Index

_

_components (pykappa.mixture.Mixture attribute)

_embeddings (pykappa.mixture.Mixture attribute) _max_embedding_width (pykappa.mixture.Mixture attribute)

A

add() (pykappa.mixture.Mixture method) (pykappa.pattern.Component method) (pykappa.utils.IndexedSet method) (pykappa.utils.OrderedSet method) add_rule() (pykappa.system.System method) Agent (class in pykappa.pattern) agent (pykappa.pattern.Site attribute), [1] agent_name (pykappa.pattern.SiteType attribute)

agents (pykappa.mixture.Mixture attribute), [1] (pykappa.pattern.Component attribute) (pykappa.pattern.Pattern attribute), [1] agents_changed (pykappa.mixture.MixtureUpdate attribute) agents_to_add (pykappa.mixture.MixtureUpdate attribute) agents_to_kappa_str() (pykappa.pattern.Pattern static method) agents_to_remove (pykappa.mixture.MixtureUpdate attribute) apply_rule() (pykappa.system.System method) apply_update() (pykappa.mixture.Mixture method)

B

bound (pykappa.pattern.Site property)

C

choose_rule() (pykappa.system.System method) Component (class in pykappa.pattern) component_tracking (pykappa.mixture.Mixture property) component_weights (pykappa.rule.KappaRuleBimolecular attribute) (pykappa.rule.KappaRuleUnimolecular attribute) components (pykappa.mixture.Mixture property) (pykappa.pattern.Pattern property)

connect_sites() (pykappa.mixture.MixtureUpdate method) Counted (class in pykappa.utils) counter (pykappa.utils.Counted attribute) coupled (pykappa.pattern.Site property) create_agent() (pykappa.mixture.MixtureUpdate method) create_index() (pykappa.utils.IndexedSet method)

D

dataframe (pykappa.system.Monitor property) depth_first_traversal (pykappa.pattern.Agent property)

detached() (pykappa.pattern.Agent method) diameter (pykappa.pattern.Component property) disconnect_site() (pykappa.mixture.MixtureUpdate method)

E

Edge (class in pykappa.mixture) edges_to_add (pykappa.mixture.MixtureUpdate attribute) edges_to_remove (pykappa.mixture.MixtureUpdate attribute) Embedding (class in pykappa.pattern) embeddings() (pykappa.mixture.Mixture method) (pykappa.pattern.Component method)

embeddings_in_component() (pykappa.mixture.Mixture method) embeds_in() (pykappa.pattern.Agent method) (pykappa.pattern.Site method) enable_component_tracking() (pykappa.mixture.Mixture method) equilibrated() (in module pykappa.utils) (pykappa.system.Monitor method)

F

from_ka() (pykappa.system.System class method) from_kappa() (pykappa.mixture.Mixture class method) (pykappa.pattern.Agent class method) (pykappa.pattern.Component class method) (pykappa.pattern.Pattern class method) (pykappa.rule.KappaRule class method) (pykappa.system.System class method)

G

group_by_isomorphism() (in module pykappa.mixture)

H

history (pykappa.system.Monitor attribute), [1]

I

IndexedSet (class in pykappa.utils) indices (pykappa.utils.IndexedSet attribute) instantiable (pykappa.pattern.Agent property) instantiate() (pykappa.mixture.Mixture method)

interface (pykappa.pattern.Agent attribute) isomorphic() (pykappa.pattern.Agent method) (pykappa.pattern.Component method) isomorphisms() (pykappa.pattern.Component method)

K

kappa_partner_str (pykappa.pattern.Site property) kappa_state_str (pykappa.pattern.Site property) kappa_str (pykappa.mixture.Mixture property) (pykappa.pattern.Agent property) (pykappa.pattern.Component property) (pykappa.pattern.Pattern property) (pykappa.pattern.Site property) (pykappa.rule.KappaRule property) (pykappa.rule.KappaRuleBimolecular property) (pykappa.rule.KappaRuleUnimolecular property) (pykappa.system.System property)

KappaRule (class in pykappa.rule) KappaRuleBimolecular (class in pykappa.rule) KappaRuleUnimolecular (class in pykappa.rule) kinetic_to_stochastic_on_rate() (in module pykappa.rule)

