def __init__(self, length=1, terminal_group=None):
super(Pegsilane, self).__init__()
module = __import__('atools.lib.moieties.one_port.'+terminal_group)
class_ = getattr(module.lib.moieties.one_port, terminal_group.title())
t_group = class_()
self.add(t_group, 'terminal_group')
chain = mb.recipes.Polymer(monomers=[CH2(), O()], sequence='AAB',
n=math.floor(length/3), port_labels=('up', 'down'))
mb.force_overlap(self['terminal_group'],
self['terminal_group']['down'],
to_positions=chain['up'])
self.add(chain)
silane = Silane()
self.add(silane)
mb.force_overlap(move_this=silane,
from_positions=silane.all_ports()[1],
to_positions=chain['down'])
self.add(silane['down'], 'down', containment=False)
def __init__(self, chain_length, terminal_group):
super(Alkylsilane, self).__init__()
terminal_group_dict = \
{'acetyl':Acetyl, 'amino':Amino, 'biphenyl':Biphenyl,
'carboxyl':Carboxyl, 'cyano':Cyano, 'cyclopropyl':Cyclopropyl,
'ethylene':Ethylene, 'fluorophenyl':Fluorophenyl,
'formyl':Formyl, 'hydroxyl':Hydroxyl, 'isopropyl':Isopropyl,
'methoxy':Methoxy, 'methyl':Methyl, 'nitro':Nitro,
'nitrophenyl':Nitrophenyl, 'pentafluorophenyl':
Pentafluorophenyl, 'perfluoromethyl':Perfluoromethyl,
'phenyl':Phenyl, 'pyrrole':Pyrrole, 'triazole':Triazole,
'difluoromethyl':Difluoromethyl, 'phenol':Phenol,
'toluene':Toluene, 'benzoicacid':Benzoicacid,
'isopropylbenzene':Isopropylbenzene, 'amide':Amide,
'cyclohexyl':Cyclohexyl, 'sulfhydryl':Sulfhydryl,
'nitroso':Nitroso}
tgroup = terminal_group_dict[terminal_group]()
alkane = Alkane(chain_length, cap_front=False, cap_end=False)
self.add(alkane, 'alkane')
self.add(tgroup, 'terminal_group')
mb.force_overlap(self['alkane'], self['alkane']['up'],
self['terminal_group']['down'])
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(self['silane'], self['silane']['up'],
self['alkane']['down'])
self.add(silane['down'], 'down', containment=False)
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, chain_length):
super(AlkylSilane, self).__init__()
alkane = mb.recipes.Alkane(chain_length, cap_end=False)
self.add(alkane, 'alkane')
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(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, terminal_group):
super(Alkylsilane, self).__init__()
terminal_group_dict = {"methyl":Methyl}
tgroup = terminal_group_dict[terminal_group]()
alkane = Alkane(chain_length, cap_front=False, cap_end=False)
self.add(alkane, 'alkane')
self.add(tgroup, 'terminal_group')
mb.force_overlap(self['alkane'], self['alkane']['up'],
self['terminal_group']['down'])
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(self['silane'], self['silane']['up'], self['alkane']['down'])
self.add(silane['down'], 'down', containment=False)
def __init__(self, n, ch2_cap=False):
super(PEGSilane, self).__init__()
tgroup = CH3()
peg = PEG(n, cap_front=False, cap_end=False)
self.add(peg, 'peg')
self.add(tgroup, 'terminal_group')
mb.force_overlap(self['peg'], self['peg']['up'],
self['terminal_group']['down'])
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(self['silane'], self['silane']['up'],
self['peg']['down'])
self.add(silane['down'], 'down', containment=False)
def __init__(self, chain_length, terminal_group):
super(Alkylsilane, self).__init__()
module = __import__('atools.lib.moieties.one_port.'+terminal_group)
class_ = getattr(module.lib.moieties.one_port, terminal_group.title())
tgroup = class_()
alkane = Alkane(chain_length, cap_front=False, cap_end=False)
self.add(alkane, 'alkane')
self.add(tgroup, 'terminal_group')
mb.force_overlap(self['alkane'], self['alkane']['up'],
self['terminal_group']['down'])
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(self['silane'], self['silane']['up'], self['alkane']['down'])
self.add(silane['down'], 'down', containment=False)
def __init__(self, chain_length):
super(nC_APD, self).__init__()
alkane = Alkane(chain_length, cap_end=False)
self.add(alkane, 'alkane')
apd = APD()
self.add(apd, 'apd')
mb.force_overlap(self['alkane'], self['alkane']['down'],
self['apd']['up'])
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(self['silane'], self['silane']['up'],
self['apd']['down'])
# Hoist silane port to AlkylSilane level.
self.add(silane['down'], 'down', containment=False)
self.spin(np.pi/2, [1, 0, 0])
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, chain_length, internal_group, locations):
super(Alkylsilane, self).__init__()
hmodule = __import__('atools.lib.moieties.multiple_ports.' +
internal_group)
hclass_ = getattr(hmodule.lib.moieties.multiple_ports,
internal_group.title())
hgroup = hclass_()
# Determine alkane segments
if isinstance(locations, int):
locations = [locations]
locations.sort()
silane = Silane()
self.add(silane, 'silane')
self.add(silane['down'], 'down', containment=False)
if 0 in locations:
'''
self.add(hgroup, 'hgroup')
mb.force_overlap(self['silane'], self['silane']['up'],
self['hgroup']['down'])
'''
current_segment = silane
else:
first_length = locations[0]
first_segment = Alkane(first_length,
cap_front=False,
cap_end=False)
self.add(first_segment, 'bottom_chain')
mb.force_overlap(self['silane'], self['silane']['up'],
self['bottom_chain']['down'])
current_segment = first_segment
c_remove = 0
if internal_group in ['amide', 'hemiacetal']:
c_remove += 1
for i, loc in enumerate(locations[1:]):
hgroup_clone = mb.clone(hgroup)
self.add(hgroup_clone, 'hgroup{}'.format(i + 1))
mb.force_overlap(self['hgroup{}'.format(i + 1)],
self['hgroup{}'.format(i + 1)]['down'],
current_segment['up'])
current_segment = hgroup_clone
length = loc - locations[i] - 1 - c_remove
if length > 0:
segment = Alkane(length, cap_front=False, cap_end=False)
self.add(segment, 'internal_chain{}'.format(i + 1))
current_segment = segment
mb.force_overlap(
self['internal_chain{}'.format(i + 1)],
self['internal_chain{}'.format(i + 1)]['down'],
self['hgroup{}'.format(i + 1)]['up'])
self.add(hgroup, 'hgroup')
mb.force_overlap(self['hgroup'], self['hgroup']['down'],
current_segment['up'])
last_length = chain_length - locations[-1] - 1 - c_remove
if last_length:
last_segment = Alkane(last_length, cap_front=True, cap_end=False)
self.add(last_segment, 'top_chain')
mb.force_overlap(self['top_chain'], self['top_chain']['down'],
self['hgroup']['up'])
else:
hydrogen = H()
self.add(hydrogen, 'H-cap')
mb.force_overlap(self['H-cap'], self['H-cap']['up'],
self['hgroup']['up'])
def silane(self):
from mbuild.lib.moieties import Silane
return Silane()