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complex_sim.py
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complex_sim.py
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import logging
import os
import random
import string
import time
#from __future__ import print_function
import h5py as h5
import matplotlib.cm as cm
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import revreaddy as rdy
reload(logging)
logging.basicConfig(
format='%(asctime)s %(levelname)s: %(message)s',
datefmt='%Y/%m/%d %I:%M:%S',
level=logging.DEBUG
)
class Sim_Complex():
def __init__(self,Diffusion,reactiondistance,micro_reactionrate_forward,micro_reactionrate_backward,micro_reactionrate_complex,alpha,trajectory_length,boxsize,particles,timestep):
"""
order of prameters: first reaction paramters later algorythmic paramter.
:param boxsize:
:param Diffusion_S:
:param Diffusion_P:
:param reactiondistance:
:param intrinsikreaction:
:param length:
:param particles:
:param alpha:
:param Diffusion_E:
:return:
"""
self.boxsize = boxsize
self.Diffusion = Diffusion
self.reactiondistance = reactiondistance
self.micro_reactionrate_forward = micro_reactionrate_forward
self.micro_reactionrate_backward = micro_reactionrate_backward
self.micro_reactionrate_complex = micro_reactionrate_complex
self.length = trajectory_length
self.particles = particles
self.positions, self.posenzyme = self.envirement()
self.alpha=alpha
self.observables={}
self.timestep=timestep
self.path=self.path()
self.radial_time_range=np.arange(100,2**14,1)
def info(self):
name='Info'+'.txt'
with open(self.path+name, 'w') as info:
info.write("This is the description of the setup of the Simulation")
info.write("boxsize= %d" %self.boxsize)
info.write("Diffusion= %d" %self.Diffusion)
info.write("reactiondistance= %d" %self.reactiondistance)
info.write("reactionrate_f= %d" %self.micro_reactionrate_forward)
info.write("reactionrate_b= %d" %self.micro_reactionrate_backward)
info.write("reactionrate_c= %d" %self.micro_reactionrate_complex)
info.write("alpha= %d" %self.alpha)
info.write("trajectory length= %d" %self.length)
info.write("amount of particles= %d" %self.particles)
info.write("timestep=%d" %self.timestep)
def stamp(self):
timestamp = time.strftime("%Y_%m_%d-%H_%M_%S")
randomstamp = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
stamp = timestamp + "_" + randomstamp
return stamp
def path(self):
path= "/srv/data/Janekg89/revdata/gute/" +"rate_f"+str(self.micro_reactionrate_forward)+"rate_b"+str(self.micro_reactionrate_backward)+"rate_c"+str(self.micro_reactionrate_complex)+"alpha"+str(self.alpha)+"S_num"+str(self.particles)+"length"+str(self.length)+"R"+str(self.reactiondistance)+"boxsize"+str(self.boxsize)+"D"+str(self.Diffusion)+"/"
if not os.path.exists(path):
os.makedirs(path)
return path
def envirement(self):
positions = []
posenzyme = [0, 0, 0]
amountenzyme = 0
while amountenzyme < self.particles:
# todo periodic boundaryconditions !!!! not anymore couse position of enyzme is 0, 0, 0 .
pos = np.random.random(3) * (self.boxsize - 0.00001) - (self.boxsize * 0.5 - 0.00001)
distance = np.sqrt(
(posenzyme[0] - pos[0]) ** 2 + (posenzyme[1] - pos[1]) ** 2 + (posenzyme[2] - pos[2]) ** 2)
#if distance > self.reactiondistance:
amountenzyme += 1
positions.append(pos)
positions = np.array(positions)
return positions, posenzyme
def observales(self, which_observables):
for i in range(which_observables):
if which_observables[i] == "all":
self.observables={0 : "MSD",1:"radial",2:"concentration",3:"number_of_particle"}
elif which_observables == "MSD":
self.observables[0] = which_observables[i]
elif which_observables[i] == "radial":
self.observables[1] = which_observables[i]
elif which_observables[i] == "number_of_particle":
self.observables[2] = which_observables[i]
elif which_observables[i] == "reaction":
self.observables[3] = which_observables[i]
def run(self):
"""
runs the simulation
"""
if self.alpha==1.0:
sim = rdy.Sim("")
else:
sim=rdy.Sim("FractionalDiffusion")
sim.kt = 1 # kJ/mol -> ~300 K
sim.alpha = self.alpha
sim.timestep = self.timestep # ns
sim.boxsize = self.boxsize # nm
sim.delete_all_particle_types() # also deletes all interactions etc.
