slv-utils
Version:
Utilities for working with SLV and DAT files.
1,846 lines • 283 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 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"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& "
],
"parsedValue": [
{
"type": "arrayNumber",
"value": [
[
1,
1,
-1
],
[
1,
2,
1
],
[
2,
2,
-1
],
[
0,
0,
0
]
]
}
]
},
{
"key": "Elementary Constants ",
"rawValue": [
"1.944853e+00 1.931480e+00 1.084404e+00 1.097818e+00 "
],
"parsedValue": [
{
"type": "arrayNumber",
"value": [
1.944853,
null,
1.93148,
null,
1.084404,
null,
1.097818
]
}
]
},
{
"key": "Initial concentrations ",
"rawValue": [
"0.000000e+00 0.000000e+00 "
],
"parsedValue": [
{
"type": "arrayNumber",
"value": [
0,
null,
0
]
}
]
},
{
"key": "Initial Stiffness",
"rawValue": [
"0.000000e+00 0.000000e+00 "
],
"parsedValue": [
{
"type": "arrayNumber",
"value": [
0,
0
]
}
]
},
{
"key": "Initial Family Steps",
"rawValue": [
"1.000000e+00 1.000000e+00 "
],
"parsedValue": [
{
"type": "arrayNumber",
"value": [
1,
null,
1
]
}
]
},
{
"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",
"",
"",
"",
"####"
]
}
]
},
{
"key": "Variables for FileOutputOn ",
"rawValue": [
" #### "
],
"parsedValue": [
{
"type": "strings",
"value": [
"####"
]
}
]
},
{
"key": "(Internal) Temporary Print Option ",
"rawValue": [
"767476298 "
],
"parsedValue": [
{
"type": "number",
"value": 767476298
}
]
},
{
"key": "LeastFitting ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "Output File Name ",
"rawValue": [
"output.txt "
],
"parsedValue": [
[
{
"type": "string",
"value": "output"
},
{
"type": "strings",
"value": [
".txt"
]
}
]
]
},
{
"key": "Experimental Data File Name ",
"rawValue": [
"example4_include2.dat "
],
"parsedValue": [
[
{
"type": "string",
"value": "example4_include2"
},
{
"type": "strings",
"value": [
".dat"
]
}
]
]
},
{
"key": "\nRight Hand Sides && \nInitial Values && \nComments Or Selkov DB record",
"rawValue": [
"\n// if-else check 1 (time) \ncheck = 1; \nif (t>50) {check=100;} \nelse {check=0;} \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//!!! F0=-91.566265 12:31:06 PM 3/16/2017 \n/*{ \nvariable:{ \n index: \"knew\", \n name: \"New parameter.\", \n notes: \"This is another example of structural comments.\" , \n rhs: {value:1} \n} \n}*/ \n/*{ \ncompartment:{ \n index: \"com1\", \n variableRef: \"com1\" \n} \n}*/ \nkcat=7.282813e-01; \nVd=5.275000e+00; \nKm=5.257432e+00; \nkabs=2.090394e+00; \n/*{ \nvariable:{ \n index: \"Vd\", \n name: \"Volume of distribution.\", \n notes: \"This is an example of structural comments.\" , \n rhs: {value:1} \n} \n}*/ ",
"\n//!kfdsklj \ndkklj \nlkal; \nll;l \n//!! hello \n';dsld \n/*{ \n\"reaction\": { \n \"index\": \"vabs_test\", \n \"rate\": \"vabs\", \n \"reactants\": [ \n {\"speciesReference\": \"C0\", \"stoichiometry\": -1}, \n {\"speciesReference\": \"C1\", \"stoichiometry\": 1} \n ] \n } \n}*/ \n\n#dbs# "
],
"parsedValue": [
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{
"type": "lineComment",
"header": 0,
"value": " if-else check 1 (time) ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "check",
"rhs": "1",
"newLine": true
}
},
{
"type": "conditionExpression",
"condition": {
"lhs": "t",
"rhs": "50",
"sign": ">"
},
"then": [
{
"type": "numeric",
"value": {
"lhs": "check",
"rhs": "100",
"newLine": false
}
}
],
"else": [
[
{
"type": "numeric",
"value": {
"lhs": "check",
"rhs": "0",
"newLine": false
}
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]
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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
},
{
"type": "expression",
"value": {
"lhs": "vabs",
"rhs": "Default*(kabs*C0)",
"newLine": true
}
},
{
"type": "lineComment",
"header": 2,
"value": "vel ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "vel",
"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",
"value": {
"lhs": "F[1]",
"rhs": "(-vabs)/Default",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "for C1 ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[2]",
"rhs": "(vabs-vel)/Vd",
"newLine": true
}
},
{
"type": "lineComment",
"header": 1,
"value": " Explicit Functions ",
"newLine": true
},
{
"type": "lineComment",
"header": 0,
"value": " Explicit Functions text",
"newLine": true
}
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[
{
"type": "lineComment",
"header": 1,
"value": " Data comments ",
