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 = 93
sizeStates = 38
sizeConstants = 21
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 (second)"
legend_states[0] = "NatP in component NatP (molecules)"
legend_constants[17] = "v1 in component v1 (flux)"
legend_algebraic[0] = "v2 in component v2 (flux)"
legend_algebraic[1] = "v3 in component v3 (flux)"
legend_states[1] = "MisP in component MisP (molecules)"
legend_algebraic[3] = "v5 in component v5 (flux)"
legend_algebraic[21] = "v23 in component v23 (flux)"
legend_algebraic[2] = "v4 in component v4 (flux)"
legend_algebraic[37] = "v39 in component v39 (flux)"
legend_algebraic[38] = "v40 in component v40 (flux)"
legend_algebraic[47] = "v49 in component v49 (flux)"
legend_algebraic[48] = "v50 in component v50 (flux)"
legend_algebraic[49] = "v51 in component v51 (flux)"
legend_algebraic[50] = "v52 in component v52 (flux)"
legend_algebraic[51] = "v53 in component v53 (flux)"
legend_algebraic[52] = "v54 in component v54 (flux)"
legend_algebraic[53] = "v55 in component v55 (flux)"
legend_algebraic[54] = "v56 in component v56 (flux)"
legend_states[2] = "Ub in component Ub (molecules)"
legend_algebraic[14] = "v16 in component v16 (flux)"
legend_algebraic[15] = "v17 in component v17 (flux)"
legend_algebraic[16] = "v18 in component v18 (flux)"
legend_algebraic[17] = "v19 in component v19 (flux)"
legend_algebraic[18] = "v20 in component v20 (flux)"
legend_algebraic[19] = "v21 in component v21 (flux)"
legend_algebraic[20] = "v22 in component v22 (flux)"
legend_algebraic[27] = "v29 in component v29 (flux)"
legend_algebraic[28] = "v30 in component v30 (flux)"
legend_algebraic[29] = "v31 in component v31 (flux)"
legend_algebraic[30] = "v32 in component v32 (flux)"
legend_algebraic[31] = "v33 in component v33 (flux)"
legend_algebraic[32] = "v34 in component v34 (flux)"
legend_algebraic[33] = "v35 in component v35 (flux)"
legend_algebraic[34] = "v36 in component v36 (flux)"
legend_algebraic[35] = "v37 in component v37 (flux)"
legend_algebraic[36] = "v38 in component v38 (flux)"
legend_algebraic[4] = "v6 in component v6 (flux)"
legend_states[3] = "E1 in component E1 (molecules)"
legend_algebraic[5] = "v7 in component v7 (flux)"
legend_states[4] = "E2 in component E2 (molecules)"
legend_algebraic[6] = "v8 in component v8 (flux)"
legend_algebraic[7] = "v9 in component v9 (flux)"
legend_algebraic[8] = "v10 in component v10 (flux)"
legend_algebraic[9] = "v11 in component v11 (flux)"
legend_algebraic[10] = "v12 in component v12 (flux)"
legend_algebraic[11] = "v13 in component v13 (flux)"
legend_algebraic[12] = "v14 in component v14 (flux)"
legend_algebraic[13] = "v15 in component v15 (flux)"
legend_states[5] = "E3 in component E3 (molecules)"
legend_states[6] = "DUB in component DUB (molecules)"
legend_states[7] = "Proteasome in component Proteasome (molecules)"
legend_algebraic[22] = "v24 in component v24 (flux)"
legend_algebraic[23] = "v25 in component v25 (flux)"
legend_algebraic[24] = "v26 in component v26 (flux)"
legend_algebraic[25] = "v27 in component v27 (flux)"
legend_algebraic[26] = "v28 in component v28 (flux)"
legend_algebraic[92] = "v94 in component v94 (flux)"
legend_states[8] = "ROS in component ROS (molecules)"
legend_states[9] = "E1_Ub in component E1_Ub (molecules)"
legend_states[10] = "E2_Ub in component E2_Ub (molecules)"
legend_states[11] = "E3_MisP in component E3_MisP (molecules)"
legend_states[12] = "MisP_Ub in component MisP_Ub (molecules)"
