Rxn

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checkRXNFiles(model, RXNFileDir)

Checks whether the set of RXN files coresponding to a model have the consistent stoichiometry and are elementally balanced

USAGE:

[modelOut, nTotalAtomTransitions] = checkRXNFiles (model, RXNFileDir)

INPUTS:

• model – Directed stoichiometric hypergraph Represented by a matlab structure with following fields:

  • .S - The m x n stoichiometric matrix for the metabolic network

  • .model.mets - An m x 1 array of metabolite identifiers. Should match metabolite identifiers in RXNfiles.

  • .model.rxns - An n x 1 array of reaction identifiers. Should match RXNfile names in RXNFileDir.

  • .lb - An n x 1 vector of lower bounds on fluxes.

  • .ub - An n x 1 vector of upper bounds on fluxes.

• RXNFileDir – Path to directory containing RXNfiles with atom mappings for internal reactions in S. File names should correspond to reaction identifiers in input model.rxns. e.g. git clone https://github.com/opencobra/ctf ~/fork-ctf

  then RXNFileDir = ~/fork-ctf/rxns/atomMapped

OUTPUTS:

• modelOut – The input model returned with the RXN-file quality-check results added as fields:

  • .metRXNBool - m x 1 vector, true if metabolite identified in at least one RXN file

  • .RXNBool - n x 1 boolean vector, true if RXN file exists

  • .RXNParsedBool - n x 1 boolean vector, true if RXN file could be parsed

  • .RXNAtomsConservedBool - n x 1 boolean vector, true if atoms in RXN file are conserved

  • .RXNStoichiometryMatchBool - n x 1 boolean vector, true if RXN stoichiometry matches model.S stoichiometry

  • .RXNStoichiometryMatchUptoProtonsBool - n x 1 boolean vector, true if RXN stoichiometry matches model.S stoichiometry when ignoring protons

  • .RXNSubstrateTransitionNumbersOrdered - n x 1 boolean vector, true if RXN file with substrate transition numbers ordered 1:q

  • .RXNProductTransitionNumbersOrdered - n x 1 boolean vector, true if RXN file with product transition numbers ordered 1:q

  • .RXNTransitionNumbersMatching - n x 1 boolean vector, true if RXN file with matching numbering of atoms between substrates and products

  • .RXNMatchingElementBool - n x 1 boolean vector, true if RXN file with matching elements between substrates and products

• nTotalAtomTransitions – total number of atom transitions across all atom mapped RXN files

findRXNFiles(model, rxnfileDir)

Identify the model metabolites and reactions that have a corresponding atom mapped RXN file

USAGE:

[metRXNBool, rxnRXNBool, internalRxnBool] = findRXNFiles (model, rxnfileDir)

INPUTS:

• model – COBRA model structure with the fields:

  • .rxns - n x 1 array of reaction identifiers

  • .S - m x n stoichiometric matrix

  • .SConsistentRxnBool - n x 1 boolean vector, true for stoichiometrically consistent reactions (used if present)

  • .SIntRxnBool - n x 1 boolean vector, true for internal reactions (used when .SConsistentRxnBool is absent)

• rxnfileDir – path to directory containing atom mapped reactions. One .RXN file per reaction with each filename matching to model.rxns{i}

OUTPUTS:

• metRXNBool – m x 1 boolean vector true for metabolites in atom mapped reactions

• rxnRXNBool – n x 1 boolean vector true for atom mapped reactions

• internalRxnBool – n x 1 boolean vector true for reactions considered internal

readRXNFile(rxnfileName, rxnfileDirectory)

Read atom mappings from a MDL rxn file.

USAGE:

[mets, elements, metNrs, atomTransitionNrs, isSubstrate, instances] = readRXNFile (rxnfileName, rxnfileDirectory)

INPUT:

rxnfileName – The file name.

OPTIONAL INPUT:

rxnfileDirectory – Path to directory containing the rxnfile. Defaults to current directory.

OUTPUTS:

• mets – A p x 1 cell array of metabolite identifiers for atoms.

• elements – A p x 1 cell array of element symbols for atoms.

• metNrs – A p x 1 vector containing the numbering of atoms within each metabolite molfile.

• atomTransitionNrs – A p x 1 vector of atom transition indices.

• isSubstrate – A p x 1 logical array. True for substrates, false for products in the reaction.

• instances – A p x 1 vector indicating which instance of a repeated metabolite atom i belongs to.

writeRxnfile(s, mets, molfileNames, molfileDirectory, rxnfileName, rxnfileDirectory)

Writes a rxnfile (Accelrys, San Diego, CA) for a metabolic reaction.

USAGE:

writeRxnfile (s, mets, molfileNames, molfileDirectory, rxnfileName, rxnfileDirectory)

INPUTS:

• s – An m x 1 vector of stoichiometric coefficients.

• mets – An m x 1 cell array of metabolite identifiers.

OPTIONAL INPUTS:

• molfileNames – An m x 1 cell array of molfile names for metabolites in mets. Defaults to mets.

• molfileDirectory – Path to directory containing input molfiles. Defaults to current directory.

• rxnfileName – A name for the output rxnfile. Defaults to ‘rxn.rxn’.

• rxnfileDirectory – Path to directory where the output rxnfile should be saved. Defaults to current directory.

Produces the file ‘rxnfileDirectory/rxnfileName.rxn’