Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ _embeddings (kappybara.mixture.Mixture attribute) _max_embedding_width (kappybara.mixture.Mixture attribute) A add() (kappybara.mixture.Mixture method) (kappybara.pattern.Component method) (kappybara.utils.IndexedSet method) (kappybara.utils.OrderedSet method) add_rule() (kappybara.system.System method) Agent (class in kappybara.pattern) agent (kappybara.pattern.Site attribute), [1] agent() (kappybara.grammar.PatternBuilder method) agent_name (kappybara.pattern.SiteType attribute) agent_name() (kappybara.grammar.AgentBuilder method) AgentBuilder (class in kappybara.grammar) agents (kappybara.mixture.Mixture attribute), [1] (kappybara.pattern.Component attribute), [1] (kappybara.pattern.Pattern attribute), [1] agents_changed (kappybara.mixture.MixtureUpdate attribute), [1] agents_to_add (kappybara.mixture.MixtureUpdate attribute), [1] agents_to_kappa_str() (kappybara.pattern.Pattern static method) agents_to_remove (kappybara.mixture.MixtureUpdate attribute), [1] algebraic_expression() (kappybara.grammar.LarkTreetoExpression method) apply_rule() (kappybara.system.System method) apply_update() (kappybara.mixture.ComponentMixture method) (kappybara.mixture.Mixture method) attrs (kappybara.algebra.Expression attribute) B binary_op() (kappybara.grammar.LarkTreetoExpression method) binary_op_expression() (kappybara.grammar.LarkTreetoExpression method) bound (kappybara.pattern.Site property) C choose_rule() (kappybara.system.System method) comparison() (kappybara.grammar.LarkTreetoExpression method) Component (class in kappybara.pattern) component_weights (kappybara.rule.KappaRuleBimolecular attribute) (kappybara.rule.KappaRuleUnimolecular attribute) ComponentMixture (class in kappybara.mixture) components (kappybara.mixture.ComponentMixture attribute), [1] (kappybara.pattern.Pattern property) conditional_expression() (kappybara.grammar.LarkTreetoExpression method) connect_sites() (kappybara.mixture.MixtureUpdate method) Counted (class in kappybara.utils) counter (kappybara.utils.Counted attribute) coupled (kappybara.pattern.Site property) create_agent() (kappybara.mixture.MixtureUpdate method) create_index() (kappybara.utils.IndexedSet method) D dataframe (kappybara.system.Monitor property) declared_variable_name() (kappybara.grammar.LarkTreetoExpression method) defined_constant() (kappybara.grammar.LarkTreetoExpression method) depth_first_traversal (kappybara.pattern.Agent property) detached() (kappybara.pattern.Agent method) diameter (kappybara.pattern.Component property) disconnect_site() (kappybara.mixture.MixtureUpdate method) E Edge (class in kappybara.mixture) edges_to_add (kappybara.mixture.MixtureUpdate attribute), [1] edges_to_remove (kappybara.mixture.MixtureUpdate attribute), [1] Embedding (class in kappybara.pattern) embeddings() (kappybara.mixture.Mixture method) (kappybara.pattern.Component method) embeddings_in_component() (kappybara.mixture.ComponentMixture method) embeds_in() (kappybara.pattern.Agent method) (kappybara.pattern.Site method) evaluate() (kappybara.algebra.Expression method) Expression (class in kappybara.algebra) F FALSE() (kappybara.grammar.LarkTreetoExpression method) filter() (kappybara.algebra.Expression method) from_ka() (kappybara.system.System class method) from_kappa() (kappybara.algebra.Expression class method) (kappybara.mixture.Mixture class method) (kappybara.pattern.Agent class method) (kappybara.pattern.Component class method) (kappybara.pattern.Pattern class method) (kappybara.rule.KappaRule class method) (kappybara.system.System class method) G grouped() (in module kappybara.mixture) H history (kappybara.system.Monitor attribute), [1] I IndexedSet (class in kappybara.utils) indices (kappybara.utils.IndexedSet attribute) instantiable (kappybara.pattern.Agent property) instantiate() (kappybara.mixture.Mixture method) interface (kappybara.pattern.Agent attribute) isomorphic() (kappybara.pattern.Agent method) (kappybara.pattern.Component method) isomorphisms() (kappybara.pattern.Component method) K kappa_partner_str (kappybