Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 9
sizeStates = 13
sizeConstants = 15
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "time in component environment (second)"
legend_algebraic[0] = "v1 in component main (flux)"
legend_algebraic[1] = "v2 in component main (flux)"
legend_algebraic[2] = "v3 in component main (flux)"
legend_algebraic[3] = "v4 in component main (flux)"
legend_algebraic[4] = "v5 in component main (flux)"
legend_algebraic[5] = "v6 in component main (flux)"
legend_algebraic[6] = "v7 in component main (flux)"
legend_algebraic[7] = "v8 in component main (flux)"
legend_algebraic[8] = "v9 in component main (flux)"
legend_states[0] = "MT1 in component main (molar)"
legend_states[1] = "MT1cat in component main (molar)"
legend_states[2] = "MT1T2 in component main (molar)"
legend_states[3] = "MT1T2M2P in component main (molar)"
legend_states[4] = "M2P in component main (molar)"
legend_states[5] = "M2 in component main (molar)"
legend_states[6] = "M2T2 in component main (molar)"
legend_states[7] = "M2T2star in component main (molar)"
legend_states[8] = "M2C1 in component main (molar)"
legend_states[9] = "C1 in component main (molar)"
legend_states[10] = "C1dmt1 in component main (molar)"
legend_states[11] = "C1dm2 in component main (molar)"
legend_states[12] = "T2 in component main (molar)"
legend_constants[0] = "kshed_eff in component model_parameters (second_order_rate_constant)"
legend_constants[1] = "kon_MT1T2 in component model_parameters (second_order_rate_constant)"
legend_constants[2] = "ki_MT1T2 in component model_parameters (molar)"
legend_constants[3] = "kon_MT1T2M2P in component model_parameters (second_order_rate_constant)"
legend_constants[4] = "koff_MT1T2M2P in component model_parameters (first_order_rate_constant)"
legend_constants[5] = "kact_eff_m2 in component model_parameters (second_order_rate_constant)"
legend_constants[6] = "kon_M2T2 in component model_parameters (second_order_rate_constant)"
legend_constants[7] = "ki_M2T2 in component model_parameters (molar)"
legend_constants[8] = "kiso_M2T2 in component model_parameters (first_order_rate_constant)"
legend_constants[9] = "k_iso_M2T2 in component model_parameters (first_order_rate_constant)"
legend_constants[10] = "kon_M2C1 in component model_parameters (second_order_rate_constant)"
legend_constants[11] = "koff_M2C1 in component model_parameters (first_order_rate_constant)"
legend_constants[12] = "kcat_M2C1 in component model_parameters (first_order_rate_constant)"
legend_constants[13] = "kcat_MT1C1 in component model_parameters (first_order_rate_constant)"
legend_constants[14] = "km_MT1C1 in component model_parameters (molar)"
legend_rates[0] = "d/dt MT1 in component main (molar)"
legend_rates[1] = "d/dt MT1cat in component main (molar)"
legend_rates[2] = "d/dt MT1T2 in component main (molar)"
legend_rates[3] = "d/dt MT1T2M2P in component main (molar)"
legend_rates[4] = "d/dt M2P in component main (molar)"
legend_rates[5] = "d/dt M2 in component main (molar)"
legend_rates[6] = "d/dt M2T2 in component main (molar)"
legend_rates[7] = "d/dt M2T2star in component main (molar)"
legend_rates[8] = "d/dt M2C1 in component main (molar)"
legend_rates[9] = "d/dt C1 in component main (molar)"
legend_rates[10] = "d/dt C1dmt1 in component main (molar)"
legend_rates[11] = "d/dt C1dm2 in component main (molar)"
legend_rates[12] = "d/dt T2 in component main (molar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 100e-9
states[1] = 0
states[2] = 0
states[3] = 0
states[4] = 50e-9
states[5] = 0
states[6] = 0
states[7] = 0
states[8] = 0
states[9] = 1e-6
states[10] = 0
states[11] = 0
states[12] = 50e-9
constants[0] = 2.8e3
constants[1] = 3.54e6
constants[2] = 4.9e-9
constants[3] = 0.14e6
constants[4] = 4.7e-3
constants[5] = 2.8e3
constants[6] = 5.9e6
constants[7] = 1.07e-6
constants[8] = 33
constants[9] = 2e-8
constants[10] = 2.6e3
constants[11] = 2.1e-3
constants[12] = 4.5e-3
constants[13] = 1.97e-3
constants[14] = 2.9e-6
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[0] = constants[0]*states[0]*states[0]
rates[1] = algebraic[0]
algebraic[1] = constants[1]*states[0]*states[12]-constants[2]*constants[1]*states[2]
rates[0] = -algebraic[0]-algebraic[1]
algebraic[2] = constants[3]*states[2]*states[4]-constants[4]*states[3]
rates[2] = algebraic[1]-algebraic[2]
rates[4] = -algebraic[2]
algebraic[3] = constants[5]*states[0]*states[3]
rates[3] = algebraic[2]-algebraic[3]
algebraic[4] = constants[6]*states[5]*states[12]-constants[6]*constants[7]*states[6]
rates[12] = -algebraic[1]-algebraic[4]
algebraic[6] = constants[10]*states[5]*states[9]-constants[11]*states[8]
rates[5] = (algebraic[3]-algebraic[4])-algebraic[6]
algebraic[5] = constants[8]*states[6]-constants[9]*states[7]
rates[6] = algebraic[4]-algebraic[5]
rates[7] = algebraic[5]
algebraic[7] = constants[12]*states[8]
rates[8] = algebraic[6]-algebraic[7]
algebraic[8] = (constants[13]/constants[14])*states[0]*states[9]
rates[9] = -algebraic[6]-algebraic[8]
rates[10] = algebraic[8]
rates[11] = algebraic[7]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[0]*states[0]*states[0]
algebraic[1] = constants[1]*states[0]*states[12]-constants[2]*constants[1]*states[2]
algebraic[2] = constants[3]*states[2]*states[4]-constants[4]*states[3]
algebraic[3] = constants[5]*states[0]*states[3]
algebraic[4] = constants[6]*states[5]*states[12]-constants[6]*constants[7]*states[6]
algebraic[6] = constants[10]*states[5]*states[9]-constants[11]*states[8]
algebraic[5] = constants[8]*states[6]-constants[9]*states[7]
algebraic[7] = constants[12]*states[8]
algebraic[8] = (constants[13]/constants[14])*states[0]*states[9]
return algebraic
def solve_model():
"""Solve model with ODE solver"""
from scipy.integrate import ode
# Initialise constants and state variables
(init_states, constants) = initConsts()
# Set timespan to solve over
voi = linspace(0, 10, 500)
# Construct ODE object to solve
r = ode(computeRates)
r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1)
r.set_initial_value(init_states, voi[0])
r.set_f_params(constants)
# Solve model
states = array([[0.0] * len(voi)] * sizeStates)
states[:,0] = init_states
for (i,t) in enumerate(voi[1:]):
if r.successful():
r.integrate(t)
states[:,i+1] = r.y
else:
break
# Compute algebraic variables
algebraic = computeAlgebraic(constants, states, voi)
return (voi, states, algebraic)
def plot_model(voi, states, algebraic):
"""Plot variables against variable of integration"""
import pylab
(legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends()
pylab.figure(1)
pylab.plot(voi,vstack((states,algebraic)).T)
pylab.xlabel(legend_voi)
pylab.legend(legend_states + legend_algebraic, loc='best')
pylab.show()
if __name__ == "__main__":
(voi, states, algebraic) = solve_model()
plot_model(voi, states, algebraic)