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=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, 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=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'])