Vonbertalanffy

configureSetupThermoModelInputs(model, T, compartments, ph, is, chi, concMinDefault, concMaxDefault, confidenceLevel)[source]

Configure inputs to setupThermoModel (set defaults etc.)

All optional inputs are empty by default. Metabolite, reaction and compartment identifiers are normalised, missing compartment assignments are derived, temperature, compartment-specific pH/ionic-strength/electrical potential and metabolite concentration bounds are set, and a confidence level is assigned.

USAGE:

model = configureSetupThermoModelInputs (model, T, compartments, ph, is, chi, concMinDefault, concMaxDefault, confidenceLevel)

INPUT:

model – COBRA model structure. Fields used or configured:

  • .S - m x n stoichiometric matrix

  • .mets - m x 1 metabolite identifiers

  • .rxns - n x 1 reaction identifiers

  • .metFormulas - m x 1 metabolite formulas

  • .metCharges - m x 1 metabolite charges

  • .metCompartments - m x 1 compartment assignments

  • .compartments - c x 1 compartment identifiers

  • .T - temperature in Kelvin

  • .ph - c x 1 compartment specific pH values

  • .is - c x 1 compartment specific ionic strengths

  • .chi - c x 1 compartment specific electrical potentials

  • .concMin - m x 1 lower bounds on metabolite concentrations

  • .concMax - m x 1 upper bounds on metabolite concentrations

  • .confidenceLevel - confidence level for directionality assignment

OPTIONAL INPUTS:

  • T – temperature in Kelvin (default: 298.15)

  • compartments – c x 1 array of compartment identifiers

  • ph – c x 1 array of compartment specific pH values

  • is – c x 1 array of compartment specific ionic strengths in mol/L

  • chi – c x 1 array of compartment specific electrical potentials in mV

  • concMinDefault – default lower bound on metabolite concentrations in mol/L

  • concMaxDefault – default upper bound on metabolite concentrations in mol/L

  • confidenceLevel – confidence level for reaction directionality (default: 0.95)

OUTPUT:

model – the model structure with the fields above configured

estimateDG_temp(model)[source]

Estimates standard transformed Gibbs energies of formation for metabolites

USAGE:

model = estimateDG_temp (model)

INPUT:

model – Model structure with following fields:

  • .S - m x n stoichiometric matrix.

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

  • .metFormulas - m x 1 cell array of metabolite formulas. Formulas for protons should be ‘H’.

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

  • .T - Temperature in Kelvin.

  • .cellCompartments - c x 1 array of cell compartment identifiers.

  • .ph - c x 1 array of compartment specific pH values.

  • .is - c x 1 array of compartment specific ionic strength values in mol/L.

  • .chi - c x 1 array of compartment specific electrical potential values in mV.

  • .metCompartments - m x 1 cell array of compartment assignments for metabolites in model.mets. Compartment identifiers should be the same as in model.cellCompartments.

  • .DfG0 - m x 1 array of standard Gibbs energies of formation.

  • .pKa - m x 1 structure array with metabolite pKa values.

OUTPUT:

model – Model structure with following fields added:

  • .DfG0_pseudoisomers - Four column matrix with pseudoisomer standard Gibbs energies of formation in kJ/mol.

    • Column 1. Row index of pseudoisomer group in model.S.

    • Column 2. Standard Gibbs energy of formation.

    • Column 3. Number of hydrogen atoms.

    • Column 4. Charge.

  • .DfGt0 - Standard transformed Gibbs energies of formation in kJ/mol.

  • .DrGt0 - Standard transformed reaction Gibbs energy in kJ/mol.

estimateDfGt0(model, confidenceLevel)[source]

Estimate standard transformed Gibbs energies of formation for metabolites

Sets a default temperature and gas constant if absent, normalises compartment identifiers, then applies a Legendre transform per metabolite pseudoisomer group to obtain transformed Gibbs energies of formation and their bounds.

