def benzene_from_parts(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi / 180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi / 180.0))
benzene = mb.Compound(name='Benzene')
benzene.add(ch)
current = ch
for _ in range(5):
ch_new = mb.clone(ch)
mb.force_overlap(move_this=ch_new,
from_positions=ch_new['a'],
to_positions=current['b'])
current = ch_new
benzene.add(ch_new)
carbons = [p for p in benzene.particles_by_name('C')]
benzene.add_bond((carbons[0], carbons[-1]))
return benzene
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, 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 test_center(self, methane):
assert np.array_equal(methane.center, np.array([0, 0, 0]))
for orientation in np.identity(3):
separation = 0.2
port = mb.Port(anchor=methane[0], orientation=orientation)
assert np.allclose(port.center,
np.array([0.0, 0.0, 0.0]),
atol=1e-15)
port = mb.Port(anchor=methane[0],
orientation=orientation,
separation=separation)
assert np.allclose(port.center,
separation * orientation,
atol=1e-15)
np.random.seed(0)
for orientation in np.random.rand(5, 3):
port = mb.Port(anchor=methane[0], orientation=orientation)
assert np.allclose(port.center,
np.array([0.0, 0.0, 0.0]),
atol=1e-15)
port = mb.Port(anchor=methane[0],
orientation=orientation,
separation=separation)
assert np.allclose(port.center,
separation * orientation /
np.linalg.norm(orientation),
atol=1e-15)
def benzene_from_parts(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.translate(-ch[0].pos)
ch.add(mb.Port(anchor=ch[0], separation=0.07), 'a')
ch['a'].rotate(120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
ch.add(mb.Port(anchor=ch[0], separation=0.07), 'b')
ch['b'].rotate(-120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
ch_copy = mb.clone(ch)
benzene = mb.Compound(name='Benzene')
benzene.add(ch)
current = ch
for _ in range(5):
ch_new = mb.clone(ch_copy)
mb.force_overlap(move_this=ch_new,
from_positions=ch_new['a'],
to_positions=current['b'])
current = ch_new
benzene.add(ch_new)
carbons = [p for p in benzene.particles_by_name('C')]
benzene.add_bond((carbons[0],carbons[-1]))
return benzene
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 __init__(self):
super(O, self).__init__()
mb.load('o.pdb', compound=self, relative_to_module=self.__module__)
self.add(mb.Port(anchor=self[0], orientation=[0, 0, 1],
separation=.075), label='up')
self.add(mb.Port(anchor=self[0], orientation=[0, 0, -1],
separation=.075), label='down')
def test_up_down_reverse_orientation_axes(self):
for vector in [[1, 0, 0], [0, 1, 0], [0, 0, 1]]:
port1 = mb.Port(orientation=vector)
port2 = mb.Port(orientation=-np.array(vector))
assert np.allclose(port1['up'].xyz_with_ports,
port2['down'].xyz_with_ports)
assert np.allclose(port1['down'].xyz_with_ports,
port2['up'].xyz_with_ports)
def test_port_separation(self, ethane):
port = mb.Port(anchor=ethane, separation=0.7)
assert np.allclose(0.7, port.separation, atol=1e-15)
port_no_anchor = mb.Port()
with pytest.warns(UserWarning):
separation = port_no_anchor.separation
assert separation is None
def test_port_separation(self, ethane):
port = mb.Port(anchor=ethane, separation=0.7)
assert (np.allclose(0.7, port.separation, atol=1e-15))
port_no_anchor = mb.Port()
with warnings.catch_warnings(record=True) as w:
separation = port_no_anchor.separation
assert w
assert (separation is None)
def __init__ (self, chain_separation=0.30):
super(CGMMM, self).__init__()
middle_bead = mb.Particle(name='_MMM')
self.add(middle_bead, 'middle_bead')
self.add(mb.Port(anchor=self['middle_bead']), label='up')
self.add(mb.Port(anchor=self['middle_bead']), label='down')
mb.Compound.translate(self['up'], [0, chain_separation, 0])
mb.Compound.translate(self['down'], [0, -(chain_separation), 0])
def __init__(self):
super(CH2UA, self).__init__()
self.add(mb.Particle(name='_CH2'))
self.add(mb.Port(anchor=self[0], separation=0.075), 'up')
self.add(
mb.Port(anchor=self[0], orientation=[0, -1, 0], separation=0.075),
'down')
def __init__(self, filepath, bond_indices):
super(Monomer, self).__init__()
mb.load(filepath, compound=self)
# mb.Compound.translate(self, -self[0].pos) # center molecule at origin
# self.add_bond((self[1], self[3]))
self.add(mb.Port(anchor=self[bond_indices[0]]), label='up')
self.add(mb.Port(anchor=self[bond_indices[1]]), label='down')
mb.Compound.translate(self['up'], [bond_length, 0, 0])
mb.Compound.translate(self['down'], [-bond_length, 0, 0])
def __init__(self):
super(MMM, self).__init__()
self.add(mb.Particle(name='_MMM'))
self.add(mb.Port(anchor=self[0], separation=0.18), 'up')
self.add(
mb.Port(anchor=self[0], orientation=[0, -1, 0], separation=0.18),
'down')
def test_up_down_reverse_orientation_random(self):
np.random.seed(84)
for _ in range(15):
vector = np.random.random(3) - 0.5
port1 = mb.Port(orientation=vector)
port2 = mb.Port(orientation=-vector)
assert np.allclose(port1['up'].xyz_with_ports,
port2['down'].xyz_with_ports)
assert np.allclose(port1['down'].xyz_with_ports,
port2['up'].xyz_with_ports)
def __init__(self):
super(C, self).__init__()
self.add(mb.Particle(name='C'))
self.add(mb.Port(anchor=self[0]), 'up')
mb.translate(self['up'], [0, 0.07, 0])
self.add(mb.Port(anchor=self[0]), 'down')
mb.translate(self['down'], [0, -0.07, 0])
def __init__(self):
super(Phenyl, self).__init__()
mb.load('phenyl.pdb', compound=self, relative_to_module=self.__module__)
self.translate(-self[0].pos)
self.add(mb.Port(anchor=self[0], orientation=[0, -1, 0], separation=0.07),
'down')
self.add(mb.Port(anchor=self[3], orientation=[0, 1, 0], separation=0.07),
'up')
def __init__(self):
super(PegMonomer, self).__init__()
mb.load('peg_monomer.pdb', compound=self, relative_to_module=self.__module__)
mb.translate(self, -self[0].pos)
self.add(mb.Port(anchor=self[0]), 'down')
mb.translate(self['down'], [0, -0.07, 0])
self.add(mb.Port(anchor=self[6]), 'up')
mb.translate(self['up'], [0, 0.073, 0])
def __init__(self):
super(CH2, self).__init__()
mb.load('ch2.pdb', compound=self, relative_to_module=self.__module__)
self.translate(-self[0].pos) # Move carbon to origin.
