def simulate(self, stop_time):
"""
Simulate after given species initial number and stoptime
Parameters:
list:the number of the species at t=0
real:the time to stop the simualtion
Returns:
list:the record of the simulation
the format of the list is : [[time,[species current number,...]],...]
"""
species_to_reaction = [[] for i in range(self.species_number)]
for i in range(self.reaction_number):
for j in self.reactant_data[i]:
species_to_reaction[j].append(i)
for j in self.product_data[i]:
species_to_reaction[j].append(i)
reaction_to_change = [[] for i in range(self.reaction_number)]
for i in range(self.reaction_number):
for j in self.reactant_data[i]:
reaction_to_change[i] += species_to_reaction[j]
for j in self.product_data[i]:
reaction_to_change[i] += species_to_reaction[j]
reaction_to_change = [list(set(i)) for i in reaction_to_change]
current = [i[1] for i in self.species]
time = 0
self.record = [[time, current]]
possibility = [i for i in self.constant]
for i in range(self.reaction_number):
for j in self.reactant_data[i]:
possibility[i] *= current[j]
possibility_sum = 0
for i in possibility:
possibility_sum += i
"""
struct current_data
{
float time;
long long *numbers;
};
struct reaction_data
{
int sub_num;
int *subs;
};
struct reaction_change_data
{
int reaction_num;
int *reacs;
};
struct record_data
{
struct current_data *ans;
int num;
};
struct record_data simulate(
float stop_time,
int species_number,
int reaction_number,
long long *current,//initial long long * species_number
float *constant,// float * reaction_number
struct reaction_data *reactant_data,// reaction_data * reaction_number
struct reaction_data *product_data,
struct reaction_change_data *reaction_link
);
"""
if C:
class c_current_data(ctypes.Structure):
_fields_ = [
("time", ctypes.c_float),
("numbers", ctypes.POINTER(ctypes.c_longlong))
]
class c_reaction_data(ctypes.Structure):
_fields_ = [
("sub_num", ctypes.c_int),
("subs", ctypes.POINTER(ctypes.c_int))
]
class c_reaction_change_data(ctypes.Structure):
_fields_ = [
("reaction_num", ctypes.c_int),
("reacs", ctypes.POINTER(ctypes.c_int))
]
class c_record_data(ctypes.Structure):
_fields_ = [
("ans",ctypes.POINTER(c_current_data)),
("num",ctypes.c_int)
]
c_stop_time = ctypes.c_float(stop_time)
c_species_number = ctypes.c_int(self.species_number)
c_reaction_number = ctypes.c_int(self.reaction_number)
STDLIB.malloc.restype = ctypes.POINTER(ctypes.c_longlong)
c_current = STDLIB.malloc(ctypes.sizeof(ctypes.c_longlong)*self.species_number)
#c_current = (ctypes.c_longlong*self.species_number)()
for i in range(self.species_number):
c_current[i] = current[i]
STDLIB.malloc.restype = ctypes.POINTER(ctypes.c_float)
c_constant = STDLIB.malloc(ctypes.sizeof(ctypes.c_float)*self.reaction_number)
for i in range(self.reaction_number):
c_constant[i] = self.constant[i]
STDLIB.malloc.restype = ctypes.POINTER(c_reaction_data)
c_reactant_data = STDLIB.malloc(ctypes.sizeof(c_reaction_data)*self.reaction_number)
c_product_data = STDLIB.malloc(ctypes.sizeof(c_reaction_data)*self.reaction_number)
STDLIB.malloc.restype = ctypes.POINTER(ctypes.c_int)
for i in range(self.reaction_number):
c_reactant_data[i].sub_num = len(self.reactant_data[i])
c_reactant_data[i].subs = STDLIB.malloc(ctypes.sizeof(ctypes.c_int)*c_reactant_data[i].sub_num)
for j in range(c_reactant_data[i].sub_num):
c_reactant_data[i].subs[j] = self.reactant_data[i][j]
c_product_data[i].sub_num = len(self.product_data[i])
c_product_data[i].subs = STDLIB.malloc(ctypes.sizeof(ctypes.c_int)*c_product_data[i].sub_num)
for j in range(c_product_data[i].sub_num):
c_product_data[i].subs[j] = self.product_data[i][j]
STDLIB.malloc.restype = ctypes.POINTER(c_reaction_change_data)
c_reaction_link = STDLIB.malloc(ctypes.sizeof(c_reaction_change_data)*self.reaction_number)
STDLIB.malloc.restype = ctypes.POINTER(ctypes.c_int)
for i in range(self.reaction_number):
c_reaction_link[i].reaction_num = len(reaction_to_change[i])
c_reaction_link[i].reacs = STDLIB.malloc(ctypes.sizeof(ctypes.c_int)*c_reaction_link[i].reaction_num)
for j in range(c_reaction_link[i].reaction_num):
c_reaction_link[i].reacs[j] = reaction_to_change[i][j]
SIMULATE.simulate.restype = c_record_data
#print "s start in py"
ans = SIMULATE.simulate(
c_stop_time,
c_species_number,
c_reaction_number,
c_current,
c_constant,
c_reactant_data,
c_product_data,
c_reaction_link)
#print "s done in py"
#print "s really done in py"
num = ans.num;
#print num
self.record = []
for i in range(num):
self.record.append([ans.ans[i].time,[ans.ans[i].numbers[j] for j in range(self.species_number)]])
#print ans.ans[i].time
#print "set done!"
