Generated Code

# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 9
sizeConstants = 20
from math import *
from numpy import *

def createLegends():
    legend_states = [""] * sizeStates
    legend_rates = [""] * sizeStates
    legend_algebraic = [""] * sizeAlgebraic
    legend_voi = ""
    legend_constants = [""] * sizeConstants
    legend_voi = "t in component environment (s)"
    legend_constants[0] = "kf1 in component PKC (per_s)"
    legend_constants[1] = "kb1 in component PKC (per_s)"
    legend_constants[2] = "kf2 in component PKC (per_um_s)"
    legend_constants[3] = "kb2 in component PKC (per_s)"
    legend_constants[4] = "kf3 in component PKC (per_s)"
    legend_constants[5] = "kb3 in component PKC (per_s)"
    legend_constants[6] = "kf4 in component PKC (per_um_s)"
    legend_constants[7] = "kb4 in component PKC (per_s)"
    legend_constants[8] = "kf5 in component PKC (per_s)"
    legend_constants[9] = "kb5 in component PKC (per_s)"
    legend_constants[10] = "kf6 in component PKC (per_s)"
    legend_constants[11] = "kb6 in component PKC (per_s)"
    legend_constants[12] = "kf7 in component PKC (per_um_s)"
    legend_constants[13] = "kb7 in component PKC (per_s)"
    legend_constants[14] = "kf8 in component PKC (per_um_s)"
    legend_constants[15] = "kb8 in component PKC (per_s)"
    legend_constants[16] = "kf9 in component PKC (per_um_s)"
    legend_constants[17] = "kb9 in component PKC (per_s)"
    legend_constants[18] = "kf10 in component PKC (per_um_s)"
    legend_constants[19] = "kb10 in component PKC (per_s)"
    legend_states[0] = "PKC_i in component PKC (um)"
    legend_states[1] = "AA in component PKC (um)"
    legend_states[2] = "DAG in component PKC (um)"
    legend_states[3] = "Ca in component PKC (um)"
    legend_states[4] = "DAGPKC in component PKC (um)"
    legend_states[5] = "AADAGPKC in component PKC (um)"
    legend_states[6] = "DAGCaPKC in component PKC (um)"
    legend_states[7] = "CaPKC in component PKC (um)"
    legend_states[8] = "PKC_a in component PKC (um)"
    legend_rates[0] = "d/dt PKC_i in component PKC (um)"
    legend_rates[4] = "d/dt DAGPKC in component PKC (um)"
    legend_rates[5] = "d/dt AADAGPKC in component PKC (um)"
    legend_rates[7] = "d/dt CaPKC in component PKC (um)"
    legend_rates[6] = "d/dt DAGCaPKC in component PKC (um)"
    legend_rates[8] = "d/dt PKC_a in component PKC (um)"
    legend_rates[1] = "d/dt AA in component PKC (um)"
    legend_rates[2] = "d/dt DAG in component PKC (um)"
    legend_rates[3] = "d/dt Ca in component PKC (um)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = 1
    constants[1] = 50
    constants[2] = 0.0000000002
    constants[3] = 0.1
    constants[4] = 1.2705
    constants[5] = 3.5026
    constants[6] = 0.000000002
    constants[7] = 0.1
    constants[8] = 1
    constants[9] = 0.1
    constants[10] = 2
    constants[11] = 0.2
    constants[12] = 0.000001
    constants[13] = 0.5
    constants[14] = 0.000000013333
    constants[15] = 8.6348
    constants[16] = 0.000000001
    constants[17] = 0.1
    constants[18] = 0.00000003
    constants[19] = 2
    states[0] = 1
    states[1] = 1
    states[2] = 0.1
    states[3] = 0.1
    states[4] = 0
    states[5] = 0
    states[6] = 0
    states[7] = 0
    states[8] = 0
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    rates[0] = ((((((-states[0]*constants[0]+states[8]*constants[1])-states[0]*states[1]*constants[2])+states[8]*constants[3])-states[0]*states[2]*constants[16])+states[4]*constants[17])-states[0]*states[3]*constants[12])+states[7]*constants[13]
    rates[4] = ((states[0]*states[2]*constants[16]-states[4]*constants[17])-states[4]*states[1]*constants[18])+states[5]*constants[19]
    rates[5] = ((states[4]*states[1]*constants[18]-states[5]*constants[19])-states[5]*constants[10])+states[8]*constants[11]
    rates[7] = ((((((states[0]*states[3]*constants[12]-states[7]*constants[13])-states[7]*constants[4])+states[8]*constants[5])-states[7]*states[1]*constants[6])+states[8]*constants[7])-states[2]*states[7]*constants[14])+states[6]*constants[15]
    rates[6] = ((states[2]*states[7]*constants[14]-states[6]*constants[15])-states[6]*constants[8])+states[8]*constants[9]
    rates[8] = ((((((((((states[0]*constants[0]-states[8]*constants[1])+states[0]*states[1]*constants[2])-states[8]*constants[3])+states[7]*constants[4])-states[8]*constants[5])+states[7]*states[1]*constants[6])-states[8]*constants[7])+states[6]*constants[8])-states[8]*constants[9])+states[5]*constants[10])-states[8]*constants[11]
    rates[1] = ((((-states[0]*states[1]*constants[2]+states[8]*constants[3])-states[7]*states[1]*constants[6])+states[8]*constants[7])-states[4]*states[1]*constants[18])+states[5]*constants[19]
    rates[2] = ((-states[0]*states[2]*constants[16]+states[4]*constants[17])-states[2]*states[7]*constants[14])+states[6]*constants[15]
    rates[3] = -states[0]*states[3]*constants[12]+states[7]*constants[13]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    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)