legend_algebraic[39] = "v41 in component v41 (flux)"
legend_algebraic[55] = "v57 in component v57 (flux)"
legend_algebraic[63] = "v65 in component v65 (flux)"
legend_algebraic[64] = "v66 in component v66 (flux)"
legend_algebraic[65] = "v67 in component v67 (flux)"
legend_algebraic[66] = "v68 in component v68 (flux)"
legend_algebraic[67] = "v69 in component v69 (flux)"
legend_algebraic[68] = "v70 in component v70 (flux)"
legend_algebraic[69] = "v71 in component v71 (flux)"
legend_states[13] = "MisP_Ub2 in component MisP_Ub2 (molecules)"
legend_algebraic[40] = "v42 in component v42 (flux)"
legend_algebraic[56] = "v58 in component v58 (flux)"
legend_algebraic[70] = "v72 in component v72 (flux)"
legend_algebraic[71] = "v73 in component v73 (flux)"
legend_algebraic[72] = "v74 in component v74 (flux)"
legend_algebraic[73] = "v75 in component v75 (flux)"
legend_algebraic[74] = "v76 in component v76 (flux)"
legend_algebraic[75] = "v77 in component v77 (flux)"
legend_states[14] = "MisP_Ub3 in component MisP_Ub3 (molecules)"
legend_algebraic[41] = "v43 in component v43 (flux)"
legend_algebraic[57] = "v59 in component v59 (flux)"
legend_algebraic[76] = "v78 in component v78 (flux)"
legend_algebraic[77] = "v79 in component v79 (flux)"
legend_algebraic[78] = "v80 in component v80 (flux)"
legend_algebraic[79] = "v81 in component v81 (flux)"
legend_algebraic[80] = "v82 in component v82 (flux)"
legend_states[15] = "MisP_Ub4 in component MisP_Ub4 (molecules)"
legend_algebraic[42] = "v44 in component v44 (flux)"
legend_algebraic[58] = "v60 in component v60 (flux)"
legend_algebraic[81] = "v83 in component v83 (flux)"
legend_algebraic[82] = "v84 in component v84 (flux)"
legend_algebraic[83] = "v85 in component v85 (flux)"
legend_algebraic[84] = "v86 in component v86 (flux)"
legend_states[16] = "MisP_Ub5 in component MisP_Ub5 (molecules)"
legend_algebraic[43] = "v45 in component v45 (flux)"
legend_algebraic[59] = "v61 in component v61 (flux)"
legend_algebraic[85] = "v87 in component v87 (flux)"
legend_algebraic[86] = "v88 in component v88 (flux)"
legend_algebraic[87] = "v89 in component v89 (flux)"
legend_states[17] = "MisP_Ub6 in component MisP_Ub6 (molecules)"
legend_algebraic[44] = "v46 in component v46 (flux)"
legend_algebraic[60] = "v62 in component v62 (flux)"
legend_algebraic[88] = "v90 in component v90 (flux)"
legend_algebraic[89] = "v91 in component v91 (flux)"
legend_states[18] = "MisP_Ub7 in component MisP_Ub7 (molecules)"
legend_algebraic[45] = "v47 in component v47 (flux)"
legend_algebraic[61] = "v63 in component v63 (flux)"
legend_algebraic[90] = "v92 in component v92 (flux)"
legend_states[19] = "MisP_Ub8 in component MisP_Ub8 (molecules)"
legend_algebraic[46] = "v48 in component v48 (flux)"
legend_algebraic[62] = "v64 in component v64 (flux)"
legend_states[20] = "MisP_Ub4_Proteasome in component MisP_Ub4_Proteasome (molecules)"
legend_states[21] = "MisP_Ub5_Proteasome in component MisP_Ub5_Proteasome (molecules)"
legend_states[22] = "MisP_Ub6_Proteasome in component MisP_Ub6_Proteasome (molecules)"
legend_states[23] = "MisP_Ub7_Proteasome in component MisP_Ub7_Proteasome (molecules)"
legend_states[24] = "MisP_Ub8_Proteasome in component MisP_Ub8_Proteasome (molecules)"
legend_states[25] = "ATP in component ATP (molecules)"
legend_states[26] = "ADP in component ADP (molecules)"
legend_states[27] = "AMP in component AMP (molecules)"
legend_states[28] = "degUb4 in component degUb4 (molecules)"
