The stoichiometric matrix of a reaction network

Given a model, described in tabular form (m is a list of data-frames). The stoichiometric matrix is the linear map between the model's flux vector and the ODE's right-gand-side vector field. If the flux vector is rr <- flux(t,x,p), which maps the state variables x and parameters p to the reaction rate rr of each reaction. The stoichiometric matrix nu (ν), will map the reaction rates to the rate of change of the state variables: dx/dt := nu %*% flux(t,x,p).

Usage

stoichiometric_matrix(m, compound.names = rownames(m$Compound))

Arguments

m

list of data frames with at least the 'Reaction' table, and the 'Compound' table

compound.names

all names of the reacting compounds

Value

the stoichimetric matrix, with some additional attributes.

Details

The matrix is usually sparse, but not extremely big. This function attaches a sparse version of the same information as attributes to the return-value, as two lists, for convenience.

Examples

the_reaction <- "A + B <=> C"
m <- list(
    Reaction=data.frame(reactants=c("A+B"),products=c("C"))
)
nu <- stoichiometric_matrix(m,c("A","B","C"))