4.2. stochsim submodule

class mod.stochsim.Simulator(*, labelSettings: mod.LabelSettings = mod.LabelSettings(mod.LabelType.String, mod.LabelRelation.Isomorphism), graphDatabase: List[mod.Graph], expandNetwork: Callable[[mod.DGBuilder, List[mod.Graph], List[mod.Graph]], None], initialState: Dict[mod.Graph, int], draw: Callable[[mod.DG], DrawFunction], drawTime: Callable[[float], float] = DrawTimeExponential(), withSetCompare: bool = True)

The main class for performing stochasim simulations.

Parameters

  • labelSettings (LabelSettings) – a settings object that will be passed to mod.DG.__init__().

  • GraphDatabase (list[mod.Graph]) – a list of graphs that will be passed to mod.DG.__init__().

  • expandNetwork (Callable[ [DGBuilder, list[mod.Graph], list[mod.Graph]], None]) –

    a callback which will be called when the simulator needs new hyperedge/reaction information. The callback will be given:

    1. the DG builder object for the underlying derivation graph.

    2. a list of graphs that were newly discovered in the last iteration.

    3. a list of all graphs in the current state.

    For example, if expansion is done via some mod.DGStrat, strat, a reasonable callback could be

    def expandNetwork(b, subset, universe):
        b.execute(addSubset(subset) >> addUniverse(universe) >> strat, verbosity=0)

    The ExpandByStrategy class is a shorthand for this type of callback.

  • initialState (dict[mod.Graph, int]) – the initial simulation state in terms of the number of copies of each graph/molecule. Graphs/molecules not mentioned are set to 0.

  • draw (Callable[[DG], DrawFunction]) – The simulator will initially create a mod.DG which is given to this function. It must then return a callable that is used in each simulation step to draw the next hyperedge/reaction. Defaults to a default constructed instance of DrawMassAction.

  • drawTime (Callable[[float], float]) – The function to use for drawing the time increment in each simulation step. The function will be given the reactivity, and must return the time increment. Defaults to an instance of DrawTimeExponential.

dg(self)

The internal derivation graph underlying the simulation.

Type

DG

simulate(self, *, time: Optional[float] = None, iterations: Optional[int] = None)

Start/continue the simulation.

Simulate an additional amount of time or number of iterations, whichever is reached first.

Parameters

  • time (Optional[float]) – the additional amount of time to simulate, or None for unbounded.

  • iterations (Optional[int]) – the additional number of iterations to simulate, or None for unbounded.

Returns

a references to the event trace for the simulation. It should not be modified.

Return type

EventTrace

class mod.stochsim.ExpandByStrategy(strat: mod.DGStrat)

A shorthand for an expansion callback that executes a strategy.

Parameters

strat (DGStrat) – a strategy.

class mod.stochsim.DrawFunction

An abstract base class for draw functions.

When constructing a simulator, a draw function creator must be given. When that is invoked, it must return an object that conforms to the interface of this class.

draw(self, marking: mod.DGPetriNetMarking)

Called in order to draw the next edge event.

Parameters

marking (DGPetriNetMarking) – the current state of the simulation. This may not be changed.

Returns

one of the given hyperedges and a number indicating the reactivity of the system.

Return type

tuple[Action, float]

syncSize(self)

Called whenever the underlying derivation graph has changed size. If the drawing function has internal data structures, this method is where such data structures can be resized. The derivation graph must be given to this object by its creator.

class mod.stochsim.DrawMassAction(*, inputRate: Union[Callable[[mod.DGVertex], float], float] = 0.0, reactionRate: Union[Callable[[mod.DGHyperEdge], float], float] = 1.0, outputRate: Union[Callable[[mod.DGVertex], float], float] = 0.0)

A creator for a drawing function implementing the law of mass action.

Parameters

  • inputRate (Callable[[DGVertex], float] or float) – the rate used for pseudo-reactions for creating molecules, defaulting to 0.0.

  • reactionRate (Callable[[DGHyperEdge], float] or float) – a callback for reaction rates, defaulting to a function returning 1.0 for every reaction.

  • outputRate (Callable[[DGVertex], float] or float) – the rate used for pseudo-reactions for destroying molecules, defaulting to 0.0.

__call__(self, dg: mod.DG)
Parameters

dg (DG) – the derivation graph underlying the simulation.

Returns

a drawing function implementing the law of mass action.

Return type

MassActionKinetics

class mod.stochsim.DrawTimeExponential

A shorthand for drawing time from an exponential distribution.

__call__(self, rateSum: float)