groupContribution¶
- assignThermoToModel(model, Alberty2006, Legendre, LegendreCHI, useKeqData, printToFile, GCpriorityMetList, metGroupCont, metSpeciespKa)¶
Assigns thermodynamic data to model at given temperature, pH, ionic strength and electrical potential.
Physicochemically, this is the most important function for setting up a thermodynamic model. It takes the standard Gibbs energies of the metabolite species and uses this data to create a standard transformed Gibbs energy for each reactant. It uses the metabolite species standard Gibbs energies of formation backcalculated from equilibrium constants, in preference to the group contribution estimates.
USAGE:
[model,computedSpeciesData] = assignThermoToModel(model, Alberty2006, Legendre, LegendreCHI, useKeqData, printToFile, GCpriorityMetList, metGroupCont, metSpeciespKa)
- INPUTS:
model: structure with fields:
model.T - temperature 298.15 K to 313.15 K
model.ph(p) - real pH in compartment defined by letter p
model.is(p) - ionic strength (0 - 0.35M) in compartment defined by letter p
model.chi(p) - electrical potential (mV) in compartment defined by letter p
model.cellCompartments(p) - 1 x # cell array of distinct compartment letters
model.NaNdfG0GCMetBool(m) - m x 1 boolean vector with 1 when no group contribution data is available for a metabolite
Alberty2006: Alberty’s data
- OPTIONAL INPUTS:
Legendre: {(1), 0} Legendre Transformation for specifc real pH? LegendreCHI: {(1), 0} Legendre Transformation for specifc electrical potential? useKeqData: {(1), 0} Use dGf0 back calculated from Keq? printToFile: {(0), 1} 1 = print out repetitive material to log file metGroupCont: Structure containing output from `Jankowski et al.’s
2008 implementation of the group contribution method (GCM).` Contains the following fields for each metabolite:
.abbreviation: Metabolite ID
.formulaMarvin: Metabolite formula output by GCM
.delta_G_formation: Estimated standard Gibbs energy of formation
.delta_G_formation_uncertainty: Uncertainty in estimated delta_G_formation
.chargeMarvin: Metabolite charge output by GCM
- metSpeciespKa: Structure containing pKa for acid-base equilibria between
metabolite species. pKa are estimated with ChemAxon’s pKa calculator plugin (see function assignpKasToSpecies).
- OUTPUTS:
model: structure with fields:
model.dfG0(m) - standard Gibbs energy of formation
model.dfG(m) - Gibbs energy of formation
model.dfGt0(m) - standard transformed Gibbs energy of formation
model.dHzerot(m) - standard transformed enthalpy of formation
model.dfGt0Source(m) - origin of data, Keq or groupContFileName.txt
model.dfGt0Keq(m)
model.dfGt0GroupCont(m)
model.dfHt0Keq(m)
model.mf(m) - mole fraction of each species within a pseudoisomer group
model.aveZi(m) - average charge
model.chi - electrical potential
model.aveHbound(m) - average number of protons bound to a reactant
modelT.gasConstant - Gas Constant (deprecated)
model.faradayConstant - Faraday Constant
modelT.temp - Temperature (deprecated)
model.ph(p) - real pH in compartment defined by letter p
model.is(p) - ionic strength (0 - 0.35M) in compartment defined by letter p
model.chi(p) - electrical potential (mV) in compartment defined by letter p
- createComputedSpeciesData(metSpeciespKa, metGroupCont)¶
Use group contribution estimated standard Gibbs energies of formation for predominant metabolite species at pH 7, and ChemAxon estimated pKa for species equilibria, to calculate standard Gibbs energies of formation for nonpredominant metabolite species.
USAGE:
computedSpeciesData = createComputedSpeciesData(metSpeciespKa, metGroupCont)
- INPUTS:
- metSpeciespKa: Structure containing pKa for acid-base equilibria between
metabolite species. pKa are estimated with ChemAxon’s pKa calculator plugin (see function “assignpKasToSpecies”)
- metGroupCont: Structure array with group contribution method output
mapped to BiGG metabolites.
- OUTPUT:
- computedSpeciesData: Structure with thermodynamic data for metabolite
species. Contains two fields for each metabolite:
.abbreviation: Metabolite abbreviation
.basicData: Cell array with 4 columns; 1. dGf0 (kJ/mol), 2. dHf0, 3. charge, 4. #Hydrogens