slv-utils
Version:
Utilities for working with SLV and DAT files.
1,909 lines (1,908 loc) • 249 kB
JSON
{
"sourceFormat": "SLV",
"content": {
"header": "DBSolve Optimum (new parser) 1 Jul 2006\nSLV25.00*",
"map": [
{
"key": "Number of rows in matrix (Number of activities) ",
"rawValue": [
"2 "
],
"parsedValue": [
{
"type": "number",
"value": 2
}
]
},
{
"key": "Number of cols in matrix (Number of compounds) ",
"rawValue": [
"2 "
],
"parsedValue": [
{
"type": "number",
"value": 2
}
]
},
{
"key": "Initial System dimension ",
"rawValue": [
"2 "
],
"parsedValue": [
{
"type": "number",
"value": 2
}
]
},
{
"key": "Selected Variable(Always TIME for ODE) ",
"rawValue": [
"3 "
],
"parsedValue": [
{
"type": "number",
"value": 3
}
]
},
{
"key": "Maximum Value of the Selected Variable ",
"rawValue": [
"1.250000e+02 "
],
"parsedValue": [
{
"type": "number",
"value": 125
}
]
},
{
"key": "Minimum Value of the Selected Variable ",
"rawValue": [
"0.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "Initial Step ",
"rawValue": [
"1.000000e-03 "
],
"parsedValue": [
{
"type": "number",
"value": 0.001
}
]
},
{
"key": "Method Accuracy ",
"rawValue": [
"1.000000e-06 "
],
"parsedValue": [
{
"type": "number",
"value": 0.000001
}
]
},
{
"key": "Maximum Number of Method Steps ",
"rawValue": [
"10000 "
],
"parsedValue": [
{
"type": "number",
"value": 10000
}
]
},
{
"key": "1st Variale for plotting ",
"rawValue": [
"t "
],
"parsedValue": [
{
"type": "string",
"value": "t"
}
]
},
{
"key": "2nd Variable for plotting: ",
"rawValue": [
"C1 "
],
"parsedValue": [
{
"type": "string",
"value": "C1"
}
]
},
{
"key": "1st Value Maximum for plotting ",
"rawValue": [
"1.000000e+02 "
],
"parsedValue": [
{
"type": "number",
"value": 100
}
]
},
{
"key": "1st Value Minimum for plotting ",
"rawValue": [
"0.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "2nd Value Maximum for plotting ",
"rawValue": [
"1.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "2nd Value Minimum for plotting ",
"rawValue": [
"0.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "Distance between Plotting points ",
"rawValue": [
"1.000000e+02 "
],
"parsedValue": [
{
"type": "number",
"value": 100
}
]
},
{
"key": "Step for Numerical derivation ",
"rawValue": [
"1.000000e-05 "
],
"parsedValue": [
{
"type": "number",
"value": 0.00001
}
]
},
{
"key": "(Internal) DbsolveStep WWW Demo ",
"rawValue": [
"701 "
],
"parsedValue": [
{
"type": "number",
"value": 701
}
]
},
{
"key": "Elementary Constant ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "FileOutput ",
"rawValue": [
"0 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "TextOutput ",
"rawValue": [
"1 "
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"parsedValue": [
{
"type": "number",
"value": 1
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]
},
{
"key": "DrawOutput ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "TransferLast ",
"rawValue": [
"0 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "Stoichiometric Matrix ",
"rawValue": [
"1 1 -1 \n1 2 1 \n2 2 -1 \n0 0 0.0 \n& "
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},
{
"key": "Elementary Constants ",
"rawValue": [
"1.944853e+00 1.931480e+00 1.084404e+00 1.097818e+00 "
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"parsedValue": [
{
"type": "arrayNumber",
"value": [
1.944853,
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1.93148,
null,
1.084404,
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1.097818
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},
{
"key": "Initial concentrations ",
"rawValue": [
"0.000000e+00 0.000000e+00 "
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"parsedValue": [
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"type": "arrayNumber",
"value": [
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null,
0
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},
{
"key": "Initial Stiffness",
"rawValue": [
"0.000000e+00 0.000000e+00 "
],
"parsedValue": [
{
"type": "arrayNumber",
"value": [
0,
0
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}
]
},
{
"key": "Initial Family Steps",
"rawValue": [
"1.000000e+00 1.000000e+00 "
],
"parsedValue": [
{
"type": "arrayNumber",
"value": [
1,
null,
1
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}
]
},
{
"key": "Number of fitting parameters (Old Income Flux Constant Number) ",
"rawValue": [
"53 "
],
"parsedValue": [
{
"type": "number",
"value": 53
}
]
},
{
"key": "Number of scan parameters ",
"rawValue": [
"53 "
],
"parsedValue": [
{
"type": "number",
"value": 53
}
]
},
{
"key": "ABsolute Fitting ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "Variables for FileOutput ",
"rawValue": [
"F[0] Km Vd X[6] X[7] kabs kcat #### "
],
"parsedValue": [
{
"type": "strings",
"value": [
"F[0]",
"",
"Km",
"",
"Vd",
"",
"X[6]",
"",
"X[7]",
"",
"kabs",
"",
"kcat",
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"####"
]
}
]
},
{
"key": "Variables for FileOutputOn ",
"rawValue": [
" #### "
],
"parsedValue": [
{
"type": "strings",
"value": [
"####"
]
}
]
},
{
"key": "(Internal) Temporary Print Option ",
"rawValue": [
"151732605 "
],
"parsedValue": [
{
"type": "number",
"value": 151732605
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]
},
{
"key": "LeastFitting ",
"rawValue": [
"1 "
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"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "Output File Name ",
"rawValue": [
"output.txt "
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[
{
"type": "string",
"value": "output"
},
{
"type": "strings",
"value": [
".txt"
]
}
]
]
},
{
"key": "Experimental Data File Name ",
"rawValue": [
"example4.dat "
],
"parsedValue": [
[
{
"type": "string",
"value": "example4"
},
{
"type": "strings",
"value": [
".dat"
]
}
]
]
},
{
"key": "\nRight Hand Sides && \nInitial Values && \nComments Or Selkov DB record",
"rawValue": [
"\n//! Rate Laws \nDoseF=Dose*F; \n//!!vabs \nvabs=Default*(kabs*C0); \n//!!vel \nvel=Vd*(kcat*C1/(Km+C1)); \n//! Differential Equations \n//for C0 \nF[1]=(-vabs)/Default; \n//for C1 \nF[2]=(vabs-vel)/Vd; \n//! Explicit Functions \n// Explicit Functions text ",
"\n//! Data comments \n//! Compartments volumes \nDefault=1; // {--} \nVd=9; //{L} \nF=0.72; \n//! Initial concentration \nDose=5; // {umole} \nT=24; \nC0=0; // {umole} \nC1=0; // {uM} \n//! Kinetic parameters \nkabs=4; // {hr-1} \nkcat=0.8; // {uM/hr} \nKm=5; // {uM} \n//!!! F0=0.020335 2:16:09 PM 5/23/2014 \nkcat=7.375000e-01; \nVd=5.275000e+00; \nKm=5.528412e+00; \nkabs=2.064588e+00; ",
