Kegg

createUniversalReactionModel(KEGGFilename, KEGGBlackList)[source]

Creates the U matrix using the universal data from the KEGG database

USAGE:

KEGG = createUniversalReactionModel (KEGGFilename, KEGGBlackList)

INPUTS:

  • KEGGFilename – downloaded from KEGG database (ie. ‘reaction.lst’)

  • KEGGBlackList – KEGG reactions not to use

OUTPUT:

KEGG – U Matrix

mapKEGGID2Model(model, Dictionary)[source]

This function matches the compound abreviation in model and from CompAbr and connects with the model metabolite the corresponding KEGGID

USAGE:

model = mapKEGGID2Model (model, Dictionary)

INPUTS:

  • model – COBRA model structure

  • Dictionary – consists of:

    • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)

    • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

model – KEGG model structure

mapMetName2KEGGID(model, Dictionary)[source]

This function maps names of metabolites to KEGG IDs.

USAGE:

model = mapMetName2KEGGID (model, Dictionary)

INPUTS:

  • model – KEGG model structure

  • Dictionary – consists of:

    • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)

    • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

model – COBRA model structure

transformKEGG2Model(modelKEGG, dictionary)[source]

Translates the metabolites from KEGG to cobra model names.

USAGE:

model = mapMetName2KEGGID (model, Dictionary)

INPUTS:

  • model – KEGG model structure

  • Dictionary – consists of:

    • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)

    • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

model – COBRA model structure

transformModel2KEGG(model, Dictionary)[source]

Replaces model.mets with model.metKEGGID. If no KEGGID defined, the empty cell will be replaced with metabolite abreviation.

USAGE:

modelKEGG = transformModel2KEGG (model, Dictionary)

INPUTS:

  • model – COBRA model structure

  • Dictionary – consists of:

    • CompAbr = Dictionary(:, 1): List of compounds abreviation (non-compartelized)

    • KEGGID = Dictionary(:, 2): List of KEGGIDs for compounds in CompAbr

OUTPUT:

modelKEGG – KEGG model structure