legend_states[29] = "degUb5 in component degUb5 (molecules)"
legend_states[30] = "degUb6 in component degUb6 (molecules)"
legend_states[31] = "degUb7 in component degUb7 (molecules)"
legend_states[32] = "degUb8 in component degUb8 (molecules)"
legend_states[33] = "MisP_total in component MisP_total (molecules)"
legend_states[34] = "NatP_refolded in component NatP_refolded (molecules)"
legend_states[35] = "AggP in component AggP (molecules)"
legend_algebraic[91] = "v93 in component v93 (flux)"
legend_states[36] = "SeqAggP in component SeqAggP (molecules)"
legend_states[37] = "AggP_Proteasome in component AggP_Proteasome (molecules)"
legend_constants[0] = "k1 in component kinetic_parameters (flux)"
legend_constants[1] = "k2 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[2] = "k3 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[3] = "k61 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[4] = "k61r in component kinetic_parameters (first_order_rate_constant)"
legend_constants[5] = "k62 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[6] = "k63 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[7] = "k64 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[8] = "k65 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[9] = "k66 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[10] = "k67 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[11] = "k68 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[12] = "k69 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[13] = "k71 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[14] = "k72 in component kinetic_parameters (second_order_rate_constant)"
legend_constants[15] = "k73 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[16] = "k74 in component kinetic_parameters (second_order_rate_constant)"
legend_rates[0] = "d/dt NatP in component NatP (molecules)"
legend_rates[1] = "d/dt MisP in component MisP (molecules)"
legend_rates[2] = "d/dt Ub in component Ub (molecules)"
legend_rates[3] = "d/dt E1 in component E1 (molecules)"
legend_rates[4] = "d/dt E2 in component E2 (molecules)"
legend_rates[5] = "d/dt E3 in component E3 (molecules)"
legend_rates[6] = "d/dt DUB in component DUB (molecules)"
legend_rates[7] = "d/dt Proteasome in component Proteasome (molecules)"
legend_rates[8] = "d/dt ROS in component ROS (molecules)"
legend_rates[9] = "d/dt E1_Ub in component E1_Ub (molecules)"
legend_rates[10] = "d/dt E2_Ub in component E2_Ub (molecules)"
legend_rates[11] = "d/dt E3_MisP in component E3_MisP (molecules)"
legend_rates[12] = "d/dt MisP_Ub in component MisP_Ub (molecules)"
legend_rates[13] = "d/dt MisP_Ub2 in component MisP_Ub2 (molecules)"
legend_rates[14] = "d/dt MisP_Ub3 in component MisP_Ub3 (molecules)"
legend_rates[15] = "d/dt MisP_Ub4 in component MisP_Ub4 (molecules)"
legend_rates[16] = "d/dt MisP_Ub5 in component MisP_Ub5 (molecules)"
legend_rates[17] = "d/dt MisP_Ub6 in component MisP_Ub6 (molecules)"
legend_rates[18] = "d/dt MisP_Ub7 in component MisP_Ub7 (molecules)"
legend_rates[19] = "d/dt MisP_Ub8 in component MisP_Ub8 (molecules)"
legend_rates[20] = "d/dt MisP_Ub4_Proteasome in component MisP_Ub4_Proteasome (molecules)"
legend_rates[21] = "d/dt MisP_Ub5_Proteasome in component MisP_Ub5_Proteasome (molecules)"
legend_rates[22] = "d/dt MisP_Ub6_Proteasome in component MisP_Ub6_Proteasome (molecules)"
legend_rates[23] = "d/dt MisP_Ub7_Proteasome in component MisP_Ub7_Proteasome (molecules)"
legend_rates[24] = "d/dt MisP_Ub8_Proteasome in component MisP_Ub8_Proteasome (molecules)"
