kappybara.mixture#

Functions

`grouped`(components)	Group components by isomorphism.
`neighborhood`(agents, radius)	Get all agents within a distance radius of the given agents.

Classes

`ComponentMixture`([patterns])	A mixture that explicitly tracks connected components.
`Edge`(site1, site2)	Represents bonds between sites.
`Mixture`([patterns])	A collection of agents and their connections.
`MixtureUpdate`([agents_to_add, ...])	Specifies changes to be applied to a mixture.

class kappybara.mixture.ComponentMixture(patterns=None)[source]#

A mixture that explicitly tracks connected components.

Parameters:: patterns (Iterable[Pattern] | None)

components#

Indexed set of all components in the mixture.

Type:: kappybara.utils.IndexedSet[kappybara.pattern.Component]

apply_update(update)[source]#

Apply a collection of changes to the mixture.

Parameters:: update (MixtureUpdate) – MixtureUpdate specifying changes to apply.
Return type:: None

components: IndexedSet[Component]#

embeddings_in_component(match_pattern, mixture_component)[source]#

Get embeddings of a pattern within a specific component.

Parameters:

match_pattern (Component) – Pattern to find embeddings for.
mixture_component (Component) – Component to search within.

Returns:

List of embeddings within the specified component.

Return type:

list[dict[Agent, Agent]]

track_component(component)[source]#

Start tracking embeddings of a component pattern.

Parameters:: component (Component) – Component pattern to track.

class kappybara.mixture.Edge(site1, site2)[source]#

Represents bonds between sites.

Note

Edge(x, y) is the same as Edge(y, x).

Parameters:

site1 (Site)
site2 (Site)

site1#

First site in the bond.

Type:: kappybara.pattern.Site

site2#

Second site in the bond.

Type:: kappybara.pattern.Site

site1: Site#

site2: Site#

class kappybara.mixture.Mixture(patterns=None)[source]#

A collection of agents and their connections.

Parameters:: patterns (Iterable[Pattern] | None)

agents#

Indexed set of all agents in the mixture.

Type:: kappybara.utils.IndexedSet[kappybara.pattern.Agent]

_embeddings#

Cache of embeddings for tracked components.

Type:: dict[kappybara.pattern.Component, kappybara.utils.IndexedSet[kappybara.pattern.Embedding]]

_max_embedding_width#

Maximum diameter of tracked components.

Type:: int

add(component)[source]#

Add a component to the mixture.

Parameters:: component (Component) – Component to add with its agents and connections.
Return type:: None

agents: IndexedSet[Agent]#

apply_update(update)[source]#

Apply a collection of changes to the mixture.

Parameters:: update (MixtureUpdate) – MixtureUpdate specifying changes to apply.
Return type:: None

embeddings(component)[source]#

Get embeddings of a tracked component.

Notes

Returns the number of matches directly returned by subgraph isomorphism, i.e. not accounting for symmetries.

Parameters:: component (Component) – Component to get embeddings for.
Returns:: Set of embeddings for the component.
Raises:: KeyError – If component is not being tracked.
Return type:: IndexedSet[Embedding]

classmethod from_kappa(patterns)[source]#

Create a mixture from Kappa pattern strings and counts.

Parameters:: patterns (dict[str, int]) – Dictionary mapping pattern strings to copy counts.
Returns:: New Mixture with instantiated patterns.
Return type:: Self

instantiate(pattern, n_copies=1)[source]#

Add instances of a pattern to the mixture.

Parameters:

pattern (Pattern | str) – Pattern to instantiate, or Kappa string.
n_copies (int) – Number of copies to create.

Raises:

AssertionError – If pattern is underspecified.

Return type:

None

property kappa_str: str#

The mixture representation in Kappa format.

Returns:: Kappa string with %init declarations for each component type.

remove(component)[source]#

Remove a component from the mixture.

Parameters:: component (Component) – Component to remove.
Return type:: None

track_component(component)[source]#

Start tracking embeddings of a component.

Parameters:: component (Component) – Component pattern to track.

class kappybara.mixture.MixtureUpdate(agents_to_add=<factory>, agents_to_remove=<factory>, edges_to_add=<factory>, edges_to_remove=<factory>, agents_changed=<factory>)[source]#

Specifies changes to be applied to a mixture.

Parameters:

agents_to_add (list[Agent])
agents_to_remove (list[Agent])
edges_to_add (set[Edge])
edges_to_remove (set[Edge])
agents_changed (set[Agent])

agents_to_add#

Agents to be added to the mixture.

Type:: list[kappybara.pattern.Agent]

agents_to_remove#

Agents to be removed from the mixture.

Type:: list[kappybara.pattern.Agent]

edges_to_add#

Edges to be created.

Type:: set[kappybara.mixture.Edge]

edges_to_remove#

Edges to be removed.

Type:: set[kappybara.mixture.Edge]

agents_changed#

Agents with internal state changes.

Type:: set[kappybara.pattern.Agent]

agents_changed: set[Agent]#

agents_to_add: list[Agent]#

agents_to_remove: list[Agent]#

connect_sites(site1, site2)[source]#

Specify to create an edge between two sites.

If the sites are bound to other sites, indicates to remove those edges.

Parameters:

site1 (Site) – First site to connect.
site2 (Site) – Second site to connect.

Return type:

None

create_agent(agent)[source]#

Create a new agent based on a template.

Note

Sites in the created agent will be emptied.

Parameters:: agent (Agent) – Template agent to base the new agent on.
Returns:: New agent with empty sites.
Return type:: Agent

disconnect_site(site)[source]#

Specify that a site should be unbound.

Parameters:: site (Site) – Site to disconnect from its partner.
Return type:: None

edges_to_add: set[Edge]#

edges_to_remove: set[Edge]#

register_changed_agent(agent)[source]#

Parameters:: agent (Agent) – Agent that has been internally modified.
Return type:: None

remove_agent(agent)[source]#

Specify to remove an agent and its edges from the mixture.

Parameters:: agent (Agent) – Agent to remove.
Return type:: None

property touched_after: set[Agent]#

The agents that will be changed or added after this update.

Returns:: Set of agents affected by the update.

property touched_before: set[Agent]#

The agents that will be changed or removed by this update.

Returns:: Set of agents affected before the update is applied.

kappybara.mixture.grouped(components)[source]#

Group components by isomorphism.

Parameters:: components (Iterable[Component]) – Components to group.
Returns:: Dictionary mapping representative components to lists of isomorphic components.
Return type:: dict[Component, list[Component]]

kappybara.mixture.neighborhood(agents, radius)[source]#

Get all agents within a distance radius of the given agents.

Parameters:

agents (Iterable[Agent]) – Starting agents for the neighborhood.
radius (int) – Maximum distance to include.

Returns:

Set of all agents within the specified radius.

Return type:

set[Agent]