L

label (pykappa.pattern.Site attribute) left (pykappa.rule.KappaRule attribute), [1]

list_from_kappa() (pykappa.rule.KappaRule class method) lookup() (pykappa.utils.IndexedSet method) lookup_one() (pykappa.utils.IndexedSet method)

M

measure() (pykappa.system.Monitor method) Mixture (class in pykappa.mixture) mixture (pykappa.system.System attribute), [1] MixtureUpdate (class in pykappa.mixture) module pykappa.mixture pykappa.pattern pykappa.rule pykappa.system pykappa.utils

Monitor (class in pykappa.system) monitor (pykappa.system.System attribute), [1]

N

n_automorphisms (pykappa.pattern.Component property) n_copies (pykappa.pattern.Component attribute) n_embeddings() (pykappa.rule.KappaRule method) (pykappa.rule.KappaRuleBimolecular method) (pykappa.rule.KappaRuleUnimolecular method) (pykappa.rule.Rule method)

n_isomorphisms() (pykappa.pattern.Pattern method) n_symmetries (pykappa.rule.KappaRule property) names (pykappa.system.System property) neighborhood() (in module pykappa.mixture) neighbors (pykappa.pattern.Agent property)

O

observables (pykappa.system.System attribute), [1]

OrderedSet (class in pykappa.utils)

P

partner (pykappa.pattern.Site attribute) Pattern (class in pykappa.pattern) plot() (pykappa.pattern.Component method) (pykappa.system.Monitor method) properties (pykappa.utils.IndexedSet attribute) pykappa.mixture module

pykappa.pattern module pykappa.rule module pykappa.system module pykappa.utils module

R

rate() (pykappa.rule.KappaRule method) (pykappa.rule.Rule method) reactivity (pykappa.system.System property) reactivity() (pykappa.rule.KappaRule method) (pykappa.rule.Rule method) read_ka() (pykappa.system.System class method) register_changed_agent() (pykappa.mixture.MixtureUpdate method) rejection_sample() (in module pykappa.utils) remove() (pykappa.mixture.Mixture method) (pykappa.utils.IndexedSet method) (pykappa.utils.OrderedSet method)

remove_agent() (pykappa.mixture.MixtureUpdate method) remove_by() (pykappa.utils.IndexedSet method) remove_rule() (pykappa.system.System method) right (pykappa.rule.KappaRule attribute), [1] rng (pykappa.system.System attribute), [1] Rule (class in pykappa.rule) rule_reactivities (pykappa.system.System property) rules (pykappa.system.System attribute), [1]

S

select() (pykappa.rule.KappaRule method) (pykappa.rule.KappaRuleBimolecular method) (pykappa.rule.KappaRuleUnimolecular method) (pykappa.rule.Rule method) set_mixture() (pykappa.system.System method) Site (class in pykappa.pattern) site1 (pykappa.mixture.Edge attribute) site2 (pykappa.mixture.Edge attribute)

site_name (pykappa.pattern.SiteType attribute) sites (pykappa.pattern.Agent property) SiteType (class in pykappa.pattern) state (pykappa.pattern.Site attribute) stated (pykappa.pattern.Site property) stochastic_rate (pykappa.rule.KappaRule attribute), [1] str_table() (in module pykappa.utils) System (class in pykappa.system) system (pykappa.system.Monitor attribute), [1]

T

tail_mean() (pykappa.system.Monitor method) tallies (pykappa.system.System attribute), [1] tallies_str (pykappa.system.System property) time (pykappa.system.System attribute), [1]

to_ka() (pykappa.system.System method) touched_after (pykappa.mixture.MixtureUpdate property) touched_before (pykappa.mixture.MixtureUpdate property) track_component() (pykappa.mixture.Mixture method) type (pykappa.pattern.Agent attribute)

U

underspecified (pykappa.pattern.Agent property) (pykappa.pattern.Pattern property) (pykappa.pattern.Site property) undetermined (pykappa.pattern.Site property)

update() (pykappa.system.Monitor method) (pykappa.system.System method) update_until() (pykappa.system.System method) update_via_kasim() (pykappa.system.System method)

V

variables (pykappa.system.System attribute), [1]

W

wait() (pykappa.system.System method)