"""#free
STDLIB.free(c_current)
STDLIB.free(c_constant)
for i in range(self.reaction_number):
STDLIB.free(c_reactant_data[i].subs)
STDLIB.free(c_product_data[i].subs)
STDLIB.free(c_reactant_data)
STDLIB.free(c_product_data)
for i in range(self.reaction_number):
STDLIB.free(c_reaction_link[i].reacs)
STDLIB.free(c_reaction_link)
#free ans TODO"""
return self.record
else:
if DEBUG:
sw_alloc("Sum")
sw_start("Sum")
sw_alloc("1")
sw_alloc("2")
sw_alloc("3")
sw_alloc("4")
while time < stop_time:
if DEBUG:
sw_start("1")
current = [x for x in current]
if possibility_sum == 0:
break
delta_time = -math.log(random.random()) / possibility_sum
if DEBUG:
sw_accmu("1")
sw_start("2")
randomer = random.random()*possibility_sum
sumer = 0
next_reaction = 0
while True:
sumer += possibility[next_reaction]
if sumer >= randomer:
break
next_reaction += 1
if DEBUG:
sw_accmu("2")
sw_start("3")
for species_temp in self.reactant_data[next_reaction]:
current[species_temp] -= 1
for species_temp in self.product_data[next_reaction]:
current[species_temp] += 1
time += delta_time
self.record.append([time+0, current])
if DEBUG:
sw_accmu("3")
sw_start("4")
for i in reaction_to_change[next_reaction]:
possibility_sum -= possibility[i]
possibility[i] = self.constant[i]
for j in self.reactant_data[i]:
possibility[i] *= current[j]
possibility_sum += possibility[i]
if DEBUG:
sw_accmu("4")
if DEBUG:
sw_accmu("Sum")
sw_print("1")
sw_print("2")
sw_print("3")
sw_print("4")
sw_print("Sum")
return self.record
#!/usr/bin/env python
from django.test import TestCase
from data_test import system_data
from bio_system import bio_system
from stopwatch import sw_alloc, sw_start, sw_accmu, sw_print
systems_data = [
{'simulation_parameters': [{'device_parameter': {'initial': [10, 10, 10]}, 'e5': {'reg': 20}, 'e4': {'reg': 20}, 'e6': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e1': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e3': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e2': {'reg': 20}}, {'device_parameter': {'initial': [0]}}], 'nodes': ['NOT3', 'INPUT'], 'system_parameter': {'time': 100}, 'arcs': [{'to': 0, 'from': 1}]},
{'simulation_parameters': [{'device_parameter': {'initial': [10, 10, 10]}, 'e5': {'reg': 20}, 'e4': {'reg': 20}, 'e6': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e1': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e3': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e2': {'reg': 20}}, {'device_parameter': {'initial': [0]}}], 'nodes': ['NOT5', 'INPUT'], 'system_parameter': {'time': 100}, 'arcs': [{'to': 0, 'from': 1}]},
{'simulation_parameters': [{'device_parameter': {'initial': [10, 10, 10]}, 'e8': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e5': {'reg': 20}, 'e4': {'reg': 20}, 'e7': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e6': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e1': {'decay1': 0.1, 'decay2': 0.05, 'trans1': 0.01, 'trans2': 0.5}, 'e3': {'reg': 20}, 'e2': {'reg': 20}}, {'device_parameter': {'initial': [0]}}, {'device_parameter': {'initial': [10]}}], 'nodes': ['OR1', 'INPUT', 'INPUT'], 'system_parameter': {'time': 100}, 'arcs': [{'to': 0, 'from': 1}, {'to': 0, 'from': 2}]}]
if __name__ == "__main__":
sw_alloc('s')
sw_start('s')
reaction = bio_system(system_data)
reaction.simulation()
sw_accmu('s')
sw_print('s')
reaction.show_record(map(lambda x:"S"+str(x), range(len(reaction.nodes))))
exit()
else:
class TestSystem(TestCase):
def test_system(self):
[bio_system(i) for i in systems_data]