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.recipes.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):
"""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.recipes.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, n=1, cap_start=True):
super(Alkane, self).__init__()
if n < 1:
raise ValueError('n must be 1 or more')
if cap_start:
#if n == 1, will simply return a a methane molecule
if n == 1:
self.add(CH4(), 'methyl_start')
if n > 1:
self.add(Backbone(n=n-1, cap_start_mol=CH3(),
cap_start_name= 'methyl_start', cap_start_port = 'up',
cap_end_mol = CH3_down(), cap_end_name='methyl_end',
cap_end_port= 'dow'))
else:
#if n == 1, will simply return a a methane molecule,
#with an available 'down' port.
#We will label this as 'methyl_start', again for consistency
#with longer chain molecules.
if n == 1:
self.add(CH3_down(), 'methyl_start')
if n > 1:
self.add(Backbone(n=n-1, cap_start_mol=CH2(),
cap_start_name= 'methyl_start', cap_start_port = 'up',
cap_end_mol = CH3_down(), cap_end_name='methyl_end',
cap_end_port= 'down'))
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.recipes.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)
def __init__(self, n=1, cap_start_mol=CH3(),
cap_start_name= 'methyl_start', cap_start_port = 'up',
cap_end_mol = OH(), cap_end_name='OH',
cap_end_port= 'down'):
super(Backbone, self).__init__()
if n < 1:
raise ValueError('n must be 1 or more')
if n == 1:
cap1 = cap_start_mol
self.add(cap1, cap_start_name)
cap2 = cap_end_mol
self.add(cap2, cap_end_name)
mb.force_overlap(cap1, cap1[cap_start_port], cap2[cap_end_port])
if n == 2:
cap1 = cap_start_mol
self.add(cap1, cap_start_name)
chain = CH2()
self.add(chain, 'chain')
mb.force_overlap(move_this=chain,
from_positions=chain['down'],
to_positions=cap1[cap_start_port], )
cap2 = cap_end_mol
self.add(cap2, cap_end_name)
mb.force_overlap(move_this=cap2,
from_positions=cap2[cap_end_port],
to_positions=chain['up'])
if n > 2:
cap1 = cap_start_mol
self.add(cap1, cap_start_name)
chain = mb.recipes.Polymer(CH2(), n=n-1, port_labels=('up', 'down'))
self.add(chain, 'chain')
mb.force_overlap(move_this=chain,
from_positions=chain['down'],
to_positions=cap1[cap_start_port])
cap2 = cap_end_mol
self.add(cap2, cap_end_name)
mb.force_overlap(move_this=cap2,
from_positions=cap2[cap_end_port],
to_positions=chain['up'])
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 __init__(self, n=1, cap_start=True):
super(Alcohol, self).__init__()
if n < 1:
raise ValueError('n must be 1 or more')
if cap_start:
self.add(Backbone(n=n, cap_start_mol=CH3(),
cap_start_name= 'methyl_start', cap_start_port = 'up',
cap_end_mol = OH(), cap_end_name='OH_end',
cap_end_port= 'down'))
else:
self.add(Backbone(n=n, cap_start_mol=CH2(),
cap_start_name= 'methyl_start', cap_start_port = 'up',
cap_end_mol = OH(), cap_end_name='OH_end',
cap_end_port= 'down'))
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.lib.recipes.Polymer([CH2()])
chain.build(n=chain_length)
self.add(chain, 'chain')
def __init__(self, n=1, cap_start=True):
super(Acid, self).__init__()
if n < 1:
raise ValueError('n must be 1 or more')
if cap_start:
if n ==1:
self.add(Methanol())
if n > 1:
self.add(Backbone(n=n-1, cap_start_mol=CH3(),
cap_start_name= 'methyl_start', cap_start_port = 'up',
cap_end_mol = COOH(), cap_end_name='COOH_end',
cap_end_port= 'down'))
else:
if n ==1:
self.add(COOH())
if n > 1:
self.add(Backbone(n=n-1, cap_start_mol=CH2(),
cap_start_name= 'methyl_start', cap_start_port = 'up',
cap_end_mol = COOH(), cap_end_name='COOH_end',
cap_end_port= 'down'))
def __init__(self, n=3, cap_front=True, cap_end=True):
"""Initialize an Alkane Compound.
Args:
n: Number of carbon atoms.
cap_front: Add a methyl group to the beginning of chain ('down' port).
cap_end: Add a methyl group to the end of chain ('up' port).
"""
if n < 1:
raise ValueError('n must be 1 or more')
super(Alkane, self).__init__()
# Handle the case of Methane and Ethane separately
if n < 3:
if n == 1:
if cap_front and cap_end:
self.add(Methane(), 'chain')
elif cap_front != cap_end:
chain = CH3()
self.add(chain, 'chain')
if cap_front:
self.add(chain['up'], 'down', containment=False)
else:
self.add(chain['up'], 'up', containment=False)
else:
chain = CH2()
self.add(chain)
self.add(chain['down'], 'down', containment=False)
self.add(chain['up'], 'up', containment=False)
elif n == 2:
if cap_front and cap_end:
self.add(Ethane(), 'chain')
elif cap_front != cap_end:
chain = CH2()
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'])
self.add(chain['down'], 'down', containment=False)
else:
self.add(CH3(), 'methyl_end')
mb.force_overlap(self['methyl_end'],
self['methyl_end']['up'],
self['chain']['down'])
self.add(chain['up'], 'up', containment=False)
else:
chain = CH2()
self.add(chain, 'chain')
self.add(chain['down'], 'down', containment=False)
self.add(chain['up'], 'up', containment=False)
# Handle general case of n >= 3
else:
# Adjust length of Polmyer for absence of methyl terminations.
if not cap_front:
n += 1
if not cap_end:
n += 1
chain = mb.recipes.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)
def ch2(self):
from mbuild.lib.moieties import CH2
return CH2()
def __init__(self, n=3, cap_front=True, cap_end=True):
"""Initialize an Alkane Compound.
