Auxillaryfiles

assignRxnWeights(MatricesSUX, weights, WeightsPerRxn, NoWeight)[source]

Assigns reaction weights

USAGE

MatricesSUX = assignRxnWeights (MatricesSUX, weights, WeightsPerRxn, NoWeight)

INPUTS

  • MatricesSUX – Input model structure

  • weights – Weight structure that permits to add weights to non-core reactions (it is recommended to use values other than 0 and 1, with lower weight corresponding to higher priority. Format:

    • weights.MetabolicRxns = 10; % Universal database metabolic reactions

    • weights.ExchangeRxns = 10; % Exchange reactions

    • weights.TransportRxns = 10; % Transport reactions

    Default: weigth of 10 for all non-core reactions.

  • WeightsPerRxn – Structure containing a list of reactions that should be assined with individual weights (WeightsPerRxn.rxns) AND a list of Reaction weights (WeightsPerRxn.weights) in the same order.

  • NoWeight – Weight that should be assigned to those reactions NOT in core reaction set and NOT in WeightsPerRxn (default:1000)

OUTPUT

MatricesSUX – Output model structure

createUniversalReactionModel2(KEGGFilename, KEGGBlackList)[source]

Creates the U matrix using the universal data from the KEGG

USAGE

KEGG = createUniversalReactionModel2 (KEGGFilename, KEGGBlackList)

INPUTS

  • KEGGFilename – File name containing universal database (e.g., KEGG; optional input, default: reaction.lst)

  • KEGGblackList – List of excluded reactions from the universal database (e.g., KEGG) (optional input, default: no blacklist)

OUTPUT

KEGG – Contains universal database (U matrix) in matrix format

Note

This file is KEGG-specific: if non-KEGG-type metabolite IDs are used it will not parse the reactions correctly and will throw an error.

createXMatrix2(compoundsIn, transport, compartment, model)[source]

Creates a matrix full of exchange reactions based on the input list (creates an exchange reaction for each of the metabolites present in the model)

USAGE

ExchangeRxnMatrix = createXMatrix2 (compoundsIn, transport, compartment, model)

INPUTS

  • compoundsIn – List of metabolites

  • transport – if 1, transport reactions will be defined as well for every compounds (default: 0, which corresponds to only exchange reactions)

  • compartment – [c] –> transport from cytoplasm [c] to extracellular space [e] (default), [p] creates transport from [c] to [p] and from [p] to [c]

  • model – model structure - used to check if exchange reaction exists already before adding it to ExchangeRxnMatrix

OUTPUT

ExchangeRxnMatrix – Model structure containing all exchange and transport reactions

findIntracellularRxns(model)[source]

This function finds all reactions that do not contain metabolites in [e] comparment.

USAGE

[intracellRxnList] = findIntracellularRxns (model)

INPUT

model – Model structure

OUTPUT

intracellRxnList – List of intracellular reactions in model

generateSUXComp(model, dictionary, KEGGFilename, KEGGBlackList, listCompartments, KEGGMatrixLoad)[source]

Creates the matrices for gap filling for compartmentalized metabolic models (S) such that the universal database (U, e.g., KEGG) is placed in each compartment specified and reversible transport reactions (X) are added for each compound present in U and S, between the compartment and the cytosol. Additionally, exchange reactions are added for each metabolite in the extracellular space.

USAGE

MatricesSUX =generateSUXComp (model, dictionary, KEGGFilename, KEGGBlackList, listCompartments)

INPUTS

  • model – Model structure

  • dictionary – List of universal database IDs and their counterpart in the model (e.g., KEGG_dictionary.xls)

  • KEGGFilename – File name containing the universal database (e.g., KEGG - reaction.lst)

  • KEGGBlackList – List of excluded reactions from the universal database (e.g., KEGG)

  • listCompartments – List of intracellular compartments in the model (optional input, default compartments to be considered: ‘[c]’ ,’[m]’, ‘[l]’, ‘[g]’, ‘[r]’, ‘[x]’, ‘[n]’)

  • KEGGMatrixLoad load precomputed KEGG matrix (default – 0)

OUTPUT

MatricesSUX – SUX matrix

Based on generateSUX.m but updated and expanded for compartmentalized gap filling efforts.

  • Ines Thiele, Jan 2021, added the option to preload KEGG matrix and

KeggExchangeRxnMatrix, if multiple reconstructions will be tested this is faster