Jankowski

createGroupContributionStruct(primaryFile, pH, secondaryFile)[source]

Generates a matlab structure out of the tab delimited group contribuion data

The matlab structure with the group contibution data for each metabolite uses the primaryFile file in preference to the secondaryFile file but these can be any first and second preference files as long as they are in the correct format see webCGMtoTabDelimitedFile.m

USAGE

metGroupCont = createGroupContributionStruct (primaryFile, pH, secondaryFile)

INPUT

primaryFile – tab delimited text file with group contribution data (Janowski et al Biophysical Journal 95:1487-1499 (2008)) i.e. output such as webCGM.txt from webCGMtoTabDelimitedFile.m

OPTIONAL INPUTS

  • pH – ph at which group contribution data given for, default = 7

  • secondaryFile – tab delimited text file with group contribution data (Janowski et al Biophysical Journal 95:1487-1499 (2008)) i.e. output such as webCGM.txt from webCGMtoTabDelimitedFile.m If the same metabolite abbreviation occurs in both files, then the data in the primary file takes precedence.

Comment on input file format - the first two text columns in both files should correspond to: abbreviation, formulaMarvin, the next three columns in both files should correspond to: delta_G_formation, delta_G_formation_Uncertainty, chargeMarvin

OUTPUTS

metGroupCont – structure with fields:

  • metGroupCont(m).abbreviation - metabolite abbreviation

  • metGroupCont(m).formulaMarvin - metabolite formula (Marvin)

  • metGroupCont(m).delta_G_formation

  • metGroupCont(m).delta_G_formation_uncertainty

  • metGroupCont(m).chargeMarvin - metabolite charge (Marvin)

  • metGroupCont(m).pH

  • metGroupCont(m).file - file data came from

createGroupIncidenceMatrix_jankowski(model, gcmOutputFile, gcmMetList, jankowskiGroupData)[source]

Creates groupData struct to calculate reaction Gibbs energies with reduced error in vonB.

USAGE

G = createGroupIncidenceMatrix_old (model, gcmOutputFile, gcmMetList, jankowskiGroupData)

INPUTS

  • model

  • gcmOutputFile

  • gcmMetList

  • jankowskiGroupData

OUTPUT

G

plotConcVSdGft0GroupContUncertainty(modelT)[source]

Compares the difference between minimum & maximum concentration, on a logarithmic scale, and the group contribution uncertainty for each metabolite.

USAGE

[D, DGC] = plotConcVSdGft0GroupContUncertainty (modelT)

INPUT

modelT – structure with fields:

  • modelT.concMax

  • modelT.concMin

  • modelT.dfGt0GroupContUncertainty

OUTPUTS

  • D

  • DGC

setupComponentContribution(model, molFileDir, cid, printLevel)[source]

Estimates standard transformed reaction Gibbs energy and directionality at in vivo conditions in multicompartmental metabolic reconstructions. Has external dependencies on the COBRA toolbox, the component contribution method, Python (with numpy and Open Babel bindings), ChemAxon’s Calculator Plugins, and Open Babel. See details on availability at the end of help text.

modelT = setupThermoModel(model,molfileDir,cid,T,cellCompartments,ph,…

is,chi,concMin,concMax,confidenceLevel)

INPUTS model Model structure with following fields: .S m x n stoichiometric matrix. .mets m x 1 array of metabolite identifiers. .rxns n x 1 array of reaction identifiers. .metFormulas m x 1 cell array of metabolite formulas. Formulas for

protons should be H, and formulas for water should be H2O.

.metCharges m x 1 numerical array of metabolite charges.

OPTIONAL INPUTS molFileDir Path to a directory containing molfiles for the

major tautomer of the major microspecies of each metabolite at pH 7. Molfiles should be named with the metabolite identifiers in model.mets (without compartment assignments). Not required if cid are specified.

cid m x 1 cell array of KEGG Compound identifiers.

Not required if molfiledir is specified.

model.metCompartments m x 1 array of metabolite compartment

assignments. Not required if metabolite identifiers are strings of the format ID[*] where * is the appropriate compartment identifier.

OUTPUTS model Model structure with following additional fields: .inchi Structure containing four m x 1 cell array’s of

IUPAC InChI strings for metabolites, with varying levels of structural detail.

.pKa m x 1 structure containing metabolite pKa values

estimated with ChemAxon’s Calculator Plugins.

.pseudoisomers p x 4 matrix with the following columns:

  1. Metabolite index.

  2. Estimated pseudoisomer standard Gibbs energy.

3. Number of hydrogen atoms in pseudoisomer chemical formula. 4. Charge on pseudoisomer.

WRITTEN OUTPUTS MetStructures.sdf An SDF containing all structures input to the

component contribution method for estimation of standard Gibbs energies.

Ronan M. T. Fleming, Sept. 2012 Version 1.0 Hulda S. H., Dec. 2012 Version 2.0

webCGMtoTabDelimitedFile(model, webCGMoutputFile, gcmMetList)[source]

Parses a webCGM output file and prepare a tab delimited file with group contribution data mapped to the metabolite abbreviations in the given model.

Parses webCGM output file and creates an input file for createGroupContributionStruct.m

USAGE

webCGMtoTabDelimitedFile (model, webCGMoutputFile, gcmMetList)

INPUTS

  • model – structure with fields:

    • model.S - m x n, stoichiometric matrix

    • model.mets - m x 1, cell array of metabolite abbreviations

    • model.metFormulas - m x 1, cell array of metabolite formulae

  • webCGMoutputFile – filename of output from webCG server

  • metList – m x 1, cell array of metabolite ID for metabolites in webCGMoutputFile. Metabolite order must be the same in metList and webGCMoutputFile.

OUTPUT

gc_data_webCGM.txt – tab delimited text file with group contribution data for createGroupContributionStruct.m. The first two text columns in both files should correspond to: abbreviation, formulaMarvin, the next three columns in both files should correspond to: delta_G_formation, delta_G_formation_Uncertainty, chargeMarvin.

Note

By default, any group contribution data for metabolites with underdefined formulae ( e.g. R group), are ignored, even if there is group contribution data available for this metabolite.