def __init__(self, chain_length):
"""Initialize an Alkane Compound.
Parameters
----------
chain_length : int
Length of the alkane chain (in number of carbons)
"""
# Make sure the user inputs a chain length of at least 1
if chain_length < 1:
raise ValueError('Chain length must be greater than 1')
super(Alkane, self).__init__()
# Create a polymer of CH2 units
chain = mb.Polymer(CH2(), n=chain_length, port_labels=('up', 'down'))
self.add(chain, 'chain')
# Cap one end of the polymer with a hydrogen
self.add(H(), 'up_cap')
mb.force_overlap(move_this=self['up_cap'],
from_positions=self['up_cap']['up'],
to_positions=self['chain']['up'])
# Cap the other end of the polymer with a hydrogen
self.add(H(), 'down_cap')
mb.force_overlap(move_this=self['down_cap'],
from_positions=self['down_cap']['up'],
to_positions=self['chain']['down'])
def __init__(self, ball_radius=10, n_chains=4, chain_length=10, monomer=None):
"""Initialize a tethered nanoparticle.
Args:
ball_radius (float): Radius of the nanoparticle.
n_chains (int): Number of chains to attach to the nanoparticle.
chain_length (int): Length of the chains being attached.
monomer (Compound, optional): Type of chain being attached.
"""
super(Tnp, self).__init__()
if not monomer:
monomer = Bead(particle_kind='t')
n = 129 # TODO: make this tweakable
self.add(Sphere(n=n, radius=ball_radius, port_distance_from_surface=0.7), label="np")
# Generate 65 points on the surface of a unit sphere.
pattern = mb.SpherePattern(n_chains)
# Magnify it a bit.
pattern.scale(ball_radius)
chain_proto = mb.Polymer(monomer, n=chain_length)
# Apply chains to pattern.
chain_protos, empty_backfill = pattern.apply_to_compound(chain_proto,
guest_port_name="down", host=self['np'])
self.add(chain_protos)
self.generate_bonds('np', 'np', sqrt(4 * ball_radius ** 2 * pi / n) - 0.5,
sqrt(4 * ball_radius**2 * pi / n) + 0.5)
self.generate_bonds('np', 't', 0.1, 0.3)
self.generate_bonds('t', 'np', 0.1, 0.3)
def __init__(self, n, cap_front=True, cap_end=True):
if n < 2:
raise ValueError('n must be 2 or more')
super(Alkane, self).__init__()
if not cap_front:
n += 1
if not cap_end:
n += 1
chain = mb.Polymer(CH2(), n=n - 2, port_labels=('up', 'down'))
self.add(chain, 'chain')
if cap_front:
self.add(CH3(), 'methyl_front')
mb.force_overlap(move_this=self['chain'],
from_positions=self['chain']['up'],
to_positions=self['methyl_front']['up'])
else:
self.add(chain['up'], 'up', containment=False)
if cap_end:
self.add(CH3(), 'methyl_end')
mb.force_overlap(self['methyl_end'], self['methyl_end']['up'],
self['chain']['down'])
else:
self.add(chain['down'], 'down', containment=False)
def __init__(self, n, cap_front=True, cap_end=True):
"""Initialize an united atom Alkane Compound.
Parameters
----------
n: int
Number of backbone particles.
cap_front: bool, optional, default=True
Add methyl group to beginning of chain ('down' port).
cap_end: bool, optional, default=True
Add methyl group to end of chain ('up' port).
"""
super(Alkane, self).__init__()
if n == 1:
if cap_front and cap_end:
ch4 = CH4()
self.add(ch4)
else:
ch3 = CH3()
self.add(ch3, 'ch3')
self.add(self['ch3']['up'], 'up', containment=False)
elif n == 2:
if cap_front:
ua1 = CH3()
else:
ua1 = CH2()
if cap_end:
ua2 = CH3()
else:
ua2 = CH2()
self.add(ua1, 'ua1')
self.add(ua2, 'ua2')
mb.force_overlap(self['ua2'], self['ua2']['up'], self['ua1']['up'])
else:
if not cap_front:
n += 1
if not cap_end:
n += 1
chain = mb.Polymer(CH2(), n=n - 2, port_labels=('up', 'down'))
self.add(chain, 'chain')
if cap_front:
self.add(CH3(), "methyl_front")
mb.force_overlap(self['chain'], self['chain']['up'],
self['methyl_front']['up'])
else:
self.add(chain['up'], 'up', containment=False)
if cap_end:
self.add(CH3(), 'methyl_end')
mb.force_overlap(self['methyl_end'], self['methyl_end']['up'],
self['chain']['down'])
else:
self.add(chain['down'], 'down', containment=False)
def test_mixed_monolayer(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
fractions = [0.75, 0.25]
chain_a = mb.Polymer(ch2, n=5)
chain_b = mb.Polymer(ch2, n=15)
monolayer = mb.Monolayer(surface=Betacristobalite(),
chains=[chain_a, chain_b],
fractions=fractions,
backfill=H(),
pattern=pattern)
n_a = round(n * m * 0.75)
n_b = round(n * m * 0.25)
assert monolayer.n_particles == 1900 + n_a * 5 * 3 + n_b * 15 * 3 + (
100 - (n_a + n_b))
assert monolayer.n_bonds == 2400 + n_a * (5 * 2 + 4 + 1) + n_b * (
15 * 2 + 14 + 1) + (100 - (n_a + n_b))
def __init__(self, n=3, cap_front=True, cap_end=True):
"""Initialize an Alkane Compound.
