SBML Compile Options

class RoadRunner.LoadSBMLOptions

The LoadSBMLOptions object allows tuning a variety of SBML loading and compilations options.

This object can be passed in as the second, optional argument of the RoadRunner.__init__() constructor, or the RoadRunner.load() method.

LoadSBMLOptions.conservedMoieties bool

Performs conservation analysis.

This causes a re-ordering of the species, so results generated with this flag enabled can not be compared index wise to results generated otherwise.

Moiety conservation is only compatable with simple models which do NOT have any events or rules which define or alter any floating species, and which have simple constant stiochiometries.

LoadSBMLOptions.mutableInitialConditions bool

Generates accessor functions to allow changing of initial conditions.

LoadSBMLOptions.noDefaultSelections bool

If True, do not create a default selection list when the model is loaded.

LoadSBMLOptions.readOnly bool

Should the model be recompiled? The LLVM ModelGenerator maintains a hash table of currently running models. If this flag is NOT set, then the generator will look to see if there is already a running instance of the given model and use the generated code from that one.

If only a single instance of a model is run, there is no need to cache the models, and this can safely be enabled, realizing some performance gains.

LoadSBMLOptions.recompile bool

If this is set, then a read-only model is generated. A read-only model can be simulated, but no code is generated to set model values, i.e. parameters, amounts, values, etc…

It takes a finite amount of time to generate the model value setting functions, and if they are not needed, one may see some performance gains, especially in very large models.