Jankowski

• Groupcontribution

createGroupContributionStruct(primaryFile, pH, secondaryFile)

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)

Create a group incidence matrix from group contribution method (GCM) output, mapping each metabolite to its structural groups (Jankowski et al. data)

USAGE:

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

INPUTS:

• model – COBRA model structure, read for the fields:

  • .mets - m x 1 cell array of metabolite identifiers

  • .jankowskiGroupData - struct of group data with a .groups field

  • .gcmMetList - metabolite identifiers ordered as the GCM output file rows

  • .gcmOutputFile - path to the GCM output file to parse

• gcmOutputFile – path to the group contribution method output file

• gcmMetList – cell array of metabolite identifiers matching the GCM output rows

• jankowskiGroupData – struct of Jankowski et al. group data with field:

  • .groups - cell array of structural group names

OUTPUT:

G – m x g group incidence matrix, one row per metabolite and one column per structural group

plotConcVSdGft0GroupContUncertainty(modelT)

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 – thermodynamically constrained model structure with fields:

• .mets - m x 1 cell array of metabolite identifiers

• .T - temperature in Kelvin

• .gasConstant - gas constant (consistent energy units)

• .concMax - m x 1 maximum metabolite concentrations

• .concMin - m x 1 minimum metabolite concentrations

• .dfGt0GroupContUncertainty - m x 1 group contribution uncertainty in the standard transformed Gibbs energy of formation

• .dfGt0Source - m x 1 source of each standard transformed Gibbs energy of formation estimate

OUTPUTS:

• D – m x 1 half the concentration contribution to the Gibbs energy of formation range for each metabolite

• DGC – m x 1 group contribution uncertainty for each metabolite

setupComponentContribution(model, molFileDir, cid, printLevel)

Estimate metabolite structures, pKa values and pseudoisomers for the component contribution method of standard Gibbs energy estimation

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.

USAGE:

model = setupComponentContribution (model, molFileDir, cid, printLevel)

INPUTS:

model – COBRA model structure with fields:

• .mets - m x 1 cell array of metabolite identifiers

• .metFormulas - m x 1 cell array of metabolite formulae (H for protons, H2O for water)

• .metCharges - m x 1 numeric array of metabolite charges

OPTIONAL INPUTS:

• molFileDir – path to a directory of molfiles for the major tautomer of the major microspecies of each metabolite at pH 7, named with the metabolite identifiers in model.mets (without compartment assignments); not required if cid is given

• cid – m x 1 cell array of KEGG Compound identifiers; not required if molFileDir is given

• printLevel – verbosity level (default 1)

OUTPUT:

model – COBRA model structure with the additional fields:

• .inchi - structure of m x 1 cell arrays of InChI strings at varying levels of structural detail

• .pseudoisomers - matrix of estimated pseudoisomer data (metabolite index, standard Gibbs energy, number of hydrogens, charge)

Note

Writes MetStructures.sdf, an SDF of all structures passed to the component contribution method for standard Gibbs energy estimation.

webCGMtoTabDelimitedFile(model, webCGMoutputFile, gcmMetList)

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:

  • .S - m x n stoichiometric matrix

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

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

• webCGMoutputFile – filename of output from the webCG server

• gcmMetList – m x 1 cell array of metabolite IDs for metabolites in webCGMoutputFile. Metabolite order must be the same in gcmMetList and webCGMoutputFile.

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.