.toolkit.topology import Molecule
>>> from openff.interchange.components.mbuild import offmol_to_compound
>>> mol = Molecule.from_smiles("CCO")
>>> compound = offmol_to_compound(mol)
>>> type(compound), compound.n_particles, compound.n_bonds
(<class 'mbuild.compound.Compound'>, 9, 8)
"""
if not off_mol.has_unique_atom_names:
off_mol.generate_unique_atom_names()
if off_mol.n_conformers == 0:
off_mol.generate_conformers(n_conformers=1)
comp = mb.Compound()
comp.name = off_mol.name
for a in off_mol.atoms:
atom_comp = mb.Particle(name=a.element.symbol)
comp.add(atom_comp, label=a.name)
for b in off_mol.bonds:
comp.add_bond((comp[b.atom1_index], comp[b.atom2_index]))
comp.xyz = off_mol.conformers[0].value_in_unit(unit.nanometer)
return comp
def __init__(self):
super(H, self).__init__()
self.add(mb.Particle(name="H"))
self.add(mb.Port(anchor=self[0]), "up")
self["up"].spin(np.pi, [0, 0, 1])
self["up"].translate(np.array([0, 0.07, 0]))
def __init__(self):
super(H, self).__init__()
self.add(mb.Particle(name='H'))
self.add(mb.Port(anchor=self[0]), 'up')
mb.spin_z(self['up'], np.pi)
mb.translate(self['up'], np.array([0, 0.07, 0]))
def __init__ (self, radius, bead_diameter):
super(Core, self).__init__()
core_bead = mb.Particle(name='_CGN')
# calculate n number of core particles from ratio of core total SA and single bead SA
n_core_particles = (int)((4*np.pi*(radius**2))/(4*np.pi*(bead_diameter/2)**2))
# arrange beads into a sphere pattern and add it to the compound
core_pattern = mb.SpherePattern(n_core_particles)
core_pattern.scale(radius)
core_formation = core_pattern.apply(core_bead)
self.add(core_formation)
self.generate_bonds(name_a='_CGN', name_b='_CGN', dmin=bead_diameter*2-0.4, dmax=bead_diameter*2+0.3)
print('Core beads added.')
# apply ports to each bead in core_formation
for i, pos in enumerate(core_pattern.points):
port = mb.Port(anchor=core_formation[i], orientation=pos, separation=radius/5)
self.add(port, label='port[$]')
print('Ports added to core')
def test_assert_bonds():
ff = Forcefield(name='trappe-ua')
derponium = mb.Compound()
at1 = mb.Particle(name='H')
at2 = mb.Particle(name='O')
at3 = mb.Particle(name='_CH4')
derponium.add([at1, at2, at3])
derponium.add_bond((at1, at2))
derponium.add_bond((at2, at3))
with pytest.raises(Exception):
ff.apply(derponium)
thing = ff.apply(derponium, assert_bond_params=False, assert_angle_params=False)
assert any(b.type is None for b in thing.bonds)
def __init__(self):
super(IN, self).__init__(
pos=[0, 0,
0], name='bb') #Initizlize an instance of abstract class
bead = mb.Particle(pos=[0.0, 0.0, 0.0], name='IN')
self.add(bead)
def _create_crosslinks(self):
"""Creates the crosslinks between monolayer chains. """
crosslinks = self.crosslink_graph.edges()
pos = nx.get_node_attributes(self.crosslink_graph, 'pos')
attachment = nx.get_node_attributes(self.crosslink_graph,
'surface_bound')
for crosslink in crosslinks:
atom1 = crosslink[0]
atom2 = crosslink[1]
loc1 = deepcopy(atom1.pos)
loc2 = deepcopy(atom2.pos)
for i in range(2):
if loc1[i] - loc2[i] > self.periodicity[i] / 2:
loc1[i] -= self.periodicity[i]
elif loc1[i] - loc2[i] < -self.periodicity[i] / 2:
loc1[i] += self.periodicity[i]
# Add an oxygen atom midway between the two silicon atoms
midpoint = (loc1 + loc2) / 2
oxygen = mb.Particle(name='O', pos=midpoint)
self.add(oxygen, 'crosslink_oxygen[$]')
self.add_bond((atom1, oxygen))
self.add_bond((atom2, oxygen))
# Add hydroxyls to dangling bonds of silane silicons
for node in self.crosslink_graph.nodes():
neighbors = len(self.bond_graph.neighbors(node))
if neighbors == 2:
self._add_hydroxyls(node, 2)
elif neighbors == 3:
self._add_hydroxyls(node, 1)
def __init__(self):
super(H, self).__init__()
self.add(mb.Particle(name='H'))
self.add(mb.Port(anchor=self[0]), 'down')
self['down'].spin(np.pi, [0, 0, 1])
self['down'].translate(np.array([0, 0.07, 0]))
def __init__(self):
super(Methane, self).__init__()
carbon = mb.Particle(name='C')
self.add(carbon)
hydrogen = mb.Particle(name='H', pos=[0.1, 0, -0.07])
self.add(hydrogen)
self.add_bond((self[0], self[1]))
self.add(mb.Particle(name='H', pos=[-0.1, 0, -0.07]))
self.add(mb.Particle(name='H', pos=[0, 0.1, 0.07]))
self.add(mb.Particle(name='H', pos=[0, -0.1, 0.07]))
self.add_bond((self[0], self[2]))
self.add_bond((self[0], self[3]))
self.add_bond((self[0], self[4]))
def __init__(self):
super(Methane, self).__init__()
carbon = mb.Particle(name="C")
self.add(carbon, label="C[$]")
hydrogen = mb.Particle(name="H", pos=[0.1, 0, -0.07])
self.add(hydrogen, label="HC[$]")
self.add_bond((self[0], self["HC"][0]))
self.add(mb.Particle(name="H", pos=[-0.1, 0, -0.07]), label="HC[$]")
self.add(mb.Particle(name="H", pos=[0, 0.1, 0.07]), label="HC[$]")
self.add(mb.Particle(name="H", pos=[0, -0.1, 0.07]), label="HC[$]")
self.add_bond((self[0], self["HC"][1]))
self.add_bond((self[0], self["HC"][2]))
self.add_bond((self[0], self["HC"][3]))
def __init__(self):
super(Methane, self).__init__()
carbon = mb.Particle(name="C", element="C")
self.add(carbon)
hydrogen = mb.Particle(name="H", pos=[0.1, 0, -0.07], element="H")
self.add(hydrogen)
self.add_bond((self[0], self[1]))
self.add(mb.Particle(name="H", pos=[-0.1, 0, -0.07], element="H"))
self.add(mb.Particle(name="H", pos=[0, 0.1, 0.07], element="H"))
self.add(mb.Particle(name="H", pos=[0, -0.1, 0.07], element="H"))
self.add_bond((self[0], self[2]))
self.add_bond((self[0], self[3]))
self.add_bond((self[0], self[4]))
def test_single_particle(self):
part = mb.Particle(name='A')
assert part.n_particles == 1
assert len(list(part.particles())) == 1
assert part.xyz.shape == (1, 3)
assert part.root == part
assert len(list(part.ancestors())) == 0
assert next(part.particles_by_name('A')) == part
