bionetgen.simulator package
Submodules
bionetgen.simulator.simulators module
- class bionetgen.simulator.simulators.BNGSimulator(model_file=None, model_str=None)[source]
Bases:
object
The generic simulator interface to all BNG simulators.
This is (going to be) designed to allow for a generic API to all other types of simulators so that this API can be used in the rest of the library without specifically writing code for each simulator type.
- model_filestr
path to the model file this simulator is using
- simulator: obj
the python object that runs the actual simulation. Any subclass implementing a BNGSimulator should set this property and make it so that setting the simulator object to the file path given to initialize the BNGSimulator class initializes the simulator object in turn.
- simulate(args)
Uses the arguments provided to call the underlying simulator
- property model_file
model file attribute that stores the path to the original model file and also sets up the simulator
- property model_str
model file attribute that stores the path to the original model file and also sets up the simulator
- class bionetgen.simulator.simulators.libRRSimulator(model_file=None, model_str=None)[source]
Bases:
bionetgen.simulator.simulators.BNGSimulator
libRoadRunner simulator wrapper
- sbml: str
the SBML used by the underlying libRoadRunner simulator
- simulator: obj
the python object that runs the actual simulation. Any subclass implementing a BNGSimulator should set this property and make it so that setting the simulator object to the file path given to initialize the BNGSimulator class initializes the simulator object in turn.
- simulate(args)
Uses the arguments provided to call the underlying simulator
- property sbml
sbml attribute which is just the SBML string with which the libRR instance is instantiated with
- simulate(*args, **kwargs)[source]
generic simulate front-end that passes the args and kwargs to the underlying simulator object
- property simulator
simulator attribute that stores the instantiated simulator object and also saves the SBML text in the sbml attribute
- bionetgen.simulator.simulators.sim_getter(model_file=None, model_str=None, sim_type='libRR')[source]
Convenience function to get a simulator object of a specific type. Allows you to pull a simulator object given a model file path.
Note: This likely needs to be refactored but for now it works.
- model_filestr, optional
The path to the model file, at the moment only BNGL is expected but this can change in the future.
- model_strstr, optional
Instead of the path to the model you can also supply the model string instead.
- sim_typestr, optional
The name of the type of simulator object to get. At the moment only libRoadRunner type simulators are allowed. This will get updated as differenty types of simulators are added.
- BNGSimulator
A simulator object with an API that’s supposed to be agnostic to the underlying simulator it’s running.