# Generated Code

The following is python code generated by the CellML API from this CellML file. (Back to language selection)

The raw code is available.

# Size of variable arrays: sizeAlgebraic = 2 sizeStates = 9 sizeConstants = 30 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[29] = "F_b_dopa in component gastrointestinal_compartment_L_dopa (dimensionless)" legend_states[0] = "A_dopa_b in component gastrointestinal_compartment_L_dopa (umole)" legend_constants[0] = "ka_b_dopa in component gastrointestinal_compartment_L_dopa (per_hour)" legend_constants[21] = "F_G in component gastrointestinal_compartment_L_dopa (dimensionless)" legend_constants[28] = "F_H in component gastrointestinal_compartment_L_dopa (dimensionless)" legend_constants[25] = "CL_H in component gastrointestinal_compartment_L_dopa (liter_per_hour)" legend_constants[1] = "Q in component gastrointestinal_compartment_L_dopa (liter_per_hour)" legend_constants[2] = "f_H in component gastrointestinal_compartment_L_dopa (dimensionless)" legend_constants[3] = "CL_dopa_0 in component L_dopa_clearance (liter_per_hour)" legend_states[1] = "C_dopa_b in component body_compartment_L_dopa (uM)" legend_constants[4] = "V_dopa in component body_compartment_L_dopa (liter)" legend_algebraic[1] = "CL_dopa in component L_dopa_clearance (liter_per_hour)" legend_states[2] = "C_OMD_b in component body_compartment_3_OMD (uM)" legend_constants[5] = "CL_OMD_b in component body_compartment_3_OMD (liter_per_hour)" legend_constants[6] = "V_OMD_b in component body_compartment_3_OMD (liter)" legend_constants[22] = "CL_COMT in component L_dopa_clearance (liter_per_hour)" legend_algebraic[0] = "CL_AADC in component L_dopa_clearance (liter_per_hour)" legend_constants[23] = "CL_AADC0 in component L_dopa_clearance (liter_per_hour)" legend_states[3] = "C_Ro_central in component central_compartment_Ro (uM)" legend_constants[26] = "CL_REST in component L_dopa_clearance (liter_per_hour)" legend_constants[7] = "ki in component L_dopa_clearance (uM)" legend_states[4] = "A_bens in component gastrointestinal_compartment_benserazide (umole)" legend_constants[8] = "ka_Bens in component gastrointestinal_compartment_benserazide (per_hour)" legend_constants[9] = "F_Bens in component gastrointestinal_compartment_benserazide (dimensionless)" legend_states[5] = "C_bens_central in component central_compartment_benserazide (uM)" legend_constants[10] = "V1_B in component central_compartment_benserazide (liter)" legend_constants[11] = "CLd_B in component central_compartment_benserazide (liter_per_hour)" legend_states[6] = "C_bens_peripheral in component peripheral_compartment_benserazide (uM)" legend_constants[24] = "CL_bens_total in component benserazide_clearance (liter_per_hour)" legend_constants[12] = "V2_B in component peripheral_compartment_benserazide (liter)" legend_constants[27] = "CL_Ro in component benserazide_clearance (liter_per_hour)" legend_constants[13] = "CL_B in component benserazide_clearance (liter_per_hour)" legend_constants[14] = "fm in component benserazide_clearance (dimensionless)" legend_states[7] = "A_Ro in component gastrointestinal_compartment_Ro (umole)" legend_constants[15] = "ka_M in component gastrointestinal_compartment_Ro (per_hour)" legend_constants[16] = "F_Ro in component gastrointestinal_compartment_Ro (dimensionless)" legend_constants[17] = "V1_M in component central_compartment_Ro (liter)" legend_constants[18] = "CLd_M in component central_compartment_Ro (liter_per_hour)" legend_constants[19] = "CL_M in component central_compartment_Ro (liter_per_hour)" legend_states[8] = "C_Ro_peripheral in component peripheral_compartment_Ro (uM)" legend_constants[20] = "V2_M in component peripheral_compartment_Ro (liter)" legend_rates[0] = "d/dt A_dopa_b in component gastrointestinal_compartment_L_dopa (umole)" legend_rates[1] = "d/dt C_dopa_b in component body_compartment_L_dopa (uM)" legend_rates[2] = "d/dt C_OMD_b in component body_compartment_3_OMD (uM)" legend_rates[4] = "d/dt A_bens in component gastrointestinal_compartment_benserazide (umole)" legend_rates[5] = "d/dt C_bens_central in component central_compartment_benserazide (uM)" legend_rates[6] = "d/dt C_bens_peripheral in component peripheral_compartment_benserazide (uM)" legend_rates[7] = "d/dt A_Ro in component gastrointestinal_compartment_Ro (umole)" legend_rates[3] = "d/dt C_Ro_central in component central_compartment_Ro (uM)" legend_rates[8] = "d/dt C_Ro_peripheral in component peripheral_compartment_Ro (uM)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 101 constants[0] = 2.11 constants[1] = 0.828 constants[2] = 0.13 constants[3] = 0.823 states[1] = 0 constants[4] = 0.496 states[2] = 0 constants[5] = 0.012 constants[6] = 0.196 states[3] = 0 constants[7] = 0.00246 states[4] = 19.51 constants[8] = 0.94 constants[9] = 0.022 states[5] = 0 constants[10] = 0.202 constants[11] = 0.072 states[6] = 0 constants[12] = 0.127 constants[13] = 1.67 constants[14] = 0.15 states[7] = 1.3658 constants[15] = 2.47 constants[16] = 1 constants[17] = 0.0691 constants[18] = 1.06 constants[19] = 4.29 states[8] = 0 constants[20] = 3.2 constants[21] = 0.244000 constants[22] = constants[3]*0.100000 constants[23] = constants[3]*0.690000 constants[24] = constants[13]/(1.00000-constants[14]) constants[25] = constants[2]*constants[3] constants[26] = constants[3]*0.210000 constants[27] = constants[24]*constants[14] constants[28] = 1.00000-constants[25]/constants[1] constants[29] = constants[28]*constants[21] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = -constants[0]*states[0] rates[2] = (1.00000/constants[6])*(constants[22]*states[1]-constants[5]*states[2]) rates[4] = -constants[8]*states[4] rates[5] = (1.00000/constants[10])*((constants[8]*states[4]*constants[9]-constants[24]*states[5])+constants[11]*(states[6]-states[5])) rates[6] = (1.00000/constants[12])*constants[11]*(states[5]-states[6]) rates[7] = -constants[15]*states[7] rates[3] = (1.00000/constants[17])*((constants[15]*states[7]*constants[16]-constants[19]*states[3])+constants[27]*states[5]+constants[18]*(states[8]-states[3])) rates[8] = (1.00000/constants[20])*constants[18]*(states[3]-states[8]) algebraic[0] = constants[23]/(1.00000+states[3]/constants[7]) algebraic[1] = algebraic[0]+constants[22]+constants[26] rates[1] = (1.00000/constants[4])*(constants[0]*states[0]*constants[29]-algebraic[1]*states[1]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = constants[23]/(1.00000+states[3]/constants[7]) algebraic[1] = algebraic[0]+constants[22]+constants[26] 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)