ReactionNetwork -- a mutable hash table, stores information about a reaction network

Functions and methods returning an object of class ReactionNetwork:

• nSiteAutocatalytic -- A motif for autocatalytic networks
• nSiteDiffusion -- an example for a diffusion network
• nSiteDistributiveModification -- A motif for purely distributive phosphorylation
• nSiteImmuneReaction -- A motif for an immune response network
• nSitePoreForming -- an example for a pore forming network
• nSiteSequestration -- A motif for sequestration networks
• reactionNetwork -- creates a reaction network

Methods that use an object of class ReactionNetwork:

• conservationEquations(ReactionNetwork) -- see conservationEquations -- creates the conservation equations of a reaction network
• conservationEquations(ReactionNetwork,Ring) -- see conservationEquations -- creates the conservation equations of a reaction network
• conservationEquations(ReactionNetwork,InexactFieldFamily) (missing documentation)
• createConcentrationRates(ReactionNetwork) (missing documentation)
• createInitialValues(ReactionNetwork) (missing documentation)
• createReactionRates(ReactionNetwork) (missing documentation)
• createRing(ReactionNetwork) -- see createRing -- creates a ring with generators species concentrations, reaction rates, initial values
• createRing(ReactionNetwork,Ring) -- see createRing -- creates a ring with generators species concentrations, reaction rates, initial values
• createRing(ReactionNetwork,InexactFieldFamily) (missing documentation)
• glue(List,ReactionNetwork) -- see glue -- combine two networks
• glue(ReactionNetwork,List) -- see glue -- combine two networks
• glue(ReactionNetwork,ReactionNetwork) -- see glue -- combine two networks
• negativeLaplacian(ReactionNetwork) -- see negativeLaplacian -- Computes the negative of the Laplacian matrix of a Reaction Network.
• negativeUndirectedLaplacian(ReactionNetwork) -- see negativeUndirectedLaplacian -- Computes the negative of the Laplacian matrix of an undirected graph associated with a Reaction Network.
• negativeWeightedLaplacian(ReactionNetwork) -- see negativeWeightedLaplacian -- Computes the negative of the weighted Laplacian matrix of a Reaction Network.
• net(ReactionNetwork) (missing documentation)
• reactantMatrix(ReactionNetwork) -- see reactantMatrix -- Computes the reactants matrix of a Reaction Network.
• reactionMatrix(ReactionNetwork) (missing documentation)
• steadyStateEquations(ReactionNetwork) -- see steadyStateEquations -- creates steady-state equations of a reaction network
• steadyStateEquations(ReactionNetwork,Ring) -- see steadyStateEquations -- creates steady-state equations of a reaction network
• steadyStateEquations(ReactionNetwork,InexactFieldFamily) (missing documentation)
• stoichiometricConeKer(ReactionNetwork) -- see stoichiometricConeKer -- Computes a matrix whose columns are the rays of the cone non-negative kernel of the stoichiometric matrix of a Reaction Network.
• stoichiometricMatrix(ReactionNetwork) -- see stoichiometricMatrix -- Computes the stoichiometric matrix of a Reaction Network.
• stoichiometricSubspace(ReactionNetwork) -- see stoichiometricSubspace -- Computes the stoichiometric space of a Reaction Network.
• stoichSubspaceKer(ReactionNetwork) -- see stoichSubspaceKer -- Computes the kernel of the stoichiometric matrix of a Reaction Network.
• subRandomInitVals(ReactionNetwork) (missing documentation)
• subRandomInitVals(ReactionNetwork,Ring) (missing documentation)
• subRandomReactionRates(ReactionNetwork) (missing documentation)
• subRandomReactionRates(ReactionNetwork,Ring) (missing documentation)
• substitute(ReactionNetwork,List) -- substitute species names in reaction network

For the programmer

The object ReactionNetwork is a type, with ancestor classes MutableHashTable < HashTable < Thing.

The source of this document is in ReactionNetworks/DocReactionNetworks.m2:109:0.