legend_rates[25] = "d/dt ATP in component ATP (molecules)"
legend_rates[26] = "d/dt ADP in component ADP (molecules)"
legend_rates[27] = "d/dt AMP in component AMP (molecules)"
legend_rates[28] = "d/dt degUb4 in component degUb4 (molecules)"
legend_rates[29] = "d/dt degUb5 in component degUb5 (molecules)"
legend_rates[30] = "d/dt degUb6 in component degUb6 (molecules)"
legend_rates[31] = "d/dt degUb7 in component degUb7 (molecules)"
legend_rates[32] = "d/dt degUb8 in component degUb8 (molecules)"
legend_rates[33] = "d/dt MisP_total in component MisP_total (molecules)"
legend_rates[34] = "d/dt NatP_refolded in component NatP_refolded (molecules)"
legend_rates[35] = "d/dt AggP in component AggP (molecules)"
legend_rates[36] = "d/dt SeqAggP in component SeqAggP (molecules)"
legend_rates[37] = "d/dt AggP_Proteasome in component AggP_Proteasome (molecules)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 500
states[1] = 0
states[2] = 500
states[3] = 100
states[4] = 100
states[5] = 100
states[6] = 200
states[7] = 100
states[8] = 10
states[9] = 0
states[10] = 0
states[11] = 0
states[12] = 0
states[13] = 0
states[14] = 0
states[15] = 0
states[16] = 0
states[17] = 0
states[18] = 0
states[19] = 0
states[20] = 0
states[21] = 0
states[22] = 0
states[23] = 0
states[24] = 0
states[25] = 10000
states[26] = 1000
states[27] = 1000
states[28] = 0
states[29] = 0
states[30] = 0
states[31] = 0
states[32] = 0
states[33] = 0
states[34] = 0
states[35] = 0
states[36] = 0
states[37] = 0
constants[0] = 0.01
constants[1] = 2e-6
constants[2] = 4e-6
constants[3] = 1.7e-5
constants[4] = 2e-4
constants[5] = 2e-4
constants[6] = 1e-3
constants[7] = 1e-3
constants[8] = 1e-3
constants[9] = 1e-5
constants[10] = 1e-5
constants[11] = 1e-5
constants[12] = 0
constants[13] = 1e-8
constants[14] = 1e-8
constants[15] = 1e-3
constants[16] = 1e-5
constants[17] = constants[0]
constants[18] = 0.00000
constants[19] = 0.00000
constants[20] = 0.00000
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[25] = constants[18]
rates[26] = constants[19]
rates[27] = constants[20]
algebraic[0] = constants[1]*states[0]*states[8]
rates[8] = algebraic[0]-algebraic[0]
rates[33] = algebraic[0]
algebraic[1] = constants[2]*states[1]
rates[0] = (constants[17]+algebraic[1])-algebraic[0]
rates[34] = algebraic[1]
algebraic[4] = (constants[5]*states[3]*states[2]*states[25])/(5000.00+states[25])
algebraic[5] = constants[6]*states[4]*states[9]
rates[3] = algebraic[5]-algebraic[4]
rates[9] = algebraic[4]-algebraic[5]
algebraic[3] = constants[4]*states[11]
algebraic[2] = constants[3]*states[5]*states[1]
algebraic[6] = constants[7]*states[10]*states[11]
rates[5] = (algebraic[3]+algebraic[6])-algebraic[2]
rates[11] = (algebraic[2]-algebraic[3])-algebraic[6]
algebraic[7] = constants[8]*states[10]*states[12]
algebraic[8] = constants[8]*states[10]*states[13]
algebraic[9] = constants[8]*states[10]*states[14]
algebraic[10] = constants[8]*states[10]*states[15]
algebraic[11] = constants[8]*states[10]*states[16]
algebraic[12] = constants[8]*states[10]*states[17]
algebraic[13] = constants[8]*states[10]*states[18]
rates[4] = (algebraic[6]+algebraic[7]+algebraic[8]+algebraic[9]+algebraic[10]+algebraic[11]+algebraic[12]+algebraic[13])-algebraic[5]
rates[10] = (((((((algebraic[5]-algebraic[6])-algebraic[7])-algebraic[8])-algebraic[9])-algebraic[10])-algebraic[11])-algebraic[12])-algebraic[13]
algebraic[21] = constants[9]*states[6]*states[12]
