getstoichmatrix (model)

Syntax

Arguments

Description

getstoichmatrix returns a stoichiometry matrix for a model object.

M = getstoichmatrix(modelObj) returns a stoichiometry matrix for a SimBiology^® model object (modelObj) to M.

A stoichiometry matrix is defined by listing all reactions contained by modelObj column-wise and all species contained by modelObj row-wise in a matrix. The species of the reaction are represented in the matrix with the stoichiometric value at the location of [row of species, column of reaction]. Reactants have negative values. Products have positive values. All other locations in the matrix are 0.

For example, if modelObj is a model object with two reactions with names R1 and R2 and Reaction values of 2 A + B -> 3 C and B + 3 D -> 4 A, the stoichiometry matrix would be defined as:

      R1   R2
A     -2    4
B     -1   -1
C      3    0
D      0   -3

[M,objSpecies] = getstoichmatrix(modelObj) returns the stoichiometry matrix to M and the species to objSpecies. objSpecies is defined by listing all Name property values of species contained by Obj. In the above example, objSpecies would be {'A', 'B', 'C', 'D'};.

[M,objSpecies,objReactions] = getstoichmatrix(modelObj) returns the stoichiometry matrix to M and the reactions to objReactions. objReactions is defined by listing all Name property values of reactions contained by modelObj. In the above example, objReactions would be {'R1', 'R2'}.

Examples

m1 = sbmlimport('lotka.xml');

[M,objSpecies,objReactions] = getstoichmatrix(m1)

M = 4x3 sparse double matrix (5 nonzeros)
   (2,1)        1
   (2,2)       -1
   (3,2)        1
   (3,3)       -1
   (4,3)        1

objSpecies = 4x1 cell
    {'x' }
    {'y1'}
    {'y2'}
    {'z' }

objReactions = 3x1 cell
    {'Reaction1'}
    {'Reaction2'}
    {'Reaction3'}

See Also

model object, getadjacencymatrix, Determining the Stoichiometry Matrix for a Model

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