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.equivalence_transform(self['chain'], self['chain']['up'], 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.equivalence_transform(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== --
def __init__(self):
super(Ethane, self).__init__()
self.add(CH3(), 'methyl1')
self.add(CH3(), 'methyl2')
mb.equivalence_transform(self.methyl1, self.methyl1.up,
self.methyl2.up)
def __init__(self, n=3, cap_front=True, cap_end=True):
if n < 1:
raise Exception('n must be 1 or more')
super(PegPolymer, self).__init__()
if not cap_front:
n += 1
if not cap_end:
n += 1
chain = mb.Polymer(PegMonomer(), n=n-1, port_labels=('down', 'up'))
self.add(chain, 'chain')
if cap_front:
self.add(CH3(), 'methyl_front')
mb.equivalence_transform(
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.equivalence_transform(
self.methyl_end, self.methyl_end.up, self.chain.down)
else:
self.add(chain.down, 'down', containment=False)
def __init__(self):
super(Hexane, self).__init__()
self.add(Propane(), 'propane1')
self.add(Propane(), 'propane2')
mb.equivalence_transform(
self['propane1'], self['propane1']['down'], self['propane2']['down'])
def __init__(self):
super(Hexane, self).__init__()
self.add(Propane(), 'propane1')
self.add(Propane(), 'propane2')
mb.equivalence_transform(self['propane1'], self['propane1']['down'],
self['propane2']['down'])
def __init__(self):
"""Connect two methyl groups to form an ethane. """
super(Ethane, self).__init__()
self.add(CH3(), "methyl1")
self.add(CH3(), "methyl2")
mb.equivalence_transform(self['methyl1'], self['methyl1']['up'], self['methyl2']['up'])
# -- ==ethane== --
def __init__(self, chain_length):
super(AlkylSilane, self).__init__()
alkane = Alkane(chain_length, cap_end=False)
self.add(alkane, 'alkane')
silane = Silane()
self.add(silane, 'silane')
mb.equivalence_transform(self['alkane'], self['alkane']['down'], self['silane']['up'])
# Hoist silane port to AlkylSilane level.
self.add(silane['down'], 'down', containment=False)
def __init__(self, chain_length):
super(PegPolymerSilane, self).__init__()
peg_polymer = PegPolymer(chain_length, cap_end=False)
self.add(peg_polymer, 'peg_polymer')
silane = Silane()
self.add(silane, 'silane')
mb.equivalence_transform(
self.peg_polymer, self.peg_polymer.down, self.silane.up)
self.add(silane.down, 'down', containment=False)
def __init__(self, chain_length):
super(AlkylSilane, self).__init__()
alkane = Alkane(chain_length, cap_end=False)
self.add(alkane, 'alkane')
silane = Silane()
self.add(silane, 'silane')
mb.equivalence_transform(self.alkane, self.alkane.down, self.silane.up)
# Hoist silane port to AlkylSilane level.
self.add(silane.down, 'down', containment=False)
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.equivalence_transform(self['initiator'], self['initiator']['down'], self['silane']['up'])
mb.equivalence_transform(self['pmpc'], self['pmpc']['down'], self['initiator']['up'])
mb.equivalence_transform(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 test_equivalence_transform_deprectation_warning(self, ch2):
ch22 = mb.clone(ch2)
with pytest.warns(DeprecationWarning):
mb.equivalence_transform(ch22,
from_positions=ch22['up'],
to_positions=ch2['down'])
def test_equivalence_transform_deprectation_warning(self, ch2):
ch22 = mb.clone(ch2)
with pytest.warns(DeprecationWarning):
mb.equivalence_transform(ch22,
from_positions=ch22['up'],
to_positions=ch2['down'])
