getadjacencymatrix

Get adjacency matrix from model object

The order of species in the output arguments (M and Headings) matches the order of species returned by modelObj.Species.

Syntax

M = getadjacencymatrix(modelObj)
[M, Headings] = getadjacencymatrix(modelObj)
[M, Headings, Mask] = getadjacencymatrix(modelObj)


Arguments

M	Adjacency matrix for modelObj.
modelObj	Specify the model object.
Headings	Return row and column headings. If species are in multiple compartments, species names are qualified with the compartment name in the form compartmentName.speciesName. For example, nucleus.DNA, cytoplasm.mRNA.
Mask	Return 1 for the species object and 0 for the reaction object to Mask.

Description

M = getadjacencymatrix(modelObj) returns an adjacency matrix (M) for the model object (modelObj).

An adjacency matrix is defined by listing all species contained by modelObj and all reactions contained by modelObj column-wise and row-wise in a matrix. The reactants of the reactions are represented in the matrix with a 1 at the location of [row of species, column of reaction]. The products of the reactions are represented in the matrix with a 1 at the location of [row of reaction, column of species]. All other locations in the matrix are 0.

[M, Headings] = getadjacencymatrix(modelObj) returns the adjacency matrix to M and the row and column headings to Headings. Headings is defined by listing all Name property values of species contained by modelObj and all Name property values of reactions contained by modelObj.

[M, Headings, Mask] = getadjacencymatrix(modelObj) returns an array of 1s and 0s to Mask, where a 1 represents a species object and a 0 represents a reaction object.

Examples

Get Adjacency Matrix of SimBiology Model

Load the lotka model.

m1 = sbmlimport("lotka.xml");

Get the adjacency matrix of the model.

[M,Headings] = getadjacencymatrix(m1)

M = 7×7 sparse double matrix (9 nonzeros)
   (5,1)        1
   (5,2)        1
   (6,3)        1
   (7,4)        1
   (1,5)        1
   (2,5)        1
   (2,6)        1
   (3,6)        1
   (3,7)        1

Headings = 7×1 cell
    {'x'        }
    {'y1'       }
    {'y2'       }
    {'z'        }
    {'Reaction1'}
    {'Reaction2'}
    {'Reaction3'}