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


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


  • model – COBRA model structure

Optional inputs

  • 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)


  • transRxns – transport reactions in rxnInds
  • nonTransRxns – non-transport reactions in rxnInds
  • transRxnsBool – checks if inclExc or isNonexchangeTransport rxns vector is equal to 1