def main():
args = parse_cl()
monomers = []
type = 0
space = model.CuboidPBC(args.box_len)
# Randomly insert into box and accept if there are not overlaps
for i in range(args.num_particles):
overlap = True
pv = random_unit_vector()
ov = random_unit_vector()
particle = model.OrientedPatchyParticle(i,
'A',
type,
patch_norm=pv,
patch_orient=ov)
monomer = model.SingleParticleMonomer([particle], args.diameter / 2, i)
while overlap:
monomer.pos = args.box_len * (np.random.rand(3) - 0.5)
overlap = model.hard_sphere_overlap(monomer, monomers,
args.diameter, space)
monomers.append(monomer)
# Write files
pdb_file = model.PDBConfigOutputFile(args.output_filebase + '.pdb')
pdb_file.write(monomers)
json_file = model.JSONConfigOutputFile(args.output_filebase + '.json')
json_file.write(monomers, args.box_len)
return overlap
def main():
args = parse_cl()
monomers = []
type = 0
space = model.CuboidPBC(args.box_len)
# Randomly insert into box and accept if there are no overlaps
radius = args.diameter / 2
acd_ntd_angle = 0.6236561373425675
blob_angle1 = -0.318827603743
blob_angle2 = -0.534300804011
s_monomers = cso.construct_monomers(radius, radius, 2, 2,
args.num_monomers, acd_ntd_angle,
blob_angle1, blob_angle2)
monomers = []
for m in s_monomers:
overlap = True
while overlap:
x1r = trans.axangles.axangle2aff([1, 0, 0],
2 * math.pi * random.random(),
m.center)
yr = trans.axangles.axangle2aff([0, 1, 0],
2 * math.pi * random.random(),
m.center)
x2r = trans.axangles.axangle2aff([1, 0, 0],
2 * math.pi * random.random(),
m.center)
m.apply_transformation(x1r)
m.apply_transformation(yr)
m.apply_transformation(x2r)
pos = np.concatenate(
[args.box_len * (np.random.rand(3) - 0.5), [0]])
ref_pos = copy.deepcopy(m.particles[0].pos)
m.particles[0].pos = pos
for p in m.particles[1:]:
pdiff = p.pos - ref_pos
p.pos = space.wrap(pos + pdiff)
overlap = model.hard_sphere_overlap(m, monomers, args.diameter,
space)
monomers.append(m)
# Write files
pdb_file = model.PDBConfigOutputFile(args.output_filebase + '.pdb')
pdb_file.write(monomers)
json_file = model.JSONConfigOutputFile(args.output_filebase + '.json')
json_file.write(monomers, args.box_len)
return overlap
def main():
args = parse_cl()
type = 0
space = model.CuboidPBC(args.box_len)
# Randomly insert into box and accept if there are no overlaps
radius = args.diameter / 2
acd_ntd_angle = 0.6236561373425675
blob_angle1 = -0.318827603743
blob_angle2 = -0.534300804011
set_monomers = []
monomers = cso.construct_monomers(radius, radius, 2, 2,
6 * args.num_hexamers, acd_ntd_angle,
blob_angle1, blob_angle2)
for i in range(args.num_hexamers):
h_monomers = [m for m in monomers[i * 6:i * 6 + 6]]
dimers = []
for j in range(0, 5, 2):
monomer1 = h_monomers[j]
monomer2 = h_monomers[j + 1]
dimer = cso.construct_dimer(monomer1, monomer2)
dimers.append(dimer)
hexamer = cso.construct_hexamer(dimers[0], dimers[1], dimers[2])
overlap = [True] * 6
while np.any(overlap):
#angle1 = 2*math.pi*random.random()
#angle2 = 2*math.pi*random.random()
#angle3 = 2*math.pi*random.random()
delta_pos = args.box_len * (np.random.rand(3) - 0.5)
delta_pos = np.concatenate([delta_pos, [0]])
for j, m in enumerate(h_monomers):
#x1r = trans.axangles.axangle2aff([1, 0, 0], angle1, m.center)
#yr = trans.axangles.axangle2aff([0, 1, 0], angle2, m.center)
#x2r = trans.axangles.axangle2aff([1, 0, 0], angle3, m.center)
#m.apply_transformation(x1r)
#m.apply_transformation(yr)
#m.apply_transformation(x2r)
for p in m.particles:
p.pos = space.wrap(p.pos + delta_pos)
overlap[j] = model.hard_sphere_overlap(m, set_monomers,
args.diameter, space)
set_monomers.extend(h_monomers)
# Write files
json_file = model.JSONConfigOutputFile(args.output_filebase + '.json')
json_file.write(set_monomers, args.box_len)