Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ _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() (pykappa.grammar.PatternBuilder method) agent_name (pykappa.pattern.SiteType attribute) agent_name() (pykappa.grammar.AgentBuilder method) AgentBuilder (class in pykappa.grammar) agents (pykappa.mixture.Mixture attribute), [1] (pykappa.pattern.Component attribute), [1] (pykappa.pattern.Pattern attribute), [1] agents_changed (pykappa.mixture.MixtureUpdate attribute), [1] agents_to_add (pykappa.mixture.MixtureUpdate attribute), [1] agents_to_kappa_str() (pykappa.pattern.Pattern static method) agents_to_remove (pykappa.mixture.MixtureUpdate attribute), [1] algebraic_expression() (pykappa.grammar.LarkTreetoExpression method) apply_rule() (pykappa.system.System method) apply_update() (pykappa.mixture.ComponentMixture method) (pykappa.mixture.Mixture method) attrs (pykappa.algebra.Expression attribute) B binary_op() (pykappa.grammar.LarkTreetoExpression method) binary_op_expression() (pykappa.grammar.LarkTreetoExpression method) bound (pykappa.pattern.Site property) C choose_rule() (pykappa.system.System method) comparison() (pykappa.grammar.LarkTreetoExpression method) Component (class in pykappa.pattern) component_weights (pykappa.rule.KappaRuleBimolecular attribute) (pykappa.rule.KappaRuleUnimolecular attribute) ComponentMixture (class in pykappa.mixture) components (pykappa.mixture.ComponentMixture attribute), [1] (pykappa.pattern.Pattern property) conditional_expression() (pykappa.grammar.LarkTreetoExpression method) 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) declared_variable_name() (pykappa.grammar.LarkTreetoExpression method) defined_constant() (pykappa.grammar.LarkTreetoExpression method) 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), [1] edges_to_remove (pykappa.mixture.MixtureUpdate attribute), [1] Embedding (class in pykappa.pattern) embeddings() (pykappa.mixture.Mixture method) (pykappa.pattern.Component method) embeddings_in_component() (pykappa.mixture.ComponentMixture method) embeds_in() (pykappa.pattern.Agent method) (pykappa.pattern.Site method) evaluate() (pykappa.algebra.Expression method) Expression (class in pykappa.algebra) F FALSE() (pykappa.grammar.LarkTreetoExpression method) filter() (pykappa.algebra.Expression method) from_ka() (pykappa.system.System class method) from_kappa() (pykappa.algebra.Expression class method) (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 grouped() (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.algebra.Expression property) (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) KappaParser (class in pykappa.grammar) 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) LarkTreetoExpression (class in pykappa.grammar) left (pykappa.rule.KappaRule attribute), [1] left_agents (pykappa.grammar.RuleBuilder attribute), [1] list_from_kappa() (pykappa.rule.KappaRule class method) list_op_expression() (pykappa.grammar.LarkTreetoExpression method) logical_and() (pykappa.grammar.LarkTreetoExpression method) logical_not() (pykappa.grammar.LarkTreetoExpression method) logical_or() (pykappa.grammar.LarkTreetoExpression method) lookup() (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.algebra pykappa.grammar 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), [1] 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 object (pykappa.grammar.AgentBuilder property) (pykappa.grammar.PatternBuilder property) (pykappa.grammar.SiteBuilder property) objects (pykappa.grammar.RuleBuilder property) observables (pykappa.system.System attribute), [1] OrderedSet (class in pykappa.utils) P parentheses() (pykappa.grammar.LarkTreetoExpression method) parse() (pykappa.grammar.KappaParser method) parse_file() (pykappa.grammar.KappaParser method) parse_operator() (in module pykappa.algebra) parse_tree_to_expression() (in module pykappa.grammar) parsed_agents (pykappa.grammar.PatternBuilder attribute), [1] parsed_interface (pykappa.grammar.AgentBuilder attribute), [1] parsed_label (pykappa.grammar.RuleBuilder attribute), [1] parsed_partner (pykappa.grammar.SiteBuilder attribute), [1] parsed_rates (pykappa.grammar.RuleBuilder attribute), [1] parsed_site_name (pykappa.grammar.SiteBuilder attribute), [1] parsed_state (pykappa.grammar.SiteBuilder attribute), [1] parsed_type (pykappa.grammar.AgentBuilder attribute), [1] partner (pykappa.pattern.Site attribute) partner() (pykappa.grammar.SiteBuilder method) Pattern (class in pykappa.pattern) pattern() (pykappa.grammar.LarkTreetoExpression method) PatternBuilder (class in pykappa.grammar) plot() (pykappa.system.Monitor method) properties (pykappa.utils.IndexedSet attribute) Property (class in pykappa.utils) pykappa.algebra module pykappa.grammar module pykappa.mixture module pykappa.pattern module pykappa.rule module pykappa.system module pykappa.utils module R rate() (pykappa.grammar.RuleBuilder method) (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) reserved_variable_name() (pykappa.grammar.LarkTreetoExpression method) rev_rule_expression() (pykappa.grammar.RuleBuilder method) right (pykappa.rule.KappaRule attribute), [1] right_agents (pykappa.grammar.RuleBuilder attribute), [1] Rule (class in pykappa.rule) rule_expression() (pykappa.grammar.RuleBuilder method) rule_reactivities (pykappa.system.System property) RuleBuilder (class in pykappa.grammar) 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) SetProperty (class in pykappa.utils) SIGNED_FLOAT() (pykappa.grammar.LarkTreetoExpression method) SIGNED_INT() (pykappa.grammar.LarkTreetoExpression method) Site (class in pykappa.pattern) site() (pykappa.grammar.AgentBuilder method) site1 (pykappa.mixture.Edge attribute), [1] site2 (pykappa.mixture.Edge attribute), [1] site_name (pykappa.pattern.SiteType attribute) site_name() (pykappa.grammar.SiteBuilder method) SiteBuilder (class in pykappa.grammar) sites (pykappa.pattern.Agent property) SiteType (class in pykappa.pattern) state (pykappa.pattern.Site attribute) state() (pykappa.grammar.SiteBuilder method) 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 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.ComponentMixture method) (pykappa.mixture.Mixture method) tree_data (pykappa.grammar.RuleBuilder attribute), [1] TRUE() (pykappa.grammar.LarkTreetoExpression method) type (pykappa.algebra.Expression attribute) (pykappa.pattern.Agent attribute) U unary_op() (pykappa.grammar.LarkTreetoExpression method) unary_op_expression() (pykappa.grammar.LarkTreetoExpression method) 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_via_kasim() (pykappa.system.System method) V variables (pykappa.system.System attribute), [1] W wait() (pykappa.system.System method)