Rxn

checkRXNFiles(model, RXNFileDir)[source]

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

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

OUTPUT: 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 ingnoring 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.

findRXNFiles(model, rxnfileDir)[source]
USAGE

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

INPUTS

  • model.rxns

  • model.SConsistentRxnBool

  • model.S

  • 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

EXAMPLE:

NOTE:

Author(s): Ronan M.T. Fleming, 2022

readRXNFile(rxnfileName, rxnfileDirectory)[source]

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)[source]

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’