Args:
n: Number of carbon atoms.
cap_front: Add methyl group to beginning of chain ('down' port).
cap_end: Add methyl group to end of chain ('up' port).
"""
if n < 1:
raise ValueError('n must be 1 or more')
elif n == 1:
if cap_front or cap_end:
warn('Returning CH3 group')
else:
warn('Returning CH2 group')
super(Alkane, self).__init__()
if n > 1:
if cap_front:
n -= 1
ch3_front = CH3()
self.add(ch3_front, 'methyl_front')
if cap_end:
n -= 1
ch3_end = clone(ch3_front)
self.add(ch3_end, 'methyl_end')
try:
chain = mb.Polymer(CH2(), n=n, port_labels=('up', 'down'))
self.add(chain, 'chain')
if cap_end:
mb.force_overlap(self['methyl_end'],
self['methyl_end']['down'],
self['chain']['down'])
else:
self.add(chain['down'], 'down', containment=False)
if cap_front:
mb.force_overlap(self['chain'], self['chain']['up'],
self['methyl_front']['down'])
else:
self.add(chain['up'], 'up', containment=False)
except ValueError:
mb.force_overlap(self['methyl_end'],
self['methyl_end']['down'],
self['methyl_front']['down'])
else:
if cap_end or cap_front:
ch3 = CH3()
self.add(ch3, 'methyl')
self.add(ch3['down'], 'down', containment=False)
else:
ch2 = CH2()
self.add(ch2, 'methylene')
self.add(ch2['up'], 'up', containment=False)
self.add(ch2['down'], 'down', containment=False)
def __init__(self, chain_length, fidelity, cap_front=True, cap_end=True):
super(Alkane, self).__init__()
if fidelity not in ['UA', 'CG']:
raise Exception("`fidelity` must be either 'UA' or 'CG'.")
if chain_length < 2:
raise Exception("Chain length must be 2 or greater.")
if fidelity == 'CG' and chain_length % 3 != 0:
raise Exception("Chain length must be divisible by three for "
"use with `fidelity`='CG'.")
if fidelity == 'CG' and chain_length == 3:
raise Exception("Chain length must be greater than 3 for "
"use with `fidelity`='CG'.")
if fidelity == 'UA':
middle_bead = CH2UA()
end_bead = CH3UA()
if fidelity == 'CG':
chain_length /= 3
middle_bead = MMM()
end_bead = MME()
if not cap_front:
chain_length += 1
if not cap_end:
chain_length += 1
if chain_length > 2:
chain = mb.Polymer(mb.clone(middle_bead),
n=chain_length - 2,
port_labels=('up', 'down'))
self.add(chain, 'chain')
if cap_front:
self.add(mb.clone(end_bead), 'front_cap')
mb.force_overlap(self['front_cap'], self['front_cap']['up'],
self['chain']['up'])
else:
# Hoist port label to `Alkane` level
self.add(chain['up'], 'up', containment=False)
if cap_end:
self.add(mb.clone(end_bead), 'end_cap')
mb.force_overlap(self['end_cap'], self['end_cap']['up'],
self['chain']['down'])
else:
# Hoist port label to `Alkane` level
self.add(chain['down'], 'down', containment=False)
else:
self.add(mb.clone(end_bead), 'front_cap')
self.add(mb.clone(end_bead), 'end_cap')
mb.force_overlap(self['end_cap'], self['end_cap']['up'],
self['front_cap']['up'])
def test_monolayer(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
chain = mb.Polymer(ch2, n=10)
monolayer = mb.Monolayer(surface=Betacristobalite(),
chains=chain,
backfill=H(),
pattern=pattern)
assert monolayer.n_particles == 1900 + n * m * (10 * 3) + (100 - n * m)
assert monolayer.n_bonds == 2400 + n * m * (10 * 2 + 9 + 1) + (100 -
n * m)
def test_pattern_kwargs(self, ch2):
n = 8
m = 8
pattern = mb.Grid2DPattern(n, m)
chain = mb.Polymer(ch2, n=10)
monolayer = mb.Monolayer(surface=Betacristobalite(),
chains=H(),
guest_port_name='up',
backfill=chain,
backfill_port_name='down',
