Transport

findTransRxns(model, inclExc, rxnInds, inclObjAsExc, irrevFlag)[source]

Identifes all transport reactions in a model, which are defined as reactions involved with metabolites in more than 1 compartment

USAGE:

[transRxns, nonTransRxns, transRxnsBool] = findTransRxns (model, inclExc, rxnInds, inclObjAsExc, irrevFlag)

INPUT:

model – COBRA model structure with fields:

  • .S - m x n stoichiometric matrix

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

  • .rxns - n x 1 cell array of reaction identifiers

OPTIONAL INPUT:

  • inclExc – includes exchange reactions as transport = true (Default = false)

  • rxnInds – indices of reactions to test for transport activity. (default = test all columns of model.S)

  • inclObjAsExc – includes objective as an exchange reaction = true - this is passed to findExcRxns. (default = false)

  • irrevFlag – model is irreversible = true - this is passed to findExcRxns. (default=false)

OUTPUTS:

  • transRxns – transport reactions in rxnInds

  • nonTransRxns – non-transport reactions in rxnInds

  • transRxnsBool – checks if inclExc or isNonexchangeTransport rxns vector is equal to 1