self.add(mb.Port(anchor=self[0]), 'up')
self['up'].translate([0, 0.07, 0])
self.add(mb.Port(anchor=self[0]), 'down')
self['down'].translate([0, -0.07, 0])
def __init__(self):
super(Ch2, self).__init__()
mb.load('ch2.pdb', compound=self, relative_to_module=self.__module__)
carbon = list(self.particles_by_name('C'))[0]
self.add(mb.Port(anchor=carbon, orientation=[0, 0, 1],
separation=.075),
label='up')
self.add(mb.Port(anchor=carbon,
orientation=[0, 0, -1],
separation=0.075),
label='down')
def __init__(self):
super(Silicon, self).__init__()
self.add(mb.Particle(name='Si'))
self.add(mb.Port(anchor=self[0], orientation=[0, 0, 1], separation=0.07),
label='up')
self.add(mb.Port(anchor=self[0], orientation=[0, 0, -1], separation=0.07),
label='down')
self.add(mb.Port(anchor=self[0], orientation=[1, 0, 0], separation=0.07),
label='right')
self.add(mb.Port(anchor=self[0], orientation=[-1, 0, 0], separation=0.07),
label='left')
def __init__(self):
super(Oxygen, self).__init__()
self.add(mb.Particle(name='O'))
up_port = mb.Port(anchor=self[0],
orientation=[0, 0, 1],
separation=.075)
down_port = mb.Port(anchor=self[0],
orientation=[0, 0, -1],
separation=.075)
self.add(up_port, label='up')
self.add(down_port, label='down')
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):
super(PegMonomer, self).__init__()
mb.load('peg_monomer.pdb', compound=self, relative_to_module=self.__module__,
infer_hierarchy=False)
self.translate(-self[0].pos)
self.rotate(pi, [1,0,0])
self.add(mb.Port(anchor=self[0]), 'up')
self['up'].translate([0, 0.07, 0])
self.add(mb.Port(anchor=self[6]), 'down')
self['down'].translate([0, -0.073, 0])
def rigid_ch(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.label_rigid_bodies()
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi / 180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi / 180.0))
return ch
def __init__(self):
super(Ester, self).__init__()
mb.load('ester.pdb', compound=self, relative_to_module=self.__module__)
mb.translate(self, -self[0].pos)
self.add(mb.Port(anchor=self[2]), 'up')
mb.spin_z(self['up'], np.pi / 2)
mb.translate_to(self['up'], np.array([0.07, 0, 0]))
self.add(mb.Port(anchor=self[0]), 'down')
mb.spin_z(self['down'], np.pi / 2)
mb.translate(self['down'], np.array([-0.07, 0, 0]))
def __init__(self):
super(C3, self).__init__()
self.add(mb.Particle(name="C"))
self.add(mb.Port(anchor=self[0]), "up")
self["up"].translate(np.array([0, 0.07, 0]))
self.add(mb.Port(anchor=self[0]), "down")
self["down"].translate(np.array([0, 0.07, 0]))
self["down"].spin(np.pi * 2 / 3, [0, 0, 1])
self.add(mb.Port(anchor=self[0]), "left")
self["left"].translate(np.array([0, 0.07, 0]))
self["left"].spin(-np.pi * 2 / 3, [0, 0, 1])
def rigid_ch(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.label_rigid_bodies()
ch.translate(-ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
ch['a'].translate([0, 0.07, 0])
ch['a'].rotate(120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
ch.add(mb.Port(anchor=ch[0]), 'b')
ch['b'].translate([0, 0.07, 0])
ch['b'].rotate(-120.0 * (np.pi/180.0), around=np.asarray([0, 0, 1]))
return ch
def __init__(self):
super(C3, self).__init__()
self.add(mb.Particle(name='C'))
self.add(mb.Port(anchor=self[0]), 'up')
self['up'].translate(np.array([0, 0.07, 0]))
self.add(mb.Port(anchor=self[0]), 'down')
self['down'].translate(np.array([0, 0.07, 0]))
self['down'].spin(np.pi * 2 / 3, [0, 0, 1])
self.add(mb.Port(anchor=self[0]), 'left')
self['left'].translate(np.array([0, 0.07, 0]))
self['left'].spin(-np.pi * 2 / 3, [0, 0, 1])