"\n//!kfdsklj \ndkklj \nlkal; \nll;l \n//!! hello \n';dsld \n\n#dbs# "
],
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{
"type": "lineComment",
"header": 1,
"value": " Rate Laws ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "DoseF",
"rhs": "Dose*F",
"newLine": true
}
},
{
"type": "lineComment",
"header": 2,
"value": "vabs ",
"newLine": true
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"type": "expression",
"value": {
"lhs": "vabs",
"rhs": "Default*(kabs*C0)",
"newLine": true
}
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"header": 2,
"value": "vel ",
"newLine": true
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"type": "expression",
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"rhs": "Vd*(kcat*C1/(Km+C1))",
"newLine": true
}
},
{
"type": "lineComment",
"header": 1,
"value": " Differential Equations ",
"newLine": true
},
{
"type": "lineComment",
"header": 0,
"value": "for C0 ",
"newLine": true
},
{
"type": "expression",
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"lhs": "F[1]",
"rhs": "(-vabs)/Default",
"newLine": true
}
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{
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"header": 0,
"value": "for C1 ",
"newLine": true
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"rhs": "(vabs-vel)/Vd",
"newLine": true
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},
{
"type": "lineComment",
"header": 1,
"value": " Explicit Functions ",
"newLine": true
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{
"type": "lineComment",
"header": 0,
"value": " Explicit Functions text",
"newLine": true
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{
"type": "lineComment",
"header": 1,
"value": " Data comments ",
"newLine": true
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{
"type": "lineComment",
"header": 1,
"value": " Compartments volumes ",
"newLine": true
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{
"type": "numeric",
"value": {
"lhs": "Default",
"rhs": "1",
"newLine": true
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"header": 0,
"value": " {--} ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "Vd",
"rhs": "9",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "{L} ",
"newLine": false
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{
"type": "numeric",
"value": {
"lhs": "F",
"rhs": "0.72",
"newLine": true
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"type": "strings",
"value": [
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""
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},
{
"type": "lineComment",
"header": 1,
"value": " Initial concentration ",
"newLine": true
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{
"type": "numeric",
"value": {
"lhs": "Dose",
"rhs": "5",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " {umole} ",
"newLine": false
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{
"type": "numeric",
"value": {
"lhs": "T",
"rhs": "24",
"newLine": true
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},
{
"type": "numeric",
"value": {
"lhs": "C0",
"rhs": "0",
"newLine": true
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{
"type": "lineComment",
"header": 0,
"value": " {umole} ",
"newLine": false
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"type": "numeric",
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"lhs": "C1",
"rhs": "0",
"newLine": true
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{
"type": "lineComment",
"header": 0,
"value": " {uM} ",
"newLine": false
},
{
"type": "lineComment",
"header": 1,
"value": " Kinetic parameters ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "kabs",
"rhs": "4",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " {hr-1} ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "kcat",
"rhs": "0.8",
"newLine": true
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{
"type": "lineComment",
"header": 0,
"value": " {uM/hr} ",
"newLine": false
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{
"type": "numeric",
"value": {
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"rhs": "5",
"newLine": true
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{
"type": "lineComment",
"header": 0,
"value": " {uM} ",
"newLine": false
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{
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"newLine": true
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{
"type": "numeric",
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"rhs": "7.375000e-01",
"newLine": true
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"newLine": true
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"rhs": "5.528412e+00",
"newLine": true
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"rhs": "2.064588e+00",
"newLine": true
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"header": 1,
"value": "kfdsklj ",
"newLine": true
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{
"type": "lineComment",
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"value": " hello ",
"newLine": true
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{
"type": "strings",
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},
{
"key": "The Number of Active P[i] for fitting ",
"rawValue": [
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"parsedValue": [
{
"type": "number",
"value": 4
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},
{
"key": "Relative step",
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"parsedValue": [
{
"type": "number",
"value": 0.2
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{
"key": "Tolerance for fitting sens",
"rawValue": [
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"parsedValue": [
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"type": "number",
"value": 0.001
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]
},
{
"key": "Tolerance for fitting ",
"rawValue": [
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"parsedValue": [
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"type": "number",
"value": -1
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]
},
{
"key": "Step for fitting ",
"rawValue": [
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"parsedValue": [
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"type": "number",
"value": 0.000001
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]
},
{
"key": "Indexes of P[i] for fitting ",
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