def __init__(self):
super(H, self).__init__()
self.add(mb.Particle(name='H'))
self.add(mb.Port(anchor=self[0]), 'up')
mb.rotate_around_z(self['up'], np.pi)
mb.translate(self['up'], np.array([0, 0.07, 0]))
def benzene_from_parts(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi/180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi/180.0))
benzene = mb.Compound(name='Benzene')
benzene.add(ch)
current = ch
for _ in range(5):
ch_new = mb.clone(ch)
mb.force_overlap(move_this=ch_new,
from_positions=ch_new['a'],
to_positions=current['b'])
current = ch_new
benzene.add(ch_new)
carbons = [p for p in benzene.particles_by_name('C')]
benzene.add_bond((carbons[0],carbons[-1]))
return benzene
def benzene_from_parts(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0], separation=0.07), 'a')
mb.rotate_around_z(ch['a'], 120.0 * (np.pi / 180.0))
ch.add(mb.Port(anchor=ch[0], separation=0.07), 'b')
mb.rotate_around_z(ch['b'], -120.0 * (np.pi / 180.0))
ch_copy = mb.clone(ch)
benzene = mb.Compound(name='Benzene')
benzene.add(ch)
current = ch
for _ in range(5):
ch_new = mb.clone(ch_copy)
mb.force_overlap(move_this=ch_new,
from_positions=ch_new['a'],
to_positions=current['b'])
current = ch_new
benzene.add(ch_new)
carbons = [p for p in benzene.particles_by_name('C')]
benzene.add_bond((carbons[0], carbons[-1]))
return benzene
def rigid_ch(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.label_rigid_bodies()
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi/180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi/180.0))
return ch
def rigid_ch(self):
ch = mb.load(get_fn('ch.mol2'))
ch.name = 'CH'
ch.label_rigid_bodies()
mb.translate(ch, -ch[0].pos)
ch.add(mb.Port(anchor=ch[0]), 'a')
mb.translate(ch['a'], [0, 0.07, 0])
mb.rotate_around_z(ch['a'], 120.0 * (np.pi / 180.0))
ch.add(mb.Port(anchor=ch[0]), 'b')
mb.translate(ch['b'], [0, 0.07, 0])
mb.rotate_around_z(ch['b'], -120.0 * (np.pi / 180.0))
return ch
def __init__(self):
super(Ester, self).__init__()
mb.load('ester.pdb', compound=self, relative_to_module=self.__module__)
mb.translate(self, -self[0].pos)
self.add(mb.Port(anchor=self[2]), 'up')
mb.rotate_around_z(self['up'], np.pi / 2)
mb.translate_to(self['up'], self[2].pos + np.array([0.07, 0, 0]))
self.add(mb.Port(anchor=self[0]), 'down')
mb.rotate_around_z(self['down'], np.pi / 2)
mb.translate(self['down'], np.array([-0.07, 0, 0]))
def __init__(self):
super(C3, self).__init__()
self.add(mb.Particle(name='C'))
self.add(mb.Port(anchor=self[0]), 'up')
mb.translate(self['up'], np.array([0, 0.07, 0]))
self.add(mb.Port(anchor=self[0]), 'down')
mb.translate(self['down'], np.array([0, 0.07, 0]))
mb.rotate_around_z(self['down'], np.pi * 2/3)
self.add(mb.Port(anchor=self[0]), 'left')
mb.translate(self['left'], np.array([0, 0.07, 0]))
mb.rotate_around_z(self['left'], -np.pi * 2/3)
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():
"""A quick test for updating a Compound and traversing its hierarchy. """
# Create a compound and write it to file.
brush1 = Brush()
brush1.save("brush1.pdb")
# Create another compound, rotate it and write it to file.
brush2 = Brush()
mb.rotate_around_z(brush2, pi/2)
brush2.save("brush2.pdb")
# Load brush2.pdb into brush1, modifying the atom positions of brush1.
brush1.update_coordinates("brush2.pdb")
brush1.save("modified_brush1.pdb")
# Access the internals of the updated brush1.
print(brush1['pmpc'])
for mpc in brush1['pmpc']['monomer']:
print(mpc)
def test_reload(self):
from mbuild.examples.pmpc.brush import Brush
from numpy import pi
# Create a compound and write it to file.
brush1 = Brush()
brush1.save("brush1.pdb")
# Create another compound, rotate it and write it to file.
brush2 = Brush()
mb.rotate_around_z(brush2, pi / 2)
brush2.save("brush2.pdb")
# Load brush2.pdb into brush1, modifying the atom positions of brush1.
brush1.update_coordinates("brush2.pdb")
brush1.save("modified_brush1.pdb")
assert brush1['pmpc'].n_particles == 164
assert brush1['pmpc'].n_bonds == 163
assert len(brush1['pmpc']['monomer']) == 4
assert brush1['pmpc']['monomer'][0].n_particles == 41
assert brush1['pmpc']['monomer'][0].n_bonds == 40
def test_reload(self):
from mbuild.examples.pmpc.brush import Brush
from numpy import pi
# Create a compound and write it to file.
brush1 = Brush()
brush1.save("brush1.pdb")
# Create another compound, rotate it and write it to file.
brush2 = Brush()
mb.rotate_around_z(brush2, pi/2)
brush2.save("brush2.pdb")
# Load brush2.pdb into brush1, modifying the atom positions of brush1.
brush1.update_coordinates("brush2.pdb")
brush1.save("modified_brush1.pdb")
assert brush1['pmpc'].n_particles == 164
assert brush1['pmpc'].n_bonds == 163
assert len(brush1['pmpc']['monomer']) == 4
assert brush1['pmpc']['monomer'][0].n_particles == 41
assert brush1['pmpc']['monomer'][0].n_bonds == 40