algebraic[14] = constants[9]*states[6]*states[19]
algebraic[15] = constants[9]*states[6]*states[18]
algebraic[16] = constants[9]*states[6]*states[17]
algebraic[17] = constants[9]*states[6]*states[16]
algebraic[18] = constants[9]*states[6]*states[15]
algebraic[19] = constants[9]*states[6]*states[14]
algebraic[20] = constants[9]*states[6]*states[13]
algebraic[27] = constants[11]*states[6]*states[20]
algebraic[28] = constants[11]*states[6]*states[21]
algebraic[29] = constants[11]*states[6]*states[22]
algebraic[30] = constants[11]*states[6]*states[23]
algebraic[31] = constants[11]*states[6]*states[24]
rates[6] = (algebraic[14]+algebraic[15]+algebraic[16]+algebraic[17]+algebraic[18]+algebraic[19]+algebraic[20]+algebraic[21]+algebraic[27]+algebraic[28]+algebraic[29]+algebraic[30]+algebraic[31])-(algebraic[14]+algebraic[15]+algebraic[16]+algebraic[17]+algebraic[18]+algebraic[19]+algebraic[20]+algebraic[21]+algebraic[27]+algebraic[28]+algebraic[29]+algebraic[30]+algebraic[31])
algebraic[32] = (constants[12]*states[20]*states[25])/(5000.00+states[25])
algebraic[22] = constants[10]*states[15]*states[7]
rates[20] = (algebraic[22]+algebraic[28])-(algebraic[27]+algebraic[32])
rates[28] = algebraic[32]
algebraic[33] = (constants[12]*states[21]*states[25])/(5000.00+states[25])
algebraic[23] = constants[10]*states[16]*states[7]
rates[21] = (algebraic[23]+algebraic[29])-(algebraic[28]+algebraic[33])
rates[29] = algebraic[33]
algebraic[34] = (constants[12]*states[22]*states[25])/(5000.00+states[25])
algebraic[24] = constants[10]*states[17]*states[7]
rates[22] = (algebraic[24]+algebraic[30])-(algebraic[29]+algebraic[34])
rates[30] = algebraic[34]
algebraic[35] = (constants[12]*states[23]*states[25])/(5000.00+states[25])
algebraic[25] = constants[10]*states[18]*states[7]
rates[23] = (algebraic[25]+algebraic[31])-(algebraic[30]+algebraic[35])
rates[31] = algebraic[35]
algebraic[36] = (constants[12]*states[24]*states[25])/(5000.00+states[25])
rates[2] = (algebraic[14]+algebraic[15]+algebraic[16]+algebraic[17]+algebraic[18]+algebraic[19]+algebraic[20]+algebraic[21]+algebraic[27]+algebraic[28]+algebraic[29]+algebraic[30]+algebraic[31]+4.00000*algebraic[32]+5.00000*algebraic[33]+6.00000*algebraic[34]+7.00000*algebraic[35]+8.00000*algebraic[36])-algebraic[4]
algebraic[26] = constants[10]*states[19]*states[7]
rates[24] = algebraic[26]-(algebraic[31]+algebraic[36])
rates[32] = algebraic[36]
algebraic[37] = (constants[13]*states[1]*(states[1]-1.00000))/2.00000
algebraic[38] = constants[13]*states[1]*states[35]
algebraic[47] = constants[14]*states[1]*states[12]
algebraic[48] = constants[14]*states[1]*states[13]
algebraic[49] = constants[14]*states[1]*states[14]
algebraic[50] = constants[14]*states[1]*states[15]
algebraic[51] = constants[14]*states[1]*states[16]
algebraic[52] = constants[14]*states[1]*states[17]
algebraic[53] = constants[14]*states[1]*states[18]
algebraic[54] = constants[14]*states[1]*states[19]
rates[1] = (algebraic[0]+algebraic[3]+algebraic[21])-(algebraic[1]+algebraic[2]+2.00000*algebraic[37]+algebraic[38]+algebraic[47]+algebraic[48]+algebraic[49]+algebraic[50]+algebraic[51]+algebraic[52]+algebraic[53]+algebraic[54])
algebraic[39] = (constants[14]*states[12]*(states[12]-1.00000))/2.00000
algebraic[55] = constants[14]*states[35]*states[12]
algebraic[63] = constants[14]*states[12]*states[13]
algebraic[64] = constants[14]*states[12]*states[14]
algebraic[65] = constants[14]*states[12]*states[15]
algebraic[66] = constants[14]*states[12]*states[16]
