conservedMoieties

classifyMoieties(L, S)

Classifies conserved moieties for a metabolic network

Usage

types = classifyMoieties(L, S)

Inputs

• L – The m x r moiety matrix with moiety vectors as columns.
• S – The m x n total stoichiometric matrix.

Output

• types – an r x 1 cell array of moiety classifications

constructElementalMatrix(metFormulas, metCharges)

Constructs the elemental matrix for a set of metabolites

Usage

[E, elements] = constructElementalMatrix(metFormulas, metCharges)

Input

• metFormulas – m x 1 cell array of metabolite formulas, e.g., CHO2

Optional input

• metCharges – m x 1 vector of metabolite charges. Used to compute the electron vector.

Outputs

• E – The m x p elemental matrix where p is the number of unique elements in metFormulas (plus the electron if metCharges is included as input)
• elements – 1 x p cell array of element symbols (e for electron)

decomposeMoietyVectors(L, N)

Decomposes moiety vectors for a metabolic network.

Usage

D = decomposeMoieties(L, N);

Inputs

• L – The m x r moiety matrix with moiety vectors as columns.
• N – The m x u internal stoichiometric matrix such that \(N^T L = 0\).

Output

• D – An m x t moiety matrix with decomposed moiety vectors as columns \((t \geq r)\).

estimateMoietyFormulas(L, E, elements)

Estimates the chemical formulas of conserved moieties in a metabolic network

Usage

moietyFormulas = estimateMoietyFormulas(L, E, elements)

Inputs

• L – The m x r moiety matrix for a metabolic network. Each column is a moiety vector.
• E – The m x p elemental matrix for metabolites in the metabolic network.
• elements – A 1 x p cell array of element symbols.

Outputs

• M – An r x p estimated elemental matrix for moieties.
• moietyFormulas – An r x 1 cell array of estimated moiety formulas.

findElementaryMoietyVectors(model, varargin)

Enumerate all possible elementary conserved moiety vectors based on the left null space of the stoichiometric matrix S.

Usage

EMV = findElementaryMoietyVectors(model, method)

Input

• model – COBRA model

OPTIONAL INPUTS (in name-value pair):

‘method’: method for finding all conserved moiety vectors

• ‘efmtool’: use EFMtool, ‘CalculateFluxModes.m’ must be in matlab path (default)
• ‘null’: use matlab rational null basis.

‘deadCMs’: include dead end metabolites or not (default true)

(will have more conserved moieties found for dead end metabolites if true)

‘printLevel’: print messages or not (default 0).

Other COBRA LP solver parameters, see solveCobraLP.m

Output

• EMV – all minimal conserved moiety vectors

identifyConservedMoieties(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] = 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)