"newLine": true
},
{
"type": "lineComment",
"header": 1,
"value": " Compartments volumes ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "Default",
"rhs": "1",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " {--} ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "Vd",
"rhs": "9",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "{L} ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "F",
"rhs": "0.72",
"newLine": true
}
},
{
"type": "strings",
"value": [
"",
""
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},
{
"type": "lineComment",
"header": 1,
"value": " Initial concentration ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "Dose",
"rhs": "5",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " {umole} ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "T",
"rhs": "24",
"newLine": true
}
},
{
"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",
"value": {
"lhs": "C1",
"rhs": "0",
"newLine": true
}
},
{
"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
}
},
{
"type": "lineComment",
"header": 0,
"value": " {uM/hr} ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "Km",
"rhs": "5",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " {uM} ",
"newLine": false
},
{
"type": "lineComment",
"header": 3,
"value": " F0=0.020335 2:16:09 PM 5/23/2014 ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "kcat",
"rhs": "7.375000e-01",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Vd",
"rhs": "5.275000e+00",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Km",
"rhs": "5.528412e+00",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "kabs",
"rhs": "2.064588e+00",
"newLine": true
}
},
{
"type": "strings",
"value": [
"",
""
]
},
{
"type": "lineComment",
"header": 3,
"value": " F0=-91.566265 12:31:06 PM 3/16/2017 ",
"newLine": true
},
{
"type": "multylineComment",
"value": "{ \nvariable:{ \n index: \"knew\", \n name: \"New parameter.\", \n notes: \"This is another example of structural comments.\" , \n rhs: {value:1} \n} \n}"
},
{
"type": "multylineComment",
"value": "{ \ncompartment:{ \n index: \"com1\", \n variableRef: \"com1\" \n} \n}"
},
{
"type": "numeric",
"value": {
"lhs": "kcat",
"rhs": "7.282813e-01",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Vd",
"rhs": "5.275000e+00",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Km",
"rhs": "5.257432e+00",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "kabs",
"rhs": "2.090394e+00",
"newLine": true
}
},
{
"type": "multylineComment",
"value": "{ \nvariable:{ \n index: \"Vd\", \n name: \"Volume of distribution.\", \n notes: \"This is an example of structural comments.\" , \n rhs: {value:1} \n} \n}"
}
],
[
{
"type": "lineComment",
"header": 1,
"value": "kfdsklj ",
"newLine": true
},
{
"type": "strings",
"value": [
"dkklj",
""
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},
{
"type": "arrayNumber",
"value": [
null
]
},
{
"type": "string",
"value": "lkal"
},
{
"type": "strings",
"value": [
";",
""
]
},
{
"type": "arrayNumber",
"value": [
null
]
},
{
"type": "string",
"value": "ll"
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{
"type": "strings",
"value": [
";l",
""
]
},
{
"type": "lineComment",
"header": 2,
"value": " hello ",
"newLine": true
},
{
"type": "strings",
"value": [
"';dsld",
""
]
},
{
"type": "multylineComment",
"value": "{ \n\"reaction\": { \n \"index\": \"vabs_test\", \n \"rate\": \"vabs\", \n \"reactants\": [ \n {\"speciesReference\": \"C0\", \"stoichiometry\": -1}, \n {\"speciesReference\": \"C1\", \"stoichiometry\": 1} \n ] \n } \n}"
}
]
]
},
{
"key": "The Number of Active P[i] for fitting ",
"rawValue": [
"4 "
],
"parsedValue": [
{
"type": "number",
"value": 4
}
]
},
{
"key": "Relative step",
"rawValue": [
"2.000000e-01 "
],
"parsedValue": [
{
"type": "number",
"value": 0.2
}
]
},
{
"key": "Tolerance for fitting sens",
"rawValue": [
"1.000000e-03 "
],
"parsedValue": [
{
"type": "number",
"value": 0.001
}
]
},
{
"key": "Tolerance for fitting ",
"rawValue": [
"-1.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": -1
}
]
},
{
"key": "Step for fitting ",
"rawValue": [
"1.000000e-06 "
],
"parsedValue": [
{
"type": "number",
"value": 0.000001
}
]
},
{
"key": "Indexes of P[i] for fitting ",
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{
"key": "Minimum for fitting ",
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