directionalityReport¶

analyseThermoConstrainedModel(model, cumNormProbCutoff, printLevel, resultsBaseFileName)[source]¶

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)[source]¶

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

Usage

model = assignQualDir(model)

Input

model – structure with fields:

model.lb

model.ub

Output

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)[source]¶

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)[source]¶

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 inputs

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)[source]¶

Creates pie charts of directionality stats

Usage

directionalityStatsFigures(directions, resultsBaseFileName, saveFigures)

Inputs

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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

Usage

generateThermodynamicTables(model, resultsBaseFileName)

Inputs

model – structure

resultsBaseFileName – default = ‘out’

plotFeasibleReactionEnergyRanges(modelT)[source]¶

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

Usage

plotFeasibleReactionEnergyRanges(modelT)

Input

modelT

singleMetaboliteThermoFigure(model, miliMolarStandard, metAbbr)[source]¶

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)[source]¶

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)[source]¶

Exports a list of reactions and bounds to a text file

Usage

writeReactionListThermo(model, FileName, start, stop)

Inputs

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