Generated Code
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# 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_c in component gastrointestinal_compartment_L_dopa (dimensionless)"
legend_states[0] = "A_dopa_c in component gastrointestinal_compartment_L_dopa (umole)"
legend_constants[0] = "ka_c 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_c 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_c in component body_compartment_3_OMD (uM)"
legend_constants[5] = "CL_OMD_c in component body_compartment_3_OMD (liter_per_hour)"
legend_constants[6] = "V_OMD_c 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_B in component gastrointestinal_compartment_benserazide (per_hour)"
legend_constants[9] = "F_B 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_c in component gastrointestinal_compartment_L_dopa (umole)"
legend_rates[1] = "d/dt C_dopa_c in component body_compartment_L_dopa (uM)"
legend_rates[2] = "d/dt C_OMD_c 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] = 1.29
constants[1] = 0.828
constants[2] = 0.13
constants[3] = 0.823
states[1] = 0
constants[4] = 0.496
states[2] = 0
constants[5] = 0.00895
constants[6] = 0.128
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] = 1.00000
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)