directionalityReport

analyseThermoConstrainedModel(model, cumNormProbCutoff, printLevel, resultsBaseFileName)

USAGE:

[out] = analyseThermoConstrainedModel(model, cumNormProbCutoff, printLevel, resultsBaseFileName)

INPUTS:

model: structure with fields:

• .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.

• .quantDir - n x 1 array indicating quantitatively assigned reaction directionality. 1 for reactions that are irreversible in the forward direction, -1 for reactions that are irreversible in the reverse direction, and 0 for reversible reactions.

cumNormProbCutoff: default = 0.2 printLevel: verbose level, default = 1 resultsBaseFileName:

OUTPUT:

out:

assignQualDir(model)

Assigns a qualitative direction to each reaction based on the upper and lower bounds

USAGE:

model = assignQualDir(model)

INPUTS:

model: structure with fields:

• model.lb

• model.ub

OUTPUTS:

model: structure with fields:

• model.quantDir - Quantitative directionality assignments.

  • quantDir = 1 for reactions that are irreversible in the forward direction.

  • quantDir = -1 for reactions that are irreversible in the reverse direction.

  • quantDir = 0 for reversible reactions.

directionalityChangeReport(model, directions, cumNormProbCutoff, printLevel, resultsBaseFileName)

Checks for changes to reconstruction reaction direction to thermodynamically constrained model direction .

Checks to see which metabolites are involved in reactions that change the reconstruction directionality then print out the reactions that these metabolites are involved in. Does not include reactions that cannot be assigned reaction directionality due to missing thermodynamic data for certain metabolites involved in that reaction.

USAGE:

directionalityChangeReport(model, directions, cumNormProbCutoff, printLevel, resultsBaseFileName)

INPUTS:

model: COBRA structure directions: a structue of boolean vectors with different directionality

assignments where some vectors contain subsets of others

qualtiative -> quantiative changed reaction directions

• .forward2Forward

• .forward2Reverse

• .forward2Reversible

• .forward2Uncertain

• .reversible2Forward

• .reversible2Reverse

• .reversible2Reversible

• .reversible2Uncertain

• .reverse2Forward

• .reverse2Reverse

• .reverse2Reversible

• .reverse2Uncertain

• .tightened

subsets of qualtiatively forward -> quantiatively reversible

• .forward2Reversible_bydGt0

• .forward2Reversible_bydGt0LHS

• .forward2Reversible_bydGt0Mid

• .forward2Reversible_bydGt0RHS

• .forward2Reversible_byConc_zero_fixed_DrG0

• .forward2Reversible_byConc_negative_fixed_DrG0

• .forward2Reversible_byConc_positive_fixed_DrG0

• .forward2Reversible_byConc_negative_uncertain_DrG0

• .forward2Reversible_byConc_positive_uncertain_DrG0

cumNormProbCutoff: {0.2} cutoff for probablity that reaction is

reversible within this cutoff of 0.5

printLevel: verbose level resultsBaseFileName:

directionalityStats(model, directions, cumNormProbCutoff, printLevel)

Build Boolean vectors with reaction directionality statistics

USAGE:

[model, directions] = directionalityStats(model, directions, cumNormProbCutoff, printLevel)

INPUTS:

model: a structue of boolean vectors with different directionality

assignments where some vectors contain subsets of others with field:

• .directions

directions: structure with field:

• .forwardProbability

qualitatively assigned internal reaction direactions

• .forwardRecon

• .reverseRecon

• .reversibleRecon

• .equilibriumRecon

quantitatively assigned internal reaction direactions thermodynamic data is lacking

• .forwardThermo

• .reverseThermo

• .reversibleThermo

• .uncertainThermo

• .equilibriumThermo

OPTIONAL INPUT

cumNormProbCutoff: {0.2} cutoff for probablity that reaction is

reversible within this cutoff of 0.5

printLevel: -1 to print out to file,

0 to silent, 1 to print out to command window

OUTPUT:

directions: a structue of boolean vectors with different directionality

assignments where some vectors contain subsets of others

qualtiative -> quantiative changed reaction directions

• .forward2Forward

• .forward2Reverse

• .forward2Reversible

• .forward2Uncertain

• .reversible2Forward

• .reversible2Reverse

• .reversible2Reversible

• .reversible2Uncertain

• .reverse2Forward

• .reverse2Reverse

• .reverse2Reversible

• .reverse2Uncertain

• .tightened

subsets of qualtiatively forward -> quantiatively reversible

• .forward2Reversible_bydGt0

• .forward2Reversible_bydGt0LHS

• .forward2Reversible_bydGt0Mid

• .forward2Reversible_bydGt0RHS

• .forward2Reversible_byConc_zero_fixed_DrG0

• .forward2Reversible_byConc_negative_fixed_DrG0

• .forward2Reversible_byConc_positive_fixed_DrG0

• .forward2Reversible_byConc_negative_uncertain_DrG0

• .forward2Reversible_byConc_positive_uncertain_DrG0

directionalityStatsFigures(directions, resultsBaseFileName, saveFigures)

Creates pie charts of directionality stats

USAGE:

directionalityStatsFigures(directions, resultsBaseFileName, saveFigures)

INPUT:

directions: a structue of boolean vectors with different directionality

assignments where some vectors contain subsets of others

qualitatively assigned directions:

