pykappa.pattern

Classes

Agent(type, sites)	Represents an agent with a type and collection of sites.
Component(agents)	A set of agents that are all in the same connected component.
Embedding	Dictionary representing a mapping from pattern agents to mixture agents.
Pattern(agents)	A pattern consisting of multiple agents, some of which may be None (empty slots).
Site(label, state, partner)	A site on an agent with state and binding partner information.

class pykappa.pattern.Site(label, state, partner)

A site on an agent with state and binding partner information.

Parameters:

• label (str)

• state (str)

• partner (str | _TypedPartner | int | Site)

agent: Agent

The agent this site belongs to (set after initialization)

label: str

Name of the site

state: str

Internal state of the site

partner: str | _TypedPartner | int | Site

property kappa_str: str

property instantiable: bool

Check if a concrete Site can be created from this pattern.

property bound: bool

class pykappa.pattern.Agent(type, sites)

Represents an agent with a type and collection of sites.

Parameters:

• type (str)

• sites (Iterable[Site])

static neighborhood(agents, radius)

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

Parameters:

• agents (Iterable[Agent])

• radius (int)

Return type:

set[Agent]

classmethod from_kappa(kappa_str)

Parse a single agent from a Kappa string.

Raises:

AssertionError – If the string doesn’t describe exactly one agent.

Parameters:

kappa_str (str)

Return type:

Self

type: str

Type name of the agent

interface: dict[str, Site]

Maps site labels to Site objects

property kappa_str

property instantiable: bool

Check if a concrete Agent can be created from this pattern.

property neighbors: list[Self]

The agents directly connected to this one.

class pykappa.pattern.Embedding

Dictionary representing a mapping from pattern agents to mixture agents.

class pykappa.pattern.Component(agents)

A set of agents that are all in the same connected component.

Note

Connectedness is not guaranteed statically and must be enforced.

Parameters:

agents (IndexedSet[Agent])

classmethod from_kappa(kappa_str)

Parse a single component from a Kappa string.

Raises:

AssertionError – If the pattern doesn’t represent exactly one component.

Parameters:

kappa_str (str)

Return type:

Self

agents: IndexedSet[Agent]

property kappa_str: str

isomorphic(other)

Parameters:

other (Self)

Return type:

bool

embeddings(other, exact=False)

Find embeddings of self in other.

Parameters:

• other (Self | Mixture | Iterable[Agent]) – Target to find embeddings in.

• exact (bool) – If True, finds isomorphisms instead of embeddings.

Return type:

Iterator[Embedding]

isomorphisms(other)

Find bijections which respect links in the site graph.

Checks for bijections ensuring that any internal site state specified in one component exists and is the same in the other.

Note

Handles isomorphism generally, between instantiated components in a mixture and potentially between rule patterns.

Parameters:

other (Self | Mixture)

Return type:

Iterator[dict[Agent, Agent]]

property diameter: int

Get the maximum minimum shortest path between any two agents.

class pykappa.pattern.Pattern(agents)

A pattern consisting of multiple agents, some of which may be None (empty slots).

Parameters:

agents (list[Agent | None])

classmethod from_kappa(kappa_str)

Raises:

AssertionError – If the string doesn’t describe exactly one pattern.

Parameters:

kappa_str (str)

Return type:

Self

agents: list[Agent | None]

property components: list[Component]

The connected components in this pattern.

property kappa_str: str

property instantiable: bool

Check if all agents in the pattern are specific enough to instantiate.

n_isomorphisms(other)

Counts the number of bijections which respect links in the site graph.

Note

Runtime is exponential in the number of components; use with caution.

Parameters:

other (Self)

Return type:

int