sim.new_type("S", 0.001, self.Diffusion)
sim.new_type("P", 0.001, self.Diffusion)
sim.new_type("E", 0.001, 0)
sim.new_type("C",0.001,0)
sim.delete_all_reactions()
sim.new_fusion("S+E<->C",0,2,3,self.micro_reactionrate_forward,self.micro_reactionrate_backward,self.reactiondistance)
sim.configure_fusion(0,[],1.,0.5*self.reactiondistance,1,1,1,0,1)
sim.new_fusion("P+E<-C", 1,2,3,0, self.micro_reactionrate_complex, self.reactiondistance)
sim.configure_fusion(1,[],1.,0.5*self.reactiondistance,1,1,1,0,1)
sim.delete_all_particles()
for i in range(self.particles):
pos = self.positions[i, :]
sim.add_particle(pos, 0)
for _ in range(1):
sim.add_particle(self.posenzyme, 2)
#sim.show_world()
sim.delete_all_observables()
for ii in self.observables:
if ii == "all":
combistamp=self.stamp()
msd=self.path+"msd/" + combistamp + "msd.h5"
if not os.path.exists(self.path+"msd/"):
os.makedirs(self.path+"msd/")
sim.new_mean_squared_displacement(1,msd,0)
S_and_E_to_C=self.path+"reaction1/" + combistamp + "reac_num_S_and_E_to_C.h5"
P_and_E_to_C=self.path+"reaction2/" + combistamp + "reac_num_S_and_P_to_C.h5"
if not os.path.exists(self.path+"reaction1/"):
os.makedirs(self.path+"reaction1/")
if not os.path.exists(self.path+"reaction2/"):
os.makedirs(self.path+"reaction2/")
sim.new_reaction_counter(1,S_and_E_to_C,"S+E<->C")
sim.new_reaction_counter(1,P_and_E_to_C,"P+E<-C")
radial_S = self.path+"radialS/" + combistamp + "radialS.h5"
radial_P = self.path+"radialP/" + combistamp + "radialP.h5"
radial_SP=self.path+"radialSP/" + combistamp + "radialSP.h5"
if not os.path.exists(self.path+"radialS/"):
os.makedirs(self.path+"radialS/")
if not os.path.exists(self.path+"radialP/"):
os.makedirs(self.path+"radialP/")
if not os.path.exists(self.path+"radialSP/"):
os.makedirs(self.path+"radialSP/")
#sim.new_radial_distribution(np.arange(1000,10000,100), radial_S, np.arange(0, (self.boxsize*1.0)/2, ((self.boxsize*1.0)/(2.0*50.0) )), np.array([[0,2],[0,3]]))
#sim.new_radial_distribution(np.arange(1000,10000,100), radial_P, np.arange(0, (self.boxsize*1.0)/2, ((self.boxsize*1.0)/(2.0*50.0) )), np.array([[1, 2],[1,3]]))
sim.new_radial_distribution(self.radial_time_range, radial_SP, np.arange(0, (self.boxsize*1.0)/2, ((self.boxsize*1.0)/(2.0*50.0) )), np.array([[0,1]]))
sim.new_radial_distribution(self.radial_time_range,radial_S, np.arange(0, (self.boxsize*1.0)/2, ((self.boxsize*1.0)/(2.0*50.0))), np.array([[0,2],[0,3]]))
sim.new_radial_distribution(np.array([1000,1020]),radial_P, np.arange(0, (self.boxsize*1.0)/2, ((self.boxsize*1.0)/(2.0*50.0))), np.array([[1, 2],[1,3]]))
number_S=self.path +"number_S/"+ combistamp + "number_s.h5"
number_P=self.path +"number_P/"+ combistamp + "number_p.h5"
number_C=self.path +"number_C/"+ combistamp + "number_c.h5"
if not os.path.exists(self.path+"number_S/"):
os.makedirs(self.path+"number_S/")
if not os.path.exists(self.path+"number_P/"):
os.makedirs(self.path+"number_P/")
if not os.path.exists(self.path+"number_C/"):
os.makedirs(self.path+"number_C/")
sim.new_particle_numbers(1,number_S,0)
sim.new_particle_numbers(1,number_P,1)
sim.new_particle_numbers(1,number_C,3)
elif ii == "MSD":
msd=self.path+"MSD/" + self.stamp() + "msd.h5"
sim.new_mean_squared_displacement(1,msd,0)
elif ii == "radial":
"""
gives the radial distribution of S around E and C and of P around E and C on the last frame of the simulation
r_momentan=1
r_radial=[r_momentan]
v=self.boxsize**3/50.0
for _ in range(30):
dr=-r_momentan+(r_momentan**3+((v*3)/(4*np.pi)))**(1.0/3.0)
r_momentan=r_momentan+dr
r_radial.append(r_momentan)
"""
combistamp=self.stamp()
