Generated Code

# Size of variable arrays:
sizeAlgebraic = 9
sizeStates = 2
sizeConstants = 13
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 (hour)"
    legend_constants[0] = "Ado in component Ado (micromolar)"
    legend_algebraic[0] = "Met in component Met (micromolar)"
    legend_algebraic[1] = "Hcy in component Hcy (micromolar)"
    legend_states[0] = "AdoHcy in component AdoHcy (micromolar)"
    legend_constants[1] = "K_AHC in component K_AHC (micromolar)"
    legend_states[1] = "AdoMet in component AdoMet (micromolar)"
    legend_algebraic[6] = "V_MET in component V_MET (flux)"
    legend_algebraic[7] = "V_GNMT in component V_GNMT (flux)"
    legend_algebraic[2] = "V_MATI in component V_MATI (flux)"
    legend_algebraic[4] = "V_MATIII in component V_MATIII (flux)"
    legend_algebraic[8] = "V_D in component V_D (flux)"
    legend_constants[2] = "V_MATImax in component V_MATI (flux)"
    legend_constants[3] = "Km_MATI in component V_MATI (micromolar)"
    legend_constants[4] = "Ki_MATI in component V_MATI (micromolar)"
    legend_constants[5] = "V_MATIIImax in component V_MATIII (flux)"
    legend_algebraic[3] = "Km1_MATIII in component V_MATIII (micromolar)"
    legend_constants[6] = "Km2_MATIII in component V_MATIII (micromolar)"
    legend_constants[7] = "V_METmax in component V_MET (flux)"
    legend_algebraic[5] = "Km1_MET in component V_MET (micromolar)"
    legend_constants[8] = "Km2_MET_A in component V_MET (dimensionless)"
    legend_constants[9] = "V_GNMTmax in component V_GNMT (flux)"
    legend_constants[10] = "Km_GNMT in component V_GNMT (micromolar)"
    legend_constants[11] = "Ki_GNMT in component V_GNMT (micromolar)"
    legend_constants[12] = "alpha_d in component V_D (first_order_rate_constant)"
    legend_rates[1] = "d/dt AdoMet in component AdoMet (micromolar)"
    legend_rates[0] = "d/dt AdoHcy in component AdoHcy (micromolar)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = 1
    states[0] = 3
    constants[1] = 0.1
    states[1] = 60
    constants[2] = 561
    constants[3] = 41
    constants[4] = 50
    constants[5] = 22870
    constants[6] = 21.1
    constants[7] = 4544
    constants[8] = 10
    constants[9] = 10600
    constants[10] = 4500
    constants[11] = 20
    constants[12] = 1333
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    algebraic[5] = 10.0000*(1.00000+states[0]/4.00000)
    algebraic[6] = constants[7]/(1.00000+algebraic[5]/states[1]+constants[8]+(constants[8]*algebraic[5])/states[1])
    algebraic[7] = ((constants[9]/(1.00000+power(constants[10]/states[1], 2.30000)))*1.00000)/(1.00000+states[0]/constants[11])
    algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 5.00000), 45.0000 , greater_equal(voi , 5.00000) & less(voi , 15.0000), 52.0000 , greater_equal(voi , 15.0000) & less(voi , 60.0000), 55.0000 , greater_equal(voi , 60.0000) & less(voi , 75.0000), 52.0000 , greater_equal(voi , 75.0000), 45.0000 , True, float('nan')])
    algebraic[2] = constants[2]/(1.00000+(constants[3]/algebraic[0])*(1.00000+states[1]/constants[4]))
    algebraic[3] = 20000.0/(1.00000+5.70000*(power(states[1]/(states[1]+600.000), 2.00000)))
    algebraic[4] = constants[5]/(1.00000+(algebraic[3]*constants[6])/(power(algebraic[0], 2.00000)+algebraic[0]*constants[6]))
    rates[1] = (algebraic[2]+algebraic[4])-(algebraic[6]+algebraic[7])
    algebraic[1] = (states[0]*constants[1])/constants[0]
    algebraic[8] = constants[12]*algebraic[1]
    rates[0] = ((algebraic[6]+algebraic[7])-algebraic[8])/(1.00000+constants[1]/constants[0])
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[5] = 10.0000*(1.00000+states[0]/4.00000)
    algebraic[6] = constants[7]/(1.00000+algebraic[5]/states[1]+constants[8]+(constants[8]*algebraic[5])/states[1])
    algebraic[7] = ((constants[9]/(1.00000+power(constants[10]/states[1], 2.30000)))*1.00000)/(1.00000+states[0]/constants[11])
    algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 5.00000), 45.0000 , greater_equal(voi , 5.00000) & less(voi , 15.0000), 52.0000 , greater_equal(voi , 15.0000) & less(voi , 60.0000), 55.0000 , greater_equal(voi , 60.0000) & less(voi , 75.0000), 52.0000 , greater_equal(voi , 75.0000), 45.0000 , True, float('nan')])
    algebraic[2] = constants[2]/(1.00000+(constants[3]/algebraic[0])*(1.00000+states[1]/constants[4]))
    algebraic[3] = 20000.0/(1.00000+5.70000*(power(states[1]/(states[1]+600.000), 2.00000)))
    algebraic[4] = constants[5]/(1.00000+(algebraic[3]*constants[6])/(power(algebraic[0], 2.00000)+algebraic[0]*constants[6]))
    algebraic[1] = (states[0]*constants[1])/constants[0]
    algebraic[8] = constants[12]*algebraic[1]
    return algebraic

def custom_piecewise(cases):
    """Compute result of a piecewise function"""
    return select(cases[0::2],cases[1::2])

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)