Args
----
n: int, default 3,
Number of carbon atoms.
cap_front: bool, default True
Whether to add a methyl group to the beginning of chain
('down' port).
cap_end: bool, default True,
Whether to add a methyl group to the end of chain ('up' port).
"""
if n < 1:
raise ValueError("n must be 1 or more")
super(Alkane, self).__init__()
# Handle the case of Methane and Ethane separately
if n < 3:
if n == 1:
if cap_front and cap_end:
self.add(Methane(), "chain")
elif cap_front != cap_end:
chain = CH3()
self.add(chain, "chain")
if cap_front:
self.add(chain["up"], "down", containment=False)
else:
self.add(chain["up"], "up", containment=False)
else:
chain = CH2()
self.add(chain)
self.add(chain["down"], "down", containment=False)
self.add(chain["up"], "up", containment=False)
elif n == 2:
if cap_front and cap_end:
self.add(Ethane(), "chain")
elif cap_front != cap_end:
chain = CH2()
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"],
)
self.add(chain["down"], "down", containment=False)
else:
self.add(CH3(), "methyl_end")
mb.force_overlap(
self["methyl_end"],
self["methyl_end"]["up"],
self["chain"]["down"],
)
self.add(chain["up"], "up", containment=False)
else:
chain = CH2()
self.add(chain, "chain")
self.add(chain["down"], "down", containment=False)
self.add(chain["up"], "up", containment=False)
# Handle general case of n >= 3
else:
end_groups = [None, None]
# Adjust length of Polmyer for absence of methyl terminations.
if cap_front:
n -= 1
end_groups[0] = CH3()
if cap_end:
n -= 1
end_groups[1] = CH3()
chain = mb.recipes.Polymer(monomers=[CH2()], end_groups=end_groups)
chain.build(n, add_hydrogens=False)
self.add(chain, "chain")
if not cap_front:
# Hoist port label to Alkane level.
self.add(self["chain"]["up"], "up", containment=False)
if not cap_end:
# Hoist port label to Alkane level.
self.add(self["chain"]["down"], "down", containment=False)
first_part = this_part
else:
# Transform this part, such that it's bottom port is rotated
# and translated to the last part's top port.
force_overlap(
this_part,
this_part.labels[port_labels[1]],
last_part.labels[port_labels[0]],
)
last_part = this_part
if n_added == n * len(sequence) - 1:
break
# Hoist the last part's top port to be the top port of the polymer.
self.add(last_part.labels[port_labels[0]],
port_labels[0],
containment=False)
# Hoist the first part's bottom port to the bottom port of the polymer.
self.add(first_part.labels[port_labels[1]],
port_labels[1],
containment=False)
if __name__ == "__main__":
from mbuild.lib.moieties import CH2
ch2 = CH2()
poly = Polymer(ch2, n=13, port_labels=("up", "down"))
poly.save("polymer.mol2")
def __init__(self, n=3, cap_front=True, cap_end=True):
"""Initialize an PEG Compound.
Args:
n: Number of carbon + oxygen atoms.
After deducted for cap front, cap end, and ch2 end
n will be divided by 3 since there are 3 element in a PEG
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(PEG, 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 = CH3()
self.add(ch3_end, 'methyl_end')
# If n is not divisible by 3, add CH2 in place of them
m = 0
while n % 3 != 0:
m += 1
n -= 1
n = n//3
chain = mb.lib.recipes.Polymer(PegMonomer(), n=n, port_labels=('up', 'down'))
self.add(chain, 'chain')
if m != 0:
ch2_chain = mb.lib.recipes.Polymer(CH2(), n=m, port_labels=('up','down'))
self.add(ch2_chain, 'ch2_chain')
mb.force_overlap(self['ch2_chain'], self['ch2_chain']['up'],
self['chain']['down'])
if cap_end:
mb.force_overlap(self['methyl_end'], self['methyl_end']['down'],
self['ch2_chain']['down'])
else:
self.add(ch2_chain['down'], 'down', containment=False)
else:
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['methyl_front'], self['methyl_front']['down'],
self['chain']['up'])
else:
self.add(chain['up'], 'up', containment=False)
else:
if cap_end or cap_front:
ch3 = CH3()
self.add(ch3, 'methyl')
self.add(ch3['down'], 'down', containment=False)
else:
peg = PegMonomer()
self.add(peg, 'PEG')
self.add(peg['up'], 'up', containment=False)
self.add(peg['down'], 'down', containment=False)