# Size of variable arrays:
sizeAlgebraic = 0
sizeStates = 6
sizeConstants = 16
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 (minute)"
    legend_constants[0] = "n in component parameters (dimensionless)"
    legend_constants[12] = "alpha_0 in component parameters (dimensionless)"
    legend_constants[13] = "alpha in component parameters (dimensionless)"
    legend_constants[14] = "beta in component parameters (dimensionless)"
    legend_constants[1] = "K_m in component parameters (dimensionless)"
    legend_constants[2] = "efficiency in component parameters (dimensionless)"
    legend_constants[3] = "mRNA_halflife in component parameters (minute)"
    legend_constants[7] = "t_ave in component parameters (minute)"
    legend_constants[8] = "kd_prot in component parameters (first_order_rate_constant)"
    legend_constants[9] = "kd_mRNA in component parameters (first_order_rate_constant)"
    legend_constants[4] = "prot_halflife in component parameters (minute)"
    legend_constants[5] = "tps_repr in component parameters (per_sec)"
    legend_constants[6] = "tps_active in component parameters (per_sec)"
    legend_constants[15] = "k_tl in component parameters (first_order_rate_constant)"
    legend_constants[10] = "a_tr in component parameters (first_order_rate_constant)"
    legend_constants[11] = "a0_tr in component parameters (first_order_rate_constant)"
    legend_states[0] = "M_lacl in component M_lacl (dimensionless)"
    legend_states[1] = "P_cl in component P_cl (dimensionless)"
    legend_states[2] = "M_tetR in component M_tetR (dimensionless)"
    legend_states[3] = "P_lacl in component P_lacl (dimensionless)"
    legend_states[4] = "M_cl in component M_cl (dimensionless)"
    legend_states[5] = "P_tetR in component P_tetR (dimensionless)"
    legend_rates[0] = "d/dt M_lacl in component M_lacl (dimensionless)"
    legend_rates[2] = "d/dt M_tetR in component M_tetR (dimensionless)"
    legend_rates[4] = "d/dt M_cl in component M_cl (dimensionless)"
    legend_rates[3] = "d/dt P_lacl in component P_lacl (dimensionless)"
    legend_rates[5] = "d/dt P_tetR in component P_tetR (dimensionless)"
    legend_rates[1] = "d/dt P_cl in component P_cl (dimensionless)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = 2
    constants[1] = 40
    constants[2] = 20
    constants[3] = 2
    constants[4] = 10
    constants[5] = 5e-4
    constants[6] = 0.5
    states[0] = 0
    states[1] = 0
    states[2] = 20
    states[3] = 0
    states[4] = 0
    states[5] = 0
    constants[7] = constants[3]/log(2.00000)
    constants[8] = log(2.00000)/constants[4]
    constants[9] = log(2.00000)/constants[3]
    constants[10] = (constants[6]-constants[5])*60.0000
    constants[11] = constants[5]*60.0000
    constants[12] = (constants[11]*constants[2])/(constants[8]*constants[1])
    constants[13] = (constants[10]*constants[2])/(constants[8]*constants[1])
    constants[14] = constants[8]/constants[9]
    constants[15] = constants[2]*constants[9]
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    rates[0] = (constants[11]+(constants[10]*(power(constants[1], constants[0])))/(power(constants[1], constants[0])+power(states[1], constants[0])))-constants[9]*states[0]
    rates[2] = ((constants[10]*(power(constants[1], constants[0])))/(power(constants[1], constants[0])+power(states[3], constants[0]))+constants[11])-constants[9]*states[2]
    rates[4] = ((constants[10]*(power(constants[1], constants[0])))/(power(constants[1], constants[0])+power(states[5], constants[0]))+constants[11])-constants[9]*states[4]
    rates[3] = constants[15]*states[0]-constants[8]*states[3]
    rates[5] = constants[15]*states[2]-constants[8]*states[5]
    rates[1] = constants[15]*states[4]-constants[8]*states[1]
    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)