def binding_prob(P, **params):
for p, result in nanopores.collect_dict(P):
pore = nanopores.get_pore(**params)
rw = randomwalk.RandomWalk(pore, **params)
receptorp = dict(receptor_params)
receptorp["p"] = p
rw.add_domain(receptor, **receptorp)
print "Start Random Walk with p = %s." % p
for t in rw.walk():
pass
# times with binding
times = rw.times[rw.bindings > 0]
result.new = dict(
p0=np.mean(rw.bindings > 0),
a0=np.mean(rw.attempts > 0),
mean_bindings=np.mean(rw.bindings),
mean_attempts=np.mean(rw.attempts),
std_bindings=np.std(rw.bindings),
std_attempts=np.std(rw.attempts),
mean_time=np.mean(times),
std_time=np.std(times),
mean_log_time=np.mean(np.log(times)),
)
return result
def setup_rw(params):
pore = nanopores.get_pore(**params)
rw = randomwalk.RandomWalk(pore, **params)
zrec = rw.zbot + rrec + (rw.ztop - rw.zbot -
2. * rrec) * params["zreceptor"]
xrec = pore.radius_at(zrec) - distrec
posrec = [xrec, 0., zrec]
print "Receptor position: %s" % posrec
receptor = randomwalk.Ball(posrec, rrec) # ztop 46.5
rw.add_domain(receptor, **receptor_params(params))
return rw
def setup_rw(params, **_):
pore = nanopores.get_pore(**params)
rw = randomwalk.RandomWalk(pore, **params)
binding_params = binding_(params)
if params["bind_everywhere"]:
rw.add_wall_binding(**binding_params)
else:
r = pore.params.l3 / 2.
z = -pore.params.hpore / 2. + pore.params.h4
wbind = 1.
lbind = params["lbind"]
bindsite = Rectangle((r, r + wbind), (z, z + lbind))
rw.add_domain(bindsite, exclusion=False, **binding_params)
#rw.domains[0].__dict__.update(exclusion=True, binding=True,
# bind_type="collision", eps=0., p=1., walldist=1.)
return rw
def setup_default(params):
pore = get_pore(**params)
return RandomWalk(pore, **params)
if params.video:
ani = video(rw, cyl=params.cyl, **aniparams)
if params.save:
save(ani, name=name)
else:
plt.show()
else:
for t in rw.walk():
pass
if plot and ((not params.video) or (not params.save)):
histogram(rw, a, b)
#plt.figure()
#hist_poisson(rw, "attempts")
#plt.figure()
#hist_poisson(rw, "bindings")
plt.show()
if __name__ == "__main__":
pore = get_pore(**params)
rw = RandomWalk(pore, **params)
receptor = Ball([15., 0., 30.], 8.)
rw.add_domain(receptor,
exclusion=True,
walldist=1.,
binding=True,
eps=1.,
t=1.5e6,
p=0.14)
run(rw, name="wei")