algebraic[67] = constants[14]*states[12]*states[17]
algebraic[68] = constants[14]*states[12]*states[18]
algebraic[69] = constants[14]*states[12]*states[19]
rates[12] = (algebraic[6]+algebraic[20])-(algebraic[7]+algebraic[21]+2.00000*algebraic[39]+algebraic[47]+algebraic[55]+algebraic[63]+algebraic[64]+algebraic[65]+algebraic[66]+algebraic[67]+algebraic[68]+algebraic[69])
algebraic[40] = (constants[14]*states[13]*(states[13]-1.00000))/2.00000
algebraic[56] = constants[14]*states[35]*states[13]
algebraic[70] = constants[14]*states[13]*states[14]
algebraic[71] = constants[14]*states[13]*states[15]
algebraic[72] = constants[14]*states[13]*states[16]
algebraic[73] = constants[14]*states[13]*states[17]
algebraic[74] = constants[14]*states[13]*states[18]
algebraic[75] = constants[14]*states[13]*states[19]
rates[13] = (algebraic[7]+algebraic[19])-(algebraic[8]+algebraic[20]+2.00000*algebraic[40]+algebraic[48]+algebraic[56]+algebraic[63]+algebraic[70]+algebraic[71]+algebraic[72]+algebraic[73]+algebraic[74]+algebraic[75])
algebraic[41] = (constants[14]*states[14]*(states[14]-1.00000))/2.00000
algebraic[57] = constants[14]*states[35]*states[14]
algebraic[76] = constants[14]*states[14]*states[15]
algebraic[77] = constants[14]*states[14]*states[16]
algebraic[78] = constants[14]*states[14]*states[17]
algebraic[79] = constants[14]*states[14]*states[18]
algebraic[80] = constants[14]*states[14]*states[19]
rates[14] = (algebraic[8]+algebraic[18]+algebraic[27])-(algebraic[9]+algebraic[19]+2.00000*algebraic[41]+algebraic[49]+algebraic[57]+algebraic[64]+algebraic[70]+algebraic[76]+algebraic[77]+algebraic[78]+algebraic[79]+algebraic[80])
algebraic[42] = (constants[14]*states[15]*(states[15]-1.00000))/2.00000
algebraic[58] = constants[14]*states[35]*states[15]
algebraic[81] = constants[14]*states[15]*states[16]
algebraic[82] = constants[14]*states[15]*states[17]
algebraic[83] = constants[14]*states[15]*states[18]
algebraic[84] = constants[14]*states[15]*states[19]
rates[15] = (algebraic[9]+algebraic[17])-(algebraic[10]+algebraic[18]+algebraic[22]+2.00000*algebraic[42]+algebraic[50]+algebraic[58]+algebraic[65]+algebraic[71]+algebraic[76]+algebraic[81]+algebraic[82]+algebraic[83]+algebraic[84])
algebraic[43] = (constants[14]*states[16]*(states[16]-1.00000))/2.00000
algebraic[59] = constants[14]*states[35]*states[16]
algebraic[85] = constants[14]*states[16]*states[17]
algebraic[86] = constants[14]*states[16]*states[18]
algebraic[87] = constants[14]*states[16]*states[19]
rates[16] = (algebraic[10]+algebraic[16])-(algebraic[11]+algebraic[17]+algebraic[23]+2.00000*algebraic[43]+algebraic[51]+algebraic[59]+algebraic[66]+algebraic[72]+algebraic[77]+algebraic[81]+algebraic[85]+algebraic[86]+algebraic[87])
algebraic[44] = (constants[14]*states[17]*(states[17]-1.00000))/2.00000
algebraic[60] = constants[14]*states[35]*states[17]
algebraic[88] = constants[14]*states[17]*states[18]
algebraic[89] = constants[14]*states[17]*states[19]
rates[17] = (algebraic[11]+algebraic[15])-(algebraic[12]+algebraic[16]+algebraic[24]+2.00000*algebraic[44]+algebraic[52]+algebraic[60]+algebraic[67]+algebraic[73]+algebraic[78]+algebraic[82]+algebraic[85]+algebraic[88]+algebraic[89])
algebraic[45] = (constants[14]*states[18]*(states[18]-1.00000))/2.00000
algebraic[61] = constants[14]*states[35]*states[18]
algebraic[90] = constants[14]*states[18]*states[19]
