def parmed_ethane(self):
from mbuild.lib.molecules import Ethane
compound = Ethane()
oplsaa = foyer.Forcefield(name="oplsaa")
pmd_structure = oplsaa.apply(compound)
return pmd_structure
def typed_ethane():
from mbuild.lib.molecules import Ethane
mb_ethane = Ethane()
oplsaa = foyer.Forcefield(name='oplsaa')
pmd_ethane = oplsaa.apply(mb_ethane)
top = from_parmed(pmd_ethane)
top.name = 'ethane'
return top
def typed_ethane(self):
from mbuild.lib.molecules import Ethane
mb_ethane = Ethane()
oplsaa = foyer.Forcefield(name='oplsaa')
# At this point, we still need to go through
# parmed Structure, until foyer can perform
# atomtyping on gmso Topology
pmd_ethane = oplsaa.apply(mb_ethane)
top = from_parmed(pmd_ethane)
return top
def ethane(self):
from mbuild.lib.molecules import Ethane
top = from_mbuild(Ethane())
return top
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 ethane(self):
from mbuild.lib.molecules import Ethane
return Ethane()
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)