Old

generateMoietyMoleculeNetwork(model, L, moietyFormulae, mbool)[source]

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

identifyConservedMoietiesLegacyInterface(model, dATM, options)[source]

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

identifyConservedMoietiesOld(model, ATN)[source]

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] = identifyConservedMoieties (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)