FR¶
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bilinearDecomposition
(S)[source]¶ Converts a stoichiometric matrix into a bilinear form.
Usage
[A, B, C] = bilinearDecomposition(S)Input
- S – m x n stoichiometric matrix
Outputs
- A – m x (m + k) matrix selecting rows such that \(S = A B C\)
- B – (m + k) x (n + k) bilinear stoichiometric matrix
- C – (n + k) x n matrix adding columns to form net reaction stoichiometry such that \(S = A B C\)
An example “bilinearisation” of the reaction
\[\begin{split}~&~ A + B + C \leftrightarrow D + E\\\end{split}\]is
\[\begin{split}~&~ A + B \leftrightarrow P \\ ~&~ P + C \leftrightarrow Q \\ ~&~ Q \leftrightarrow D + E\end{split}\]where P and Q are faux molecular species.
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checkRankFR
(model, printLevel)[source]¶ Calculates the rank of [F R] and [F; R], when restricted to certain rows and columns
Usage
[rankFR, rankFRV, rankFRvanilla, rankFRVvanilla, model] = checkRankFR(model, printLevel)Inputs
- model – model structure
- printLevel – verbose level
Outputs
- rankFR – rank of [F R], when using only FRrows
- rankFRV – rank of [F; R], when using only FRVcols
- rankFRvanilla – rank of [F R], when using all rows
- rankFRVvanilla – rank of [F; R], when using all cols
- model –
structure with fields:
- .FRrows - m x 1 boolean of rows of [F R] that are nonzero, unique upto positive scaling and part of the maximal conservation vector
- .FRVcols - n x 1 boolean of cols of [F; R] that are nonzero, unique upto positive scaling and part of the maximal conservation vector
- .FRirows - m x 1 boolean of rows of [F R] that are independent
- .FRdrows - m x 1 boolean of rows of [F R] that are dependent
- .FRwrows - m x 1 boolean of independent rows of [F R] that have dependent rows amongst model.FRdrows
- .FRVdcols - n x 1 boolean of cols of [F; R] that are dependent
- model.SConsistentMetBool - m x 1 boolean vector indicating metabolites involved in the maximal consistent vector
- .SConsistentRxnBool - n x 1 boolean vector indicating metabolites involved in the maximal consistent vector
- .FRnonZeroBool - m x 1 boolean vector indicating metabolites involved in at least one internal reaction
- .FRuniqueBool - m x 1 boolean vector indicating metabolites with reaction stoichiometry unique upto scalar multiplication
- .SIntRxnBool - n x 1 boolean vector indicating the non exchange reactions
- .FRVnonZeroBool - n x 1 boolean vector indicating non exchange reactions with at least one metabolite involved
- .FRVuniqueBool - n x 1 boolean vector indicating non exchange reactions with stoichiometry unique upto scalar multiplication
- .connectedRowsFRBool - m x 1 boolean vector indicating metabolites in connected rows of [F R]
- .connectedRowsFRVBool - n x 1 boolean vector indicating complexes in connected columns of [F; R]
- .V - \(S V = 0\); \(1^T |V| > 1\) for all flux consistent reactions
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connectedFR
(F, R)[source]¶ Computes the connected sets of rows of [F, R] and the largest connected set of columns of [F; R] using gamic
Usage
[connectedRowsFRBool, connectedColsFRVBool] = connectedFR(F, R)Inputs
- F – m x n
- R – m x n
Outputs
- connectedRowsFRBool – m x z boolean vector indicating z sets of connected rows
- connectedColsFRVBool – n x z boolean vector indicating z sets of connected cols
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largestConnectedFR
(F, R, printLevel)[source]¶ Computes the largest connected set of rows of [F, R] and the largest connected set of columns of [F; R] using gamic
Usage
[connectedRowsFRBool, connectedColsFRVBool] = largestConnectedFR(F, R, printLevel)Inputs
- F – m x n
- R – m x n
- printLevel – verbose level
Outputs
- connectedRowsFRBool – m x 1 boolean vector indicating largests set of connected rows
- connectedColsFRVBool – n x 1 boolean vector indicating largests set of connected cols
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makeFRresultsTable
(FRresults, resultsDirectory, resultsFileName, modelMetaData, tableFilename)[source]¶ Makes a table of FR results
Usage
[FRresultsTable, FRresults] = makeFRresultsTable(FRresults, resultsDirectory, resultsFileName, modelMetaData, tableFilename)Input
- FRresults – output of checkRankFRdriver
Optional inputs
- resultsDirectory – directory where output of checkRankFRdriver has been saved
- resultsFileName – filename where output of checkRankFRdriver has been saved
- modelMetaData – Cell array, where each row is metadata for one model with five columns: species, version, fileName, PMID, doi. See function modelMetaData = modelCitations()
- tableFilename – If provided, a the table of results is written out to a csv file, with specified filename
Outputs
- FRresultsTable – table displaying the results of checkRankFRdriver
- FRresults – output of checkRankFRdriver
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plotFRresults
(FRresults, nRows, nCols, resultsDirectory, resultsFileName, schematicFlag, modelMetaData)[source]¶ Plots FR results in the same order as the FRresultsTable using FRresults structure or by loading the FRresults structure
Usage
plotFRresults(FRresults, nRows, nCols, resultsDirectory, resultsFileName, schematicFlag, modelMetaData)Inputs
- FRresults – output of checkRankFRdriver
- nRows – number of rows in the subplot
- nCols – number of rows in the subplot (\(nRows*nCols \geq length(FRresults)\))
Optional inputs
- resultsDirectory – directory where output of checkRankFRdriver has been saved
- resultsFileName – filename where output of checkRankFRdriver has been saved
- schematicFlag – default = 1
- modelMetaData – metadata of model
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printFRdependencies
(model, filePathName)[source]¶ Reports on the dependencies between rows of [F, R], either to the command line (default) or to a specified text file
Usage
printFRdependencies(model, filePathName)Input
- model – model output from checkRankFR
Optional input
- filePathName – full file name for printing dependencies to file