def __init__(self):
super(TnpBox, self).__init__()
tnp_proto = Tnp(ball_radius=5, n_chains=5, chain_length=8)
pattern = mb.Grid3DPattern(3, 3, 3)
pattern.scale(100)
rnd = random.Random()
rnd.seed(1928)
for pos in pattern:
tnp = clone(tnp_proto)
mb.rotate_around_x(tnp, rnd.uniform(0, 2 * pi))
mb.rotate_around_y(tnp, rnd.uniform(0, 2 * pi))
mb.rotate_around_z(tnp, rnd.uniform(0, 2 * pi))
mb.translate(tnp, pos)
self.add(tnp)
def __init__(self, c1_pos=None, rotate_random=True):
super(C10, self).__init__()
num_particles = 10
for index in range(num_particles):
self.add(C(), label='C[$]')
if c1_pos is not None:
mb.translate(self['C'][0], c1_pos)
if rotate_random is True:
mb.rotate_around_x(self['C'][0], random.uniform(0, 2 * math.pi))
mb.rotate_around_y(self['C'][0], random.uniform(0, 2 * math.pi))
mb.rotate_around_z(self['C'][0], random.uniform(0, 2 * math.pi))
for index in range(num_particles - 1):
mb.force_overlap(move_this=self['C'][index + 1],
from_positions=self['C'][index + 1]['down'],
to_positions=self['C'][index]['up'])
def main():
from mbuild.utils.io import get_fn
from mbuild.lib.moieties import H2O
water = H2O()
ecerns = mb.load(get_fn('ecer2.pdb'))
chol = mb.load(get_fn('cg-chol.pdb'))
# Orient along the z-direction.
mb.rotate_around_x(chol, -135.0*np.pi/180)
mb.rotate_around_y(chol, -45.0*np.pi/180)
lipids = [(ecerns, 0.5), (chol, 0.5)]
bilayer = Bilayer(lipids, n_lipids_x=15, n_lipids_y=15, area_per_lipid=1.4,
solvent=water, ref_atoms=[1, 6], spacing_z=0.7,
solvent_per_lipid=20, mirror=False)
bilayer.save(filename='bilayer.pdb')
return bilayer
def __init__(self, alpha=0):
super(MPC, self).__init__()
# Look for data file in same directory as this python module.
mb.load('mpc.pdb', compound=self, relative_to_module=self.__module__)
# Transform the coordinate system of mpc such that the two carbon atoms
# that are part of the backbone are on the y axis, c_backbone at the origin.
C_top = self[37]
# this can be achieved with the following alternative syntax:
# C_top = self.labels["atom[37]"]
# C_top = self.labels["atom"][37]
C_bottom = self[1]
mb.y_axis_transform(self, new_origin=C_top, point_on_y_axis=C_bottom)
# Add top port.
self.add(mb.Port(anchor=C_top), label='up')
mb.translate(self['up'], C_top.pos - (C_top.pos - C_bottom.pos)*1.50)
# Add bottom port
self.add(mb.Port(anchor=C_bottom), 'down')
mb.rotate_around_y(self['down'], alpha)
mb.translate(self['down'], C_bottom.pos - (C_bottom.pos - C_top.pos)*1.50)