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generateMoietyMoleculeNetwork(model, L, moietyFormulae, mbool)

Generate a structure to represent a network that associates moieties to molecules

USAGE:

MMN = generateMoietyMoleculeNetwork (model, L, moietyFormulae, mbool)

INPUTS:

• model – COBRA model structure with fields:

  • .S - m x n stoichiometric matrix

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

  • .metFormulas - m x 1 cell array of metabolite chemical formulae

• L – nMoieties x nMappedMet matrix mapping moieties to the mapped metabolites

• moietyFormulae – nMoieties x 1 cell array of moiety chemical formulae

OPTIONAL INPUT:

mbool – m x 1 boolean vector indicating the metabolites mapped by the columns of L (defaults to all metabolites when the sizes of L and model.S are consistent)

OUTPUT:

MMN – moiety-molecule network structure with fields:

• .L - the (possibly transposed) moiety-to-metabolite matrix

• .moi - table of moiety properties (Name, Formula, Mass, NumMolecules)

• .mol - table of molecule properties (Name, Mets, Formula, Mass, NumMoieties)

identifyConservedMoietiesLegacyInterface(model, dATM, options)

[L, M, moietyFormulas, moieties2mets, moieties2vectors, atoms2moieties]

identifyConservedMoietiesOld(model, ATN)

Identifies conserved moieties in a metabolic network (model) by graph theoretical analysis of the corresponding atom transition network (ATN).

USAGE:

[L, M, moietyFormulas, moieties2mets, moieties2vectors, atoms2moieties, mtrans2rxns, atrans2mtrans] = identifyConservedMoietiesOld (model, ATN)

INPUTS:

• model – Structure with following fields:

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

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

  • .rxns - An n x 1 array of reaction identifiers. Should match rxnfile names in rxnFileDir.

• ATN – Structure with following fields:

  • .A - A p x q sparse incidence matrix for the atom transition network, where p is the number of atoms and q is the number of atom transitions.

  • .mets - A p x 1 cell array of metabolite identifiers to link atoms to their metabolites. The order of atoms is the same in A as in the molfile for each metabolite.

  • .rxns - A q x 1 cell array of reaction identifiers to link atom transitions to their reactions. The order of atom transitions is the same in A as in the rxnfile (with atom mappings) for each reaction.

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

OUTPUTS:

• L – An m x r matrix of r moiety vectors in the left null space of S.

• M – The u x v incidence matrix of the moiety supergraph where each connected component is a moiety graph.

• moietyFormulas – r x 1 cell array with chemical formulas of moieties

• moieties2mets – u x 1 vector mapping moieties (rows of M) to metabolites (rows of S)

• moieties2vectors – u x 1 vector mapping moieties (rows of M) to moiety vectors (columns of L)

• atoms2moieties – p x 1 vector mapping atoms (rows of A) to moieties (rows of M)

• mtrans2rxns – ‘v x 1’ vector mapping moiety transitions (columns of M) to reactions (columns of S)

• atrans2mtrans – ‘q x 1’ vector mapping atom transitions (columns of A) to moiety transitions (columns of M)