USAGE:

model = estimateDfGt0 (model, confidenceLevel)

INPUT:

model – model structure with the following fields:

  • .S - m x n stoichiometric matrix

  • .mets - m x 1 metabolite identifiers

  • .metFormulas - m x 1 metabolite formulas (protons should be H)

  • .T - temperature in Kelvin (default 310.15 if absent)

  • .gasConstant - gas constant in kJ/(K*mol) (set if absent)

  • .compartments - c x 1 compartment identifiers

  • .metCompartments - m x 1 compartment assignments for the metabolites

  • .ph - c x 1 compartment specific pH values

  • .is - c x 1 compartment specific ionic strengths in mol/L

  • .chi - c x 1 compartment specific electrical potentials in mV

  • .DfG0 - m x 1 standard Gibbs energies of formation

  • .DfH0 - m x 1 standard enthalpies of formation (optional)

  • .concMin - m x 1 lower bounds on metabolite concentrations in mol/L

  • .concMax - m x 1 upper bounds on metabolite concentrations in mol/L

  • .DfG0_Uncertainty - m x 1 uncertainty in standard Gibbs energies of formation

  • .SIntRxnBool - n x 1 true for internal reactions

OPTIONAL INPUT:

confidenceLevel – {0.50, 0.70, (0.95), 0.99}. Confidence level for DfGt0 and DrGt0 interval estimates. Default is 0.95, corresponding to 95% confidence intervals.

OUTPUT:

model – the model structure with the following fields added:

  • .DfG0_pseudoisomers - four column matrix of pseudoisomer standard Gibbs energies of formation (metabolite index, standard Gibbs energy, number of hydrogen atoms, charge)

  • .DfGt0 - m x 1 standard transformed Gibbs energies of formation in kJ/mol

  • .DfHt0 - m x 1 standard transformed enthalpies of formation in kJ/mol

  • .aveHbound - m x 1 average number of bound hydrogen ions

  • .aveZi - m x 1 average charge

  • .DfGt0Min - m x 1 lower bounds on standard transformed Gibbs energies of formation

  • .DfGt0Max - m x 1 upper bounds on standard transformed Gibbs energies of formation

  • .DfGtMin - m x 1 lower bounds on transformed Gibbs energies of formation in kJ/mol

  • .DfGtMax - m x 1 upper bounds on transformed Gibbs energies of formation in kJ/mol

  • .DfGtMean - m x 1 mean transformed Gibbs energies of formation in kJ/mol

estimateDrGt0(model, confidenceLevel)[source]

Estimate bounds on transformed Gibbs energies for metabolites and reactions in a model

Computes standard and standard transformed reaction Gibbs energies from the metabolite estimates, adds the multicompartmental (pH and electrical potential) contributions for transport reactions, and derives lower and upper bounds and a mean estimate.

USAGE:

model = estimateDrGt0 (model, confidenceLevel)

INPUT:

model – model structure with the following fields:

  • .S - m x n stoichiometric matrix

  • .mets - m x 1 metabolite identifiers

  • .metFormulas - m x 1 metabolite formulas (protons should be H)

  • .metCharges - m x 1 metabolite charges

  • .metCompartments - m x 1 compartment assignments

  • .compartments - c x 1 compartment identifiers

  • .T - temperature in Kelvin

  • .ph - c x 1 compartment specific pH values

  • .chi - c x 1 compartment specific electrical potential values in mV

  • .concMin - m x 1 lower bounds on metabolite concentrations in mol/L

  • .concMax - m x 1 upper bounds on metabolite concentrations in mol/L

  • .DfG0 - m x 1 standard Gibbs energies of formation

  • .DfGt0 - m x 1 standard transformed Gibbs energies of formation

  • .DfGtMin - m x 1 lower bounds on transformed Gibbs energies of formation

  • .DfGtMax - m x 1 upper bounds on transformed Gibbs energies of formation

  • .SIntRxnBool - n x 1 true for internal reactions

  • .DrG0_Uncertainty - n x 1 uncertainty in standard reaction Gibbs energies

  • .DrGt0_Uncertainty - n x 1 uncertainty in standard transformed reaction Gibbs energies

OPTIONAL INPUT:

confidenceLevel – {0.50, 0.70, (0.95), 0.99}. Confidence level for DfGt0 and DrGt0 interval estimates. Default is 0.95, corresponding to 95% confidence intervals.

