# 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 = 1 sizeStates = 4 sizeConstants = 9 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 Test (second)" legend_algebraic[0] = "J in component PingPongBiBi (mM_per_second)" legend_states[0] = "S1 in component Test (mM)" legend_states[1] = "S2 in component Test (mM)" legend_states[2] = "P1 in component Test (mM)" legend_states[3] = "P2 in component Test (mM)" legend_constants[0] = "V_f in component Test (mM_per_second)" legend_constants[1] = "V_b in component Test (mM_per_second)" legend_constants[2] = "Keq in component Test (dimensionless)" legend_constants[3] = "Km_S1 in component Test (mM)" legend_constants[4] = "Km_S2 in component Test (mM)" legend_constants[5] = "Km_P1 in component Test (mM)" legend_constants[6] = "Km_P2 in component Test (mM)" legend_constants[7] = "Ki_S1 in component Test (mM)" legend_constants[8] = "Ki_P2 in component Test (mM)" legend_rates[0] = "d/dt S1 in component Test (mM)" legend_rates[1] = "d/dt S2 in component Test (mM)" legend_rates[2] = "d/dt P1 in component Test (mM)" legend_rates[3] = "d/dt P2 in component Test (mM)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 2 states[1] = 1 states[2] = 1 states[3] = 0 constants[0] = 10.0000 constants[1] = 3.00000 constants[2] = 0.200000 constants[3] = 0.100000 constants[4] = 0.500000 constants[5] = 0.100000 constants[6] = 0.500000 constants[7] = 0.500000 constants[8] = 0.500000 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = (constants[0]*(states[0]*states[0]-(states[2]*states[3])/constants[2]))/(states[0]*states[0]+constants[4]*states[0]+constants[3]*states[0]*(1.00000+states[3]/constants[8])+(constants[0]/(constants[1]*constants[2]))*(constants[6]*states[2]*(1.00000+states[0]/constants[7])+states[3]*(constants[5]+states[2]))) rates[0] = -algebraic[0] rates[1] = -algebraic[0] rates[2] = algebraic[0] rates[3] = algebraic[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = (constants[0]*(states[0]*states[0]-(states[2]*states[3])/constants[2]))/(states[0]*states[0]+constants[4]*states[0]+constants[3]*states[0]*(1.00000+states[3]/constants[8])+(constants[0]/(constants[1]*constants[2]))*(constants[6]*states[2]*(1.00000+states[0]/constants[7])+states[3]*(constants[5]+states[2]))) 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)