Accessing the SBML Model Variables

The following methods allow users to obtain information on the model

Compartment Group

ExecutableModel.getCompartmentVolumes([index]) Returns a vector of compartment volumes.
ExecutableModel.getNumCompartments() Returns the number of compartments in the model.
ExecutableModel.getCompartmentIds([index]) Returns a vector of compartment identifier symbols.
ExecutableModel.setCompartmentVolumes(...) Sets a vector of compartment volumes.

Boundary Species Group

ExecutableModel.getBoundarySpeciesConcentrations([index]) Returns a vector of boundary species concentrations.
ExecutableModel.setBoundarySpeciesConcentrations(...) Use this to set the entire set of boundary species concentrations in one call.
ExecutableModel.getNumBoundarySpecies() Returns the number of boundary species in the model.
ExecutableModel.getBoundarySpeciesIds() Returns a vector of boundary species Ids.

Floating Species Group

ExecutableModel.getFloatingSpeciesConcentrations([index]) Returns a vector of floating species concentrations.
ExecutableModel.setFloatingSpeciesConcentrations(...) Use this to set the entire set of floating species concentrations in one call.
ExecutableModel.getNumFloatingSpecies() Returns the number of floating species in the model.
ExecutableModel.getFloatingSpeciesIds() Return a list of floating species sbml ids.

Initial Conditions Group

Reaction Group

ExecutableModel.getNumReactions() Returns the number of reactions in the model.
ExecutableModel.getReactionRates([index]) Returns a vector of reaction rates for the current state of the model.
ExecutableModel.getReactionIds() Returns a vector of reaction Ids.

Rates Of Change Group

ExecutableModel.getFloatingSpeciesAmountRates([index]) Return a vector of floating species amount rates.
ExecutableModel.getReactionRates([index]) Returns a vector of reaction rates for the current state of the model.
ExecutableModel.getNumReactions() Returns the number of reactions in the model.
ExecutableModel.getReactionIds() Returns a vector of reaction Ids.

Parameters Group

ExecutableModel.setGlobalParameterValues(...) Use this to set the entire set of global parameters in one call.
ExecutableModel.getGlobalParameterValues([index]) Return a vector of global parameter values.
ExecutableModel.getNumGlobalParameters() Returns the number of global parameters in the model.
ExecutableModel.getNumGlobalParameters() Returns the number of global parameters in the model.