Index

A

add() (pykappa.mixture.Mixture method) (pykappa.pattern.Component method) add_rule() (pykappa.system.System method) Agent (class in pykappa.pattern) agent (pykappa.pattern.Site attribute)

agent_name (pykappa.pattern.SiteType attribute) agents (pykappa.mixture.Mixture attribute) (pykappa.pattern.Component attribute) (pykappa.pattern.Pattern attribute) agents_to_kappa_str() (pykappa.pattern.Pattern static method)

B

BimolecularRule (class in pykappa.rule)

binding_kinetics_table() (in module pykappa.analysis) bound (pykappa.pattern.Site property)

C

Component (class in pykappa.pattern) component_tracking (pykappa.mixture.Mixture property) components (pykappa.mixture.Mixture property) (pykappa.pattern.Pattern property)

contact_map() (in module pykappa.analysis) (pykappa.system.System method) coupled (pykappa.pattern.Site property)

D

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

detached() (pykappa.pattern.Agent method) diameter (pykappa.pattern.Component property)

E

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.analysis) (pykappa.analysis.Monitor method) equilibration_time() (in module pykappa.analysis) equilibrium_value() (in module pykappa.analysis)

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.Rule class method) (pykappa.system.System class method)

H

history (pykappa.analysis.Monitor attribute)

I

instantiable (pykappa.pattern.Agent property) 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.Rule property) (pykappa.system.System property)

L

label (pykappa.pattern.Site attribute)

left (pykappa.rule.Rule attribute) list_from_kappa() (pykappa.rule.Rule class method)

M

measure() (pykappa.analysis.Monitor method) Mixture (class in pykappa.mixture) mixture (pykappa.system.System attribute) module pykappa.analysis pykappa.mixture pykappa.pattern pykappa.rule pykappa.system

Monitor (class in pykappa.analysis) monitor (pykappa.system.System attribute)

N

n_automorphisms (pykappa.pattern.Component property) n_embeddings() (pykappa.rule.BimolecularRule method) (pykappa.rule.Rule method) (pykappa.rule.UnimolecularRule method)

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

O

observables (pykappa.system.System attribute)

P

partner (pykappa.pattern.Site attribute) Pattern (class in pykappa.pattern) plot() (pykappa.analysis.Monitor method) pykappa.analysis module pykappa.mixture module

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

R

rate() (pykappa.rule.Rule method) reactivity (pykappa.system.System property) reactivity() (pykappa.rule.Rule method) read_ka() (pykappa.system.System class method) relative_slope() (in module pykappa.analysis)

remove() (pykappa.mixture.Mixture method) remove_rule() (pykappa.system.System method) right (pykappa.rule.Rule attribute) Rule (class in pykappa.rule) rule_reactivities (pykappa.system.System property) rules (pykappa.system.System attribute)

S

Site (class in pykappa.pattern) 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.Rule attribute) System (class in pykappa.system) system (pykappa.analysis.Monitor attribute)

T

tail_mean() (pykappa.analysis.Monitor method) tallies (pykappa.system.System attribute) tallies_str (pykappa.system.System property)

time (pykappa.system.System attribute) to_ka() (pykappa.system.System 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)

UnimolecularRule (class in pykappa.rule) update() (pykappa.analysis.Monitor method) (pykappa.system.System method) update_via_kasim() (pykappa.system.System method)

V

variables (pykappa.system.System attribute)

W

wait() (pykappa.system.System method)