pattern=pattern)
chains = 100 - (n * m)
assert monolayer.n_particles == 1900 + chains * (10 * 3) + (100 -
chains)
assert monolayer.n_bonds == 2400 + chains * (10 * 2 + 9 + 1) + (100 -
chains)
def test_block_copolymer(self, ch2, ester):
n = 2
sequence = 'ABBA'
abba = mb.Polymer([ch2, ester], sequence=sequence, n=n)
assert abba.n_particles == n * 3 * len(sequence)
assert len(abba.children) == len(sequence) * n
assert abba.children[0].name == 'CH2'
assert abba.children[1].name == 'Ester'
assert abba.children[2].name == 'Ester'
assert abba.children[3].name == 'CH2'
assert abba.children[4].name == 'CH2'
assert abba.children[5].name == 'Ester'
assert abba.children[6].name == 'Ester'
assert abba.children[7].name == 'CH2'
n_elements = Counter(p.name for p in abba.particles())
assert n_elements['C'] == n * len(sequence)
assert n_elements['H'] == n * len(sequence)
assert n_elements['O'] == n * len(sequence)
assert abba.n_bonds == n * 2 * len(sequence) + (n * len(sequence) - 1)
def __init__(self, chain_length=4, alpha=pi / 4):
super(Brush, self).__init__()
# Add parts
self.add(Silane(), label='silane')
self.add(Initiator(), label='initiator')
self.add(mb.Polymer(MPC(alpha=alpha),
n=chain_length,
port_labels=('up', 'down')),
label='pmpc')
self.add(CH3(), label='methyl')
mb.force_overlap(self['initiator'], self['initiator']['down'],
self['silane']['up'])
mb.force_overlap(self['pmpc'], self['pmpc']['down'],
self['initiator']['up'])
mb.force_overlap(self['methyl'], self['methyl']['up'],
self['pmpc']['up'])
# Make self.port point to silane.bottom_port
self.add(self['silane']['down'], label='down', containment=False)
def __init__(self, n=3, cap_front=True, cap_end=True):
"""Initialize an Alkane Compound.
Args:
n: Number of carbon atoms.
cap_front: Add methyl group to beginning of chain ('down' port).
cap_end: Add methyl group to end of chain ('up' port).
"""
if n < 2:
raise ValueError('n must be 1 or more')
super(Alkane, self).__init__()
# Adjust length of Polmyer for absence of methyl terminations.
if not cap_front:
n += 1
if not cap_end:
n += 1
chain = mb.Polymer(CH2(), n=n - 2, port_labels=('up', 'down'))
self.add(chain, 'chain')
if cap_front:
self.add(CH3(), "methyl_front")
mb.force_overlap(move_this=self['chain'],
from_positions=self['chain']['up'],
to_positions=self['methyl_front']['up'])
else:
# Hoist port label to Alkane level.
self.add(chain['up'], 'up', containment=False)
if cap_end:
self.add(CH3(), 'methyl_end')
mb.force_overlap(self['methyl_end'], self['methyl_end']['up'],
self['chain']['down'])
else:
# Hoist port label to Alkane level.
self.add(chain['down'], 'down', containment=False)
# -- ==alkane== --
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')
# Implicit hydrogens
# XYZ doesn't matter, we just need bonds and particle names
# So we can upload to charmm-gui
cap_with = 'H'
pvp = mb.Polymer(mvp(), n=2)
if cap_with == 'C':
c_top = mb.Particle(name='C')
cap_top = mb.Compound()
cap_top.add(c_top)
cap_top.add(mb.Port(anchor=c_top), 'down')
mb.force_overlap(cap_top, cap_top['down'], pvp['up'])
c_bot = mb.Particle(name='C')
cap_bot = mb.Compound()
cap_bot.add(c_bot)
cap_bot.add(mb.Port(anchor=c_bot), 'up')
mb.force_overlap(cap_bot, cap_bot['up'], pvp['down'])
pvp.add(cap_top)
pvp.add(cap_bot)
def test_polymer(self, ch2):
n = 6
c6 = mb.Polymer(ch2, n=n)
assert c6.n_particles == n * 3
assert c6.n_bonds == n * 2 + (n - 1)
