protons

addPseudoisomersToModel(model, printLevel)

Estimate metabolite pKa values with ChemAxon calculator plugins and determine all relevant pseudoisomers.

USAGE:

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

INPUT:
model Model structure with following fields:

  • .mets - m x 1 array of metabolite 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.

  • .metCompartments - optional 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.

  • .inchi - Structure containing four m x 1 cell array’s of IUPAC InChI strings for metabolites, with varying levels of structural detail.

  • .inchi.standard: m x 1 cell array of standard inchi

  • .inchi.standardWithStereo: m x 1 cell array of standard inchi with stereo

  • .inchi.standardWithStereoAndCharge: m x 1 cell array of standard inchi with stereo and charge

  • .inchi.nonstandard: m x 1 cell array of non-standard inchi

OPUTPUT model.pseudoisomer m x 1 structure array where each element has the fields

listed below. All fields are empty for metabolites where no InChI is given. Fields:

  • .success - Logical one (true) for metabolites where an InChI was given.

  • .pKas - p x p matrix where element (i, j) is the pKa value for the acid-base equilibrium between pseudoisomers i and j.

  • .zs - p x 1 array of pseudoisomer charges.

  • .nHs - p x 1 array of number of hydrogen atoms in each pseudoisomer’s chemical formula.

  • .majorMSpH7 - p x 1 logical array. True for the most abundant pseudoisomer at pH 7.

*.mf *.lambda *.gpfnsp

pKaErrorMets

getMetaboliteMsDistr(mets, molfiledir, msdistrdir, phs)

Calculate microspecies distributions at all pH values in phs using ChemAxon’s cxcalc. Metabolite mol files in molfiledir are input to cxcalc. Mol file names should correspond to the metabolite ID in mets (it is assumed that compartment assignments are appended to the end of metabolite ID in the format metID[c]). Microspecies distributions are returned as .sdf files in msdistrdir

USAGE:

getMetaboliteMsDistr(mets, molfiledir, msdistrdir, phs)

INPUTS:

mets: metabolites molfiledir: directory with mol files msdistrdir: directory with microspecies distributions phs: pH values

getMetabolitepKa(mets, molfiledir, pkadir)

Compute pKas of the metabolites listed in mets using ChemAxon’s cxcalc. Metabolite mol files in molfiledir are input to cxcalc. Mol file names should correspond to the metabolite ID in mets (it is assumed that compartment assignments are appended to the end of metabolite ID in the format metID[c]). Text files with pKas are returned in pkadir.

USAGE:

getMetabolitepKa(mets, molfiledir, pkadir)

INPUTS:

mets: metabolites molfiledir: directory with mol files pkadir: directory with text files with pKas

moleFraction(metAbbr, Alberty2006, metAbbrAlbertyAbbr, temp, pHa, is, chi)

Mole fraction of different metabolite species that make up a reactant

USAGE:

mf = moleFraction(metAbbr, Alberty2006, metAbbrAlbertyAbbr, temp, pHa, is, chi)

INPUT:

metAbbr: reconstruction reactant abbreviation Alberty2006: Basic data on the metabolite species that make

up a reactant, compiled by Robert A. Alberty, Massachusetts Institute of Technology. In Print: Robert A. Alberty, Biochemical Thermodynamics: Applications of Mathematica. John Wiley & Sons, 2006. p391-395 Online: BasicBioChemData3.nb http://library.wolfram.com/infocenter/MathSource/5704/

metAbbrAlbertyAbbr: mapping from model metabolite primary key to

primary key of reactants in Alberty2006

OPTIONAL INPUTS:

temp: pHa: is: temp: chi:

OUTPUT:

mf: mole fraction at equilibrium

moleFractionStats(modelT)

Plots of mole fraction statistics.

Plot a histogram of the number of metabolite species relevant between pH 5 and 9, and a stacked bar chart of the mole fractions of reactants with significant (<0.99) distributions over more than one metabolite species.

USAGE:

moleFractionStats(modelT)

INPUT:

modelT: structure with fields:

  • .S

  • .officialName

  • .mf

plotActivityCoefficients(modelT)

Plots statistics on activity coefficients.

Plots a histogram of the distribution of activity coefficients also a curve of activity coefficients for different charges at a range of ionic strengths

USAGE:

[n, edges, lambda] = plotActivityCoefficients(modelT)

INPUT:

modelT: structure with fields:

  • model.met(i).lambda - activity coefficient

  • model.temp - temperature

OUTPUTS:

n: edges: lambda:

plotMoleFraction(metAbbr, Alberty2006, metAbbrAlbertyAbbr, PHmin, PHmax, ISmin, ISmax, CHImin, CHImax, TEMPmin, TEMPmax, N)

Plot the mole fractions of metabolite species of a reactant as a function of pH, ionic strength, charge and temperature.

USAGE:

plotMoleFraction(metAbbr, Alberty2006, metAbbrAlbertyAbbr, PHmin, PHmax, ISmin, ISmax, CHImin, CHImax, TEMPmin, TEMPmax, N)

INPUTS:

metAbbr: reconstruction reactant abbreviation Alberty2006: Basic data on the metabolite species that make

up a reactant, compiled by Robert A. Alberty, Massachusetts Institute of Technology. In Print: Robert A. Alberty, Biochemical Thermodynamics: Applications of Mathematica. John Wiley & Sons, 2006. p391-395 Online: BasicBioChemData3.nb http://library.wolfram.com/infocenter/MathSource/5704/

metAbbrAlbertyAbbr: mapping from model metabolite primary key to

primary key of reactants in Alberty2006

PHmin: Minimum glass electrode pH PHmax: Maximum glass electrode pH ISmin: Ionic strength minimum ISmax: Ionic strength maximum CHImin: Electrical potential minimum CHImax: Electrical potential maximum TEMPmin: temperature minimum TEMPmax: temperature maximum N:

realpH(pHa, temp, is)

Apparent glass electrode pH is not the same as real pH for thermodynamic calculations.

Given the experimental glass electrode measurement of pH, this function returns the pH to be used for thermodynamic calculations, pHc = -log10[H+], by subtracting the effect of the ion atmosphere around H+ which reduces its activity coefficient below unity. See p49 Alberty 2003.

USAGE:

[pHr, pHAdjustment] = realpH(pHa, temp, is)

INPUTS:

pHa: apparent pH, measured by glass electrode experimentally temp: experimentally measured temperature is: estimate of ionic strength

OUTPUTS:

pHr: real pH to be used for thermodynamic calculations pHAdjustment: adjustment to pH