radial_S = self.path + combistamp + "radialS.h5"
radial_P = self.path + combistamp + "radialP.h5"
number_S=self.path + combistamp + "number_s.h5"
number_P=self.path + combistamp + "number_p.h5"
number_C=self.path + combistamp + "number_c.h5"
radial_SP=self.path + combistamp + "radialSP.h5"
sim.new_particle_numbers(1,number_S,0)
sim.new_particle_numbers(1,number_P,1)
sim.new_particle_numbers(1,number_C,3)
sim.new_radial_distribution(np.arange(1000,10000,100), radial_S, np.arange(0, self.boxsize/2, (self.boxsize/(2.0*50.0) )), np.array([[0,2],[0,3]]))
sim.new_radial_distribution(np.arange(1000,10000,100), radial_P, np.arange(0, self.boxsize/2, (self.boxsize/(2.0*50.0) )), np.array([[1, 2],[1,3]]))
sim.new_radial_distribution(np.arange(1000,10000,100), radial_SP, np.arange(0, self.boxsize/2, (self.boxsize/(2.0*50.0) )), np.array([0,1]))
#sim.new_radial_distribution(self.length, radial_P,r_radial, np.array([[2, 1],[3,1]]))
elif ii == "number_of_particle":
"""
gives number of particles of s,p and c over time
"""
for iii in self.observables:
if iii == "radial":
pass
else:
number_S=self.path + self.stamp() + "number_s.h5"
number_P=self.path + self.stamp() + "number_p.h5"
number_C=self.path + self.stamp() + "number_c.h5"
sim.new_particle_numbers(1,number_S,0)
sim.new_particle_numbers(1,number_P,1)
sim.new_particle_numbers(1,number_C,3)
elif ii == "reaction":
"""
gives number of reactions over time
"""
S_and_E_to_C=self.path + self.stamp() + "reac_num_S_and_E_to_C.h5"
P_and_E_to_C=self.path + self.stamp() + "reac_num_S_and_P_to_C.h5"
sim.new_reaction_counter(1,S_and_E_to_C,"S+E<->C")
sim.new_reaction_counter(1,P_and_E_to_C,"P+E<-C")
'''
elif ii == "distribution":
combistamp=self.stamp()
distribution_sx= self.path + combistamp + "distributionSx.h5"
distribution_sy= self.path + combistamp + "distributionSy.h5"
distribution_sz=self.path + combistamp + "distributionSz.h5"
distribution_px= self.path + combistamp + "distributionSx.h5"
distribution_py= self.path + combistamp + "distributionSy.h5"
distribution_pz=self.path + combistamp + "distributionSz.h5"
number_S=self.path + combistamp + "number_s.h5"
number_P=self.path + combistamp + "number_p.h5"
number_C=self.path + combistamp + "number_c.h5"
sim.new_particle_numbers(1,number_S,0)
sim.new_particle_numbers(1,number_P,1)
sim.new_particle_numbers(1,number_C,3)
sim.new_probability_density(self.length, distribution_sx, 0, range(-self.boxsize/2,self.boxsize/2,50),0)
sim.new_probability_density(self.length, distribution_sy, 0, range(-self.boxsize/2,self.boxsize/2,50),1)
sim.new_probability_density(self.length, distribution_sz, 0, range(-self.boxsize/2,self.boxsize/2,50),2)
sim.new_(range(100,200), radial_S, np.arange(self.reactiondistance, self.boxsize/2, (self.boxsize/2.0-self.reactiondistance)/50.0 ), np.array([[2,0],[3,0]]))
sim.new_radial_distribution(range(100,200), radial_P, np.arange(self.reactiondistance, self.boxsize/2, (self.boxsize/2.0-self.reactiondistance)/50.0 ), np.array([[2, 1],[3,1]]))
#sim.new_radial_distribution(self.length, radial_S,r_radial, np.array([[2,0],[3,0]]))
#sim.new_radial_distribution(self.length, radial_P,r_radial, np.array([[2, 1],[3,1]]))
'''
sim.run(self.length)
sim.write_observables_to_file()
sim.delete_all_observables()
#sim.show_world()
"""
particlenumber=1000
boxsize=7.0
D=1.0/6.0
R=1.0
alpha=0.5
lambda_plus=1.0
lambda_c=1.0
lambda_minus=1.0
tau=boxsize**(3)
tau= tau/(lambda_plus*(R*np.pi*particlenumber*6*D)**alpha)
print 2**13
complex=Sim_Complex(D,R,lambda_plus,lambda_minus,lambda_c,alpha,1024,boxsize,particlenumber,0.1)
complex.observables=["all"]
complex.info()
complex.run()
"""