def test_symetrie():
eps = 1e-4
P = Polymer(0, start=0, end=2, origins=[0, 2])
P.increment_time(dt=0.5)
P.add_fork(ptags=["Left", "Right"],
otag=0,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=1)
P.add_fork(ptags=["Left1", "Right1"],
otag=2,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=1)
for t in range(4):
#print("Avant",[[p,p.position] for p in P.modules])
inc = P.increment_time(dt=0.5)
#print(inc)
bind_diff, diff_diff, update_bond, passivated_origin, to_release, alone = inc
#print(P.ended[-1].position)
#print("Apres",[[p,p.position] for p in P.modules])
#print(P.end)
if t == 0:
assert ("Right1" in alone and "Left" in alone)
#print("Here")
for p in P.ended:
if p.tag in ["Left", "Right1"]:
#print("path", p.path,len)
assert (len(p.path) == 1)
elif p.tag in ["Left1", "Right"]:
assert (len(p.path) == 2)
if p.tag == "Right":
#print(p.path)
assert (p.path[0].pos == 0.5 and p.path[1].pos == 1)
if p.tag == "Left1":
#print(p.path,p.position)
assert (p.path[0].pos == 2.5 and p.path[1].pos == 1.5)
#print(p.tag,p.path)
assert (np.all(P.get_replication_profile(1) == [1, 2, 1]))
def test_remove_passivated4():
P = Polymer(0, start=0, end=2, origins=[0, 1, 2])
P.modules[1].position = 1.9
P.modules[2].position = 2.1
P.add_fork(ptags=["Left", "Right"],
otag=0,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=1)
for t in range(5):
#print("Avant",[[p,p.position] for p in P.modules])
inc = P.increment_time(dt=1)
bind_diff, diff_diff, update_bond, passivated_origin, to_release, alone = inc
#print(P.ended[-1].position)
#print("Apres",[[p,p.position] for p in P.modules])
#print(P.end)
#print(P.modules)
#print(t,passivated_origin)
if t == 0:
assert ("Left" in alone)
#print("Here")
for p in P.ended:
if p.tag in ["Right"]:
#print("path", p.path,len)
assert (len(p.path) == 1)
if t == 1:
assert (1 in passivated_origin and 2 in passivated_origin)
#print(P.get_replication_profile(1))
assert (np.all(P.get_replication_profile(1) == [1, 2, 3]))
def test_jump2():
P = Polymer(0, start=0, end=2, origins=[0, 2])
#
P.add_fork(ptags=["Left", "Right"],
otag=2,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=3)
for t in range(3):
#print([m.path for m in P.modules if m.move])
P.increment_time(dt=1)
assert (np.all(P.get_replication_profile(1) == [1, 1, 1]))
def test_It():
P = Polymer(0, start=0, end=2, origins=[0, 2])
P.increment_time(dt=0.5)
P.add_fork(ptags=["Left", "Right"],
otag=0,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=1)
P.add_fork(ptags=["Left1", "Right1"],
otag=2,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=1)
for t in range(3):
P.increment_time(dt=1)
#print([m.path for m in P.ended if m.move])
#print(P.get_replication_profile(1))
It = P.get_firing_time_It(cut=0, normed=False, dt=0.5)
#print(It)
assert (np.all(It[1] == array([0., 2., 0., 0., 0., 0., 0., 0., 0., 0.])))
assert (np.all(It[0] == array([1, 1])))
def test_simple2():
P = Polymer(0, start=0, end=2, origins=[0, 2])
P.increment_time(dt=0.5)
P.add_fork(ptags=["Left", "Right"],
otag=0,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=1)
P.add_fork(ptags=["Left1", "Right1"],
otag=2,
new_btags=[None, None],
diff_diff_tag=None,
fork_speed=1)
for t in range(3):
P.increment_time(dt=1)
#print([m.path for m in P.ended if m.move])
#print(P.get_replication_profile(1))
assert (np.all(P.get_replication_profile(1) == [1, 2, 1]))
def __init__(self,
nori,
ndiff,
lengths,
p_on,
p_off,
only_one=False,
fork_speed=1,
dt_speed=1,
tolerance=0.1,
gindin=True,
p_v=1,
random=False,
positions=None,
ramp=None,
max_ramp=None,
ramp_type="linear",
strengths=None,
fsd="uniform",
variance_fs=1):
self.p_on = p_on
self.p_off = p_off
self.ndiff = ndiff
self.oris = []
self.only_one = only_one
self.lengths = lengths
self.dt_speed = dt_speed
self.fs = fork_speed
self.fsd = fsd
self.vfs = variance_fs
self.gindin = gindin
self.p_v = p_v
self.Ndiff_libre_t = []
self.positions = positions
self.ramp = ramp
self.max_ramp = max_ramp
self.strengths = copy.deepcopy(strengths)
self.uniform_strength = False
self.ramp_type = ramp_type
if self.ramp_type not in ["linear", "exp", "pulse"]:
raise "Invalid ramp type"
if self.max_ramp and self.max_ramp > self.ndiff:
print(self.max_ramp, self.ndiff)
raise "Problem max_ramp > ndiff"
# print(nori)
assert (len(lengths) == len(nori))
starts = [0] + np.cumsum(lengths).tolist()
# print(starts)
for el, length, start in zip(nori, lengths, starts):
if type(el) in [list, np.ndarray]:
self.oris.append(el)
continue
self.oris.append([])
while (el - len(self.oris[-1])) / el > tolerance:
self.oris[-1] = [
np.random.randint(length) for ori in range(el)
]
self.oris[-1] = list(set(self.oris[-1]))
# print(self.oris)
# print(len(self.oris),(nori-len(self.oris)) / nori)
if strengths is None or strengths == []:
self.uniform_strength = True
self.strengths = [[1] * len(o) for o in self.oris]
if positions is None:
self.polys = [
Polymer(i,
start,
start + length - 1,
np.array(oris) + start,
random=random,
strengths=strengths,
max_fs=self.max_fs())
for i, (start, length, oris, strengths) in enumerate(
zip(starts, lengths, self.oris, self.strengths))
]
else:
self.polys = [
Polymer(i,
start,
start + length - 1,
np.array(oris) + start,
random=random,
positions=np.array(position) + start,
strengths=strengths,
max_fs=self.max_fs())
for i, (start, length, oris, position, strengths) in enumerate(
zip(starts, lengths, self.oris, self.positions,
self.strengths))
]
class MyD(dict):
def __init__(self, *args):
dict.__init__(self, *args)
self.set = 0
def __setitem__(self, key, value):
if key == 0 and value == 0:
self.set += 1
if self.set == 1:
raise
dict.__setitem__(self, key, value)
self.libre = {d: 0 for d in np.arange(ndiff)}
self.origins = {d: None for d in np.arange(ndiff)}
self.record_diffusing = [Diffusing(d) for d in np.arange(ndiff)]
self.fork_speeds = []