rates[18] = (algebraic[12]+algebraic[14])-(algebraic[13]+algebraic[15]+algebraic[25]+2.00000*algebraic[45]+algebraic[53]+algebraic[61]+algebraic[68]+algebraic[74]+algebraic[79]+algebraic[83]+algebraic[86]+algebraic[88]+algebraic[90])
algebraic[46] = (constants[14]*states[19]*(states[19]-1.00000))/2.00000
algebraic[62] = constants[14]*states[35]*states[19]
rates[19] = algebraic[13]-(algebraic[14]+algebraic[26]+2.00000*algebraic[46]+algebraic[54]+algebraic[62]+algebraic[69]+algebraic[75]+algebraic[80]+algebraic[84]+algebraic[87]+algebraic[89]+algebraic[90])
algebraic[91] = constants[15]*states[35]
rates[36] = algebraic[91]
algebraic[92] = constants[16]*states[35]*states[7]
rates[7] = (algebraic[27]+algebraic[32]+algebraic[33]+algebraic[34]+algebraic[35]+algebraic[36])-(algebraic[22]+algebraic[23]+algebraic[24]+algebraic[25]+algebraic[26]+algebraic[92])
rates[35] = (algebraic[37]+2.00000*algebraic[38]+algebraic[39]+algebraic[40]+algebraic[41]+algebraic[42]+algebraic[43]+algebraic[44]+algebraic[45]+algebraic[46]+algebraic[47]+algebraic[48]+algebraic[49]+algebraic[50]+algebraic[51]+algebraic[52]+algebraic[53]+algebraic[54]+2.00000*algebraic[55]+2.00000*algebraic[56]+2.00000*algebraic[57]+2.00000*algebraic[58]+2.00000*algebraic[59]+2.00000*algebraic[60]+2.00000*algebraic[61]+2.00000*algebraic[62]+algebraic[63]+algebraic[64]+algebraic[65]+algebraic[66]+algebraic[67]+algebraic[68]+algebraic[69]+algebraic[70]+algebraic[71]+algebraic[72]+algebraic[73]+algebraic[74]+algebraic[75]+algebraic[76]+algebraic[77]+algebraic[78]+algebraic[79]+algebraic[80]+algebraic[81]+algebraic[82]+algebraic[83]+algebraic[84]+algebraic[85]+algebraic[86]+algebraic[87]+algebraic[88]+algebraic[89]+algebraic[90])-(algebraic[38]+algebraic[55]+algebraic[56]+algebraic[57]+algebraic[58]+algebraic[59]+algebraic[60]+algebraic[61]+algebraic[62]+algebraic[91]+algebraic[92])
rates[37] = algebraic[92]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[1]*states[0]*states[8]
algebraic[1] = constants[2]*states[1]
algebraic[4] = (constants[5]*states[3]*states[2]*states[25])/(5000.00+states[25])
algebraic[5] = constants[6]*states[4]*states[9]
algebraic[3] = constants[4]*states[11]
algebraic[2] = constants[3]*states[5]*states[1]
algebraic[6] = constants[7]*states[10]*states[11]
algebraic[7] = constants[8]*states[10]*states[12]
algebraic[8] = constants[8]*states[10]*states[13]
algebraic[9] = constants[8]*states[10]*states[14]
algebraic[10] = constants[8]*states[10]*states[15]
algebraic[11] = constants[8]*states[10]*states[16]
algebraic[12] = constants[8]*states[10]*states[17]
algebraic[13] = constants[8]*states[10]*states[18]
algebraic[21] = constants[9]*states[6]*states[12]
algebraic[14] = constants[9]*states[6]*states[19]
algebraic[15] = constants[9]*states[6]*states[18]
algebraic[16] = constants[9]*states[6]*states[17]
algebraic[17] = constants[9]*states[6]*states[16]
algebraic[18] = constants[9]*states[6]*states[15]
algebraic[19] = constants[9]*states[6]*states[14]
algebraic[20] = constants[9]*states[6]*states[13]
algebraic[27] = constants[11]*states[6]*states[20]
algebraic[28] = constants[11]*states[6]*states[21]
algebraic[29] = constants[11]*states[6]*states[22]
algebraic[30] = constants[11]*states[6]*states[23]
algebraic[31] = constants[11]*states[6]*states[24]
algebraic[32] = (constants[12]*states[20]*states[25])/(5000.00+states[25])
algebraic[22] = constants[10]*states[15]*states[7]
algebraic[33] = (constants[12]*states[21]*states[25])/(5000.00+states[25])
algebraic[23] = constants[10]*states[16]*states[7]