OUTPUT:

model – the model structure with the following fields added:

  • .DrG0 - n x 1 standard reaction Gibbs energies in kJ/mol

  • .DrGt0 - n x 1 standard transformed reaction Gibbs energies in kJ/mol

  • .transportRxnBool - n x 1 true for transport reactions

  • .DrGt0Min - n x 1 lower bounds on standard transformed reaction Gibbs energies

  • .DrGt0Max - n x 1 upper bounds on standard transformed reaction Gibbs energies

  • .DrGtMin - n x 1 lower bounds on transformed reaction Gibbs energies in kJ/mol

  • .DrGtMax - n x 1 upper bounds on transformed reaction Gibbs energies in kJ/mol

  • .DrGtMean - n x 1 mean transformed reaction Gibbs energies in kJ/mol

getCompartment(mets)[source]

Gets the compartment for each metabolite, and the unique compartments, from metabolite abbreviation(s), each of which must have compartment symbol concatenated on the right hand side (i.e. metAbbr[*]), or using the underscore format (e.g., metAbbr_x).

USAGE:

[compartments, uniqueCompartments, abbr, uniqueAbbr] = getCompartment (mets)

INPUT:

mets – char array with a single metabolite abbreviation or m x 1 cell array of metabolite abbreviations

OUTPUTS:

  • compartments – char array with a single compartment identifier or m x 1 cell array of compartment identifiers

  • uniqueCompartments – char array with a single compartment identifier or cell array of unique compartment identifiers

  • abbr – char array with a single metabolite abbreviation, without compartment or m x 1 cell array of metabolite abbreviations, without compartments

  • uniqueAbbr – unique cell array of metabolite abbrviations without compartment

initVonBertalanffy[source]

All the installation instructions are in a separate .md file named vonBertalanffy.md in docs/source/installation Setup the paths to the data, scripts and functions Check if this COBRA toolbox extension is in the Matlab path

setupThermoModel(model, confidenceLevel)[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.

USAGE:

model = setupThermoModel (model, 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.

    • .T - Temperature in Kelvin.

    • .compartments - c x 1 array of compartment identifiers. Should match the compartment identifiers in model.metCompartments.

    • .ph - c x 1 array of compartment specific pH values in the range 4.7 to 9.3.

    • .is - c x 1 array of compartment specific ionic strength values in the range 0 to 0.35 mol/L.

    • .chi - c x 1 array of compartment specific electrical potential values in mV. Electrical potential in cytosol is assumed to be 0 mV. Electrical potential in all other compartments are relative to that in cytosol.

    • .concMin - m x 1 array of lower bounds on metabolite concentrations in mol/L.

    • .concMax - m x 1 array of upper bounds on metabolite concentrations in mol/L.

  • confidenceLevel – {0.50, 0.70, (0.95), 0.99}. Confidence level for standard transformed reaction Gibbs energies used to quantitatively assign reaction directionality. Default is 0.95, corresponding to a confidence interval of +/- 1.96 * ur.

OUTPUT:

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.

  • .DfG0 - m x 1 array of component contribution estimated standard Gibbs energies of formation.

  • .covf - m x m estimated covariance matrix for standard Gibbs energies of formation.

  • .DfG0_Uncertainty - m x 1 array of uncertainty in estimated standard Gibbs energies of formation. Will be large for metabolites that are not covered by component contributions.

  • .DrG0 - n x 1 array of component contribution estimated standard reaction Gibbs energies.

  • .DrG0_Uncertainty - n x 1 array of uncertainty in standard reaction Gibbs energy estimates. Will be large for reactions that are not covered by component contributions.

  • .DfG0_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.

  • .DfGt0 - m x 1 array of estimated standard transformed Gibbs energies of formation.

  • .DrGt0 - n x 1 array of estimated standard transformed reaction Gibbs energies.

  • .DfGtMin - m x 1 array of estimated lower bounds on transformed Gibbs energies of formation.

  • .DfGtMax - m x 1 array of estimated upper bounds on transformed Gibbs energies of formation.

  • .DrGtMin - n x 1 array of estimated lower bounds on transformed reaction Gibbs energies.

  • .DrGtMax - n x 1 array of estimated upper bounds on transformed reaction Gibbs energies.

  • .DfG0_Uncertainty - m x 1 array of uncertainty in estimated standard Gibbs energies of formation. Will be large for metabolites that are not covered by component contributions.

  • .gasConstant - gas constant in kJ/(K*mol), set from .R if present

  • .faradayConstant - Faraday constant in kJ/kmol, set from .F if present

Written output - MetStructures.sdf - An SDF containing all structures input to the component contribution method for estimation of standard Gibbs energies.