| Element
|
Description
|
| rxns
|
Vector containing the abbreviated reaction names, in the same order as they appear on The Matrix.
|
| mets
|
Vector containing the abbreviated metabolite names, in the same order as they appear on The Matrix.
|
| S
|
The grand stochiometry matrix (aka The Matrix), with dimensions nrow=metabolites & ncol=reactions. It is in a "sparse" form.
|
| rev
|
A logical vector of length rxns that hold whether the reaction is reversible.
|
| lb
|
Matrix containing the lower bounds for the fluxes. They are ordered as the reactions.
|
| ub
|
Matrix containing the upper bounds for the fluxes. They are ordered as the reactions.
|
| c
|
Vector specifying the reaction to maximize (as 1) among the others (as 0s).
|
| rules
|
Vector containing the conditional rules for successful expression of a given reaction. They are ordered by reaction.
|
| genes
|
Vector containing all the genes associated with The Matrix. They carry their own order.
|
| rxnGeneMat
|
Matrix in"sparse" format containing the association of genes and metabolites. It's dimensions are nrow=metabolites & ncol=genes.
|
| grRules
|
Vector containing the conditional rules for successful expression fo a given reaction. They are ordered by reaction. Redundant with the vector "rules", however this one implicitly cites the genes involved.
|
| subSystems
|
Vector containing annotation information for the different reactions of the Model. They are ordered by reaction.
|
| rxnNames
|
The full names of all the reactions. They are ordered by reaction.
|
| metNames
|
The full names of all the metabolites. They are ordered by metabolite.
|
| metFormulas
|
The chemical formulae for the different metabolites. Might be of use with balancing?
|
| b
|
N/A
|
| description
|
A description of the Model.
|
H2 Project
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