algebraic[34] = (constants[12]*states[22]*states[25])/(5000.00+states[25])
algebraic[24] = constants[10]*states[17]*states[7]
algebraic[35] = (constants[12]*states[23]*states[25])/(5000.00+states[25])
algebraic[25] = constants[10]*states[18]*states[7]
algebraic[36] = (constants[12]*states[24]*states[25])/(5000.00+states[25])
algebraic[26] = constants[10]*states[19]*states[7]
algebraic[37] = (constants[13]*states[1]*(states[1]-1.00000))/2.00000
algebraic[38] = constants[13]*states[1]*states[35]
algebraic[47] = constants[14]*states[1]*states[12]
algebraic[48] = constants[14]*states[1]*states[13]
algebraic[49] = constants[14]*states[1]*states[14]
algebraic[50] = constants[14]*states[1]*states[15]
algebraic[51] = constants[14]*states[1]*states[16]
algebraic[52] = constants[14]*states[1]*states[17]
algebraic[53] = constants[14]*states[1]*states[18]
algebraic[54] = constants[14]*states[1]*states[19]
algebraic[39] = (constants[14]*states[12]*(states[12]-1.00000))/2.00000
algebraic[55] = constants[14]*states[35]*states[12]
algebraic[63] = constants[14]*states[12]*states[13]
algebraic[64] = constants[14]*states[12]*states[14]
algebraic[65] = constants[14]*states[12]*states[15]
algebraic[66] = constants[14]*states[12]*states[16]
algebraic[67] = constants[14]*states[12]*states[17]
algebraic[68] = constants[14]*states[12]*states[18]
algebraic[69] = constants[14]*states[12]*states[19]
algebraic[40] = (constants[14]*states[13]*(states[13]-1.00000))/2.00000
algebraic[56] = constants[14]*states[35]*states[13]
algebraic[70] = constants[14]*states[13]*states[14]
algebraic[71] = constants[14]*states[13]*states[15]
algebraic[72] = constants[14]*states[13]*states[16]
algebraic[73] = constants[14]*states[13]*states[17]
algebraic[74] = constants[14]*states[13]*states[18]
algebraic[75] = constants[14]*states[13]*states[19]
algebraic[41] = (constants[14]*states[14]*(states[14]-1.00000))/2.00000
algebraic[57] = constants[14]*states[35]*states[14]
algebraic[76] = constants[14]*states[14]*states[15]
algebraic[77] = constants[14]*states[14]*states[16]
algebraic[78] = constants[14]*states[14]*states[17]
algebraic[79] = constants[14]*states[14]*states[18]
algebraic[80] = constants[14]*states[14]*states[19]
algebraic[42] = (constants[14]*states[15]*(states[15]-1.00000))/2.00000
algebraic[58] = constants[14]*states[35]*states[15]
algebraic[81] = constants[14]*states[15]*states[16]
algebraic[82] = constants[14]*states[15]*states[17]
algebraic[83] = constants[14]*states[15]*states[18]
algebraic[84] = constants[14]*states[15]*states[19]
algebraic[43] = (constants[14]*states[16]*(states[16]-1.00000))/2.00000
algebraic[59] = constants[14]*states[35]*states[16]
algebraic[85] = constants[14]*states[16]*states[17]
algebraic[86] = constants[14]*states[16]*states[18]
algebraic[87] = constants[14]*states[16]*states[19]
algebraic[44] = (constants[14]*states[17]*(states[17]-1.00000))/2.00000
algebraic[60] = constants[14]*states[35]*states[17]
algebraic[88] = constants[14]*states[17]*states[18]
algebraic[89] = constants[14]*states[17]*states[19]
algebraic[45] = (constants[14]*states[18]*(states[18]-1.00000))/2.00000
algebraic[61] = constants[14]*states[35]*states[18]
algebraic[90] = constants[14]*states[18]*states[19]
algebraic[46] = (constants[14]*states[19]*(states[19]-1.00000))/2.00000
algebraic[62] = constants[14]*states[35]*states[19]
algebraic[91] = constants[15]*states[35]
algebraic[92] = constants[16]*states[35]*states[7]
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)