コード例 #1
0
    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
コード例 #2
0
#!/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]