• directions.forwardRecon

• directions.reverseRecon

• directions.reversibleRecon

qualitatively assigned directions using thermo in preference to qualitative assignments but using qualitative assignments where thermodynamic data is lacking

• directions.forwardThermo

• directions.reverseThermo

• directions.reversibleThermo

• directions.uncertainThermo

qualtiative -> quantiative changed reaction directions

• directions.forward2Forward

• directions.forward2Reverse

• directions.forward2Reversible

• directions.forward2Uncertain

• directions.reversible2Forward

• directions.reversible2Reverse

• directions.reversible2Reversible

• directions.reversible2Uncertain

• directions.reverse2Forward

• directions.reverse2Reverse

• directions.reverse2Reversible

• directions.reverse2Uncertain

subsets of forward qualtiative -> reversible quantiative change

• directions.forward2Reversible_bydGt0

• directions.forward2Reversible_bydGt0LHS

• directions.forward2Reversible_bydGt0Mid

• directions.forward2Reversible_bydGt0RHS

• directions.forward2Reversible_byConc_zero_fixed_DrG0

• directions.forward2Reversible_byConc_negative_fixed_DrG0

• directions.forward2Reversible_byConc_positive_fixed_DrG0

• directions.forward2Reversible_byConc_negative_uncertain_DrG0

• directions.forward2Reversible_byConc_positive_uncertain_DrG0

resultsBaseFileName: saveFigures:

forwardProbablyReverseFigures(model, miliMolarStandard)

Figure of qualitatively forward reactions that are probably quantiatively reverse. creates a vertical errorbar figure of the qualitatively forward reactions that end up being probably quantiatively reverse by at least one metabolite group contribution estimate

USAGE:

forwardProbablyReverseFigures(model,m iliMolarStandard)

INPUTS:

model: structure with field:

• .directions (subsets of forward qualtiative -> probably quantiative reverse):

  • .forwardReversible_bydGt0RHS

  • .forwardReversible_byConc_positive_fixed_DrG0

  • .forwardReversible_byConc_positive_uncertain_DrG0

miliMolarStandard:

forwardReversibleFigures(model, directions, confidenceLevel)

Figures of different classes of reactions: qualitatively forward -> quantitatively reversible

USAGE:

forwardReversibleFigures(model, directions, confidenceLevel)

INPUTS:

model: structure with fields:

• .S

• .DrGt0

directions: subsets of qualtiatively forward -> quantiatively reversible

• .forwardReversible

• .forwardReversible_bydGt0

• .forwardReversible_bydGt0LHS

• .forwardReversible_bydGt0Mid

• .forwardReversible_bydGt0RHS

• .forwardReversible_byConc_zero_fixed_DrG0

• .forwardReversible_byConc_negative_fixed_DrG0

• .forwardReversible_byConc_positive_fixed_DrG0

• .forwardReversible_byConc_negative_uncertain_DrG0

• .forwardReversible_byConc_positive_uncertain_DrG0

confidenceLevel: default = 0.95

forwardTransportQuantReverseFigures(model)

Figure of the qualitatively forward transport reactions that are quantitatively reversible. Creates a vertical errorbar figure of the qualitatively forward transport reactions that are quantitatively reversible, whether from group contribution or Keq, that then need to be assigned to be forward, to limit the growth rate i.e. abc transporters or reactions involving protons.

USAGE:

forwardTransportQuantReverseFigures(model)

INPUT:

model: structure with fields:

• .transportRxnBool

• .dGt0Min

• .dGt0Max

• .directions.forwardReversible

generateThermodynamicTables(model, resultsBaseFileName)

Generate tab delimited tables detailing the thermodynamic estimates generated for a model

USAGE:

generateThermodynamicTables(model, resultsBaseFileName)

INPUTS:

model: structure resultsBaseFileName: default = ‘out’

plotFeasibleReactionEnergyRanges(modelT)

Plots feasible dGr0’ and dGr’ for all reactions with quantitatively determined reaction energies

USAGE:

plotFeasibleReactionEnergyRanges(modelT)

INPUT:

modelT:

qualitativeVSquantitativeChangesTable

Example of a script that can be used to set up different thermodynamic models depending on the pH temp etc

singleMetaboliteThermoFigure(model, miliMolarStandard, metAbbr)

Creates a vertical errorbar figure of the reactions involving the metabolite given by the abbreviation

USAGE:

singleMetaboliteThermoFigure(model, miliMolarStandard, metAbbr)

INPUTS:

model: structure miliMolarStandard: metAbbr:

standardGibbsFormationEnergyStats(modelT, figures)

Generate the stats +/- pie chart on the provinence of the metabolite standard Gibbs energies.

USAGE:

[nKeq, nGC, nNone] = standardGibbsFormationEnergyStats(modelT, figures)

INPUTS:

modelT: figures:

OUTPUTS:

nKeq: nGC: nNone:

writeReactionListThermo(model, FileName, start, stop)

Exports a list of reactions and bounds to a text file

USAGE:

writeReactionListThermo(model, FileName, start, stop)

INPUT:

model: model structure FileName: Name of output file

OPTIONAL INPUTS:

start: integer index of first reaction index to write out stop: integer index of last reaction index to write out