atomica.modelΒΆ

Implements the Atomica computational graph

Fundamentally, models in Atomica can be represented as a graph, with nodes corresponding to compartments, and edges corresponding to transitions/links. This module implements the graph representation of the Framework in a form that can be numerically integrated. It also implements the methods to actually perform the integration.

Functions

run_model

Build and process model

Classes

Characteristic

A characteristic represents a grouping of compartments.

Compartment

A class to wrap up data for one compartment within a cascade network.

JunctionCompartment

A TimedCompartment has a duration group by virtue of having a .parameter attribute and a flush link.

Link

A Link is a Variable that maps to a transition between compartments.

Model

A class to wrap up multiple populations within model and handle cross-population transitions.

Parameter

Integration object to represent Parameters

Population

A class to wrap up data for one population within model.

ResidualJunctionCompartment

Junction with a residual outflow

SinkCompartment

SourceCompartment

Derived class for source compartments

TimedCompartment

Instantiate the TimedCompartment

TimedLink

A TimedLink connects two TimedCompartments

Variable

Integration object to manage compartments, characteristics, parameters, and links

Exceptions

BadInitialization

Error for invalid conditions

ModelError

Exception type for general model errors