Generated Code

# Size of variable arrays:
sizeAlgebraic = 11
sizeStates = 6
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_states[0] = "q_Eb in component environment (fmol)"
    legend_states[1] = "q_NO in component environment (fmol)"
    legend_states[2] = "q_E6c in component environment (fmol)"
    legend_states[3] = "q_E5c in component environment (fmol)"
    legend_states[4] = "q_cGMP in component environment (fmol)"
    legend_states[5] = "q_NO_product in component environment (fmol)"
    legend_algebraic[6] = "v_R_1_sGC in component sGC (fmol_per_sec)"
    legend_algebraic[7] = "v_R_2_sGC in component sGC (fmol_per_sec)"
    legend_algebraic[8] = "v_R_3_sGC in component sGC (fmol_per_sec)"
    legend_algebraic[9] = "v_R_4_sGC in component sGC (fmol_per_sec)"
    legend_algebraic[10] = "v_R_DNO_sGC in component sGC (fmol_per_sec)"
    legend_constants[0] = "v_NO_generation in component environment (fmol_per_sec)"
    legend_constants[1] = "kappa_R_1_sGC in component sGC_parameters (fmol_per_sec)"
    legend_constants[2] = "kappa_R_2_sGC in component sGC_parameters (fmol_per_sec)"
    legend_constants[3] = "kappa_R_3_sGC in component sGC_parameters (fmol_per_sec)"
    legend_constants[4] = "kappa_R_4_sGC in component sGC_parameters (fmol_per_sec)"
    legend_constants[5] = "kappa_R_DNO_sGC in component sGC_parameters (fmol_per_sec)"
    legend_constants[6] = "K_Eb in component sGC_parameters (per_fmol)"
    legend_constants[7] = "K_NO in component sGC_parameters (per_fmol)"
    legend_constants[8] = "K_E6c in component sGC_parameters (per_fmol)"
    legend_constants[9] = "K_E5c in component sGC_parameters (per_fmol)"
    legend_constants[10] = "K_cGMP in component sGC_parameters (per_fmol)"
    legend_constants[11] = "K_NO_product in component sGC_parameters (per_fmol)"
    legend_constants[12] = "R in component constants (J_per_K_per_mol)"
    legend_constants[13] = "T in component constants (kelvin)"
    legend_algebraic[0] = "mu_Eb in component sGC (J_per_mol)"
    legend_algebraic[1] = "mu_NO in component sGC (J_per_mol)"
    legend_algebraic[2] = "mu_E6c in component sGC (J_per_mol)"
    legend_algebraic[3] = "mu_E5c in component sGC (J_per_mol)"
    legend_algebraic[4] = "mu_cGMP in component sGC (J_per_mol)"
    legend_algebraic[5] = "mu_NO_product in component sGC (J_per_mol)"
    legend_constants[14] = "F in component constants (C_per_mol)"
    legend_rates[0] = "d/dt q_Eb in component environment (fmol)"
    legend_rates[1] = "d/dt q_NO in component environment (fmol)"
    legend_rates[2] = "d/dt q_E6c in component environment (fmol)"
    legend_rates[3] = "d/dt q_E5c in component environment (fmol)"
    legend_rates[4] = "d/dt q_cGMP in component environment (fmol)"
    legend_rates[5] = "d/dt q_NO_product in component environment (fmol)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    states[0] = 1e-18
    states[1] = 0.00836
    states[2] = 1e-18
    states[3] = 1e-18
    states[4] = 1e-18
    states[5] = 1e-18
    constants[0] = 0.000114
    constants[1] = 996545
    constants[2] = 0.00090595
    constants[3] = 3.20816
    constants[4] = 0.00996545
    constants[5] = 0.0236081
    constants[6] = 0.0638542
    constants[7] = 0.114174
    constants[8] = 29.7524
    constants[9] = 0.297524
    constants[10] = 0.269542
    constants[11] = 0.0114174
    constants[12] = 8.31
    constants[13] = 310
    constants[14] = 96485
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    algebraic[0] = constants[12]*constants[13]*log(constants[6]*states[0])
    algebraic[1] = constants[12]*constants[13]*log(constants[7]*states[1])
    algebraic[2] = constants[12]*constants[13]*log(constants[8]*states[2])
    algebraic[6] = constants[1]*(exp((algebraic[0]+algebraic[1])/(constants[12]*constants[13]))-exp(algebraic[2]/(constants[12]*constants[13])))
    algebraic[3] = constants[12]*constants[13]*log(constants[9]*states[3])
    algebraic[7] = constants[2]*(exp(algebraic[2]/(constants[12]*constants[13]))-exp(algebraic[3]/(constants[12]*constants[13])))
    algebraic[8] = constants[3]*(exp((algebraic[2]+algebraic[1])/(constants[12]*constants[13]))-exp((algebraic[3]+algebraic[1])/(constants[12]*constants[13])))
    rates[2] = (algebraic[6]-algebraic[7])-algebraic[8]
    algebraic[4] = constants[12]*constants[13]*log(constants[10]*states[4])
    algebraic[9] = constants[4]*(exp((algebraic[3]+algebraic[4]*2.00000)/(constants[12]*constants[13]))-exp((algebraic[0]+algebraic[1])/(constants[12]*constants[13])))
    rates[0] = -algebraic[6]+algebraic[9]
    rates[3] = (algebraic[7]+algebraic[8])-algebraic[9]
    rates[4] = -2.00000*algebraic[9]
    algebraic[5] = constants[12]*constants[13]*log(constants[11]*states[5])
    algebraic[10] = constants[5]*(exp(algebraic[1]/(constants[12]*constants[13]))-exp(algebraic[5]/(constants[12]*constants[13])))
    rates[1] = ((-algebraic[6]+algebraic[9])-algebraic[10])+constants[0]
    rates[5] = algebraic[10]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[0] = constants[12]*constants[13]*log(constants[6]*states[0])
    algebraic[1] = constants[12]*constants[13]*log(constants[7]*states[1])
    algebraic[2] = constants[12]*constants[13]*log(constants[8]*states[2])
    algebraic[6] = constants[1]*(exp((algebraic[0]+algebraic[1])/(constants[12]*constants[13]))-exp(algebraic[2]/(constants[12]*constants[13])))
    algebraic[3] = constants[12]*constants[13]*log(constants[9]*states[3])
    algebraic[7] = constants[2]*(exp(algebraic[2]/(constants[12]*constants[13]))-exp(algebraic[3]/(constants[12]*constants[13])))
    algebraic[8] = constants[3]*(exp((algebraic[2]+algebraic[1])/(constants[12]*constants[13]))-exp((algebraic[3]+algebraic[1])/(constants[12]*constants[13])))
    algebraic[4] = constants[12]*constants[13]*log(constants[10]*states[4])
    algebraic[9] = constants[4]*(exp((algebraic[3]+algebraic[4]*2.00000)/(constants[12]*constants[13]))-exp((algebraic[0]+algebraic[1])/(constants[12]*constants[13])))
    algebraic[5] = constants[12]*constants[13]*log(constants[11]*states[5])
    algebraic[10] = constants[5]*(exp(algebraic[1]/(constants[12]*constants[13]))-exp(algebraic[5]/(constants[12]*constants[13])))
    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)