pykappa.pattern

Classes

Agent(type, sites)

Represents an agent with a type and collection of sites.

Component(agents[, n_copies])

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)

Represents a site on an agent with state and binding partner information.

SiteType(site_name, agent_name)

class pykappa.pattern.Agent(type, sites)[source]

Represents an agent with a type and collection of sites.

Parameters:

  • type (str)

  • sites (Iterable[Site])

type

Type name of the agent.

interface

Dictionary mapping site labels to Site objects.

property depth_first_traversal: list[Self]

Perform depth-first traversal starting from this agent.

detached()[source]

Create a clone with all sites emptied of partners.

Return type:

Self

embeds_in(other)[source]

Check whether self as a pattern matches other as a concrete agent.

Parameters:

other (Self)

Return type:

bool

classmethod from_kappa(kappa_str)[source]

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

property instantiable: bool

Check if this agent pattern can be instantiated.

isomorphic(other)[source]

Check if two Agents are equivalent locally, ignoring partners.

Note

Doesn’t assume agents of the same type will have the same site signatures.

Parameters:

other (Self)

Return type:

bool

property kappa_str

The agent representation in Kappa format.

property neighbors: list[Self]

The agents directly connected to this one.

property sites: Iterable[Site]

All sites of this agent.

property underspecified: bool

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

class pykappa.pattern.Component(agents, n_copies=1)[source]

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

Note

Connectedness is not guaranteed statically and must be enforced.

Parameters:
add(agent)[source]

Add an agent to this component.

Parameters:

agent (Agent)

agents: IndexedSet[Agent]
property diameter: int

Get the maximum minimum shortest path between any two agents.

embeddings(other, exact=False)[source]

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]

classmethod from_kappa(kappa_str)[source]

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

isomorphic(other)[source]

Check if two components are isomorphic.

Parameters:

other (Self)

Return type:

bool

isomorphisms(other)[source]

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 kappa_str: str

The component representation in Kappa format.

property n_automorphisms: int

Returns the number of automorphisms (i.e. isomorphisms onto itself) of the component.

Note

This uses a cached result, and thus should only be used for static components, i.e. the ones in rules and observables. Do not use this for components in a mixture that can change.

n_copies: int
plot(legend=True)[source]

Plot the component using graphviz.

Parameters:

legend (bool)

Return type:

None

class pykappa.pattern.Embedding[source]

Dictionary representing a mapping from pattern agents to mixture agents.

class pykappa.pattern.Pattern(agents)[source]

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

Parameters:

agents (list[Agent | None])

agents

List of agents, where None represents empty slots in rules.

Type:

list[pykappa.pattern.Agent | None]

agents: list[Agent | None]
static agents_to_kappa_str(agents)[source]

Convert a collection of agents to Kappa string representation.

Parameters:

agents (Iterable[Agent | None])

Return type:

str

property components: list[Component]

The connected components in this pattern.

classmethod from_kappa(kappa_str)[source]

Parse a pattern from a Kappa string.

Parameters:

kappa_str (str) – Kappa string describing a pattern.

Returns:

Parsed Pattern object.

Raises:

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

Return type:

Self

property kappa_str: str

The pattern representation in Kappa format.

n_isomorphisms(other)[source]

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

property underspecified: bool

Check if any agents in the pattern are underspecified.

class pykappa.pattern.Site(label, state, partner)[source]

Represents a site on an agent with state and binding partner information.

Parameters:

  • label (str)

  • state (str)

  • partner (str | SiteType | int | Site)

agent

The agent this site belongs to (set after initialization).

Type:

pykappa.pattern.Agent

label

Name of the site.

state

Internal state of the site.

partner

Binding partner specification.

agent: Agent
property bound: bool

Check if the site is bound.

property coupled: bool

Check if the site is coupled to a specific other site.

embeds_in(other)[source]

Check whether self as a pattern matches other as a concrete site.

Parameters:

other (Self)

Return type:

bool

property kappa_partner_str: str
property kappa_state_str: str
property kappa_str: str

The site representation in Kappa format.

property stated: bool

Check if the site has a specific internal state.

property underspecified: bool

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

property undetermined: bool

Check if the site is in a state equivalent to leaving it unnamed in an agent.

class pykappa.pattern.SiteType(site_name, agent_name)
Parameters:

  • site_name (str)

  • agent_name (str)

agent_name: str

Alias for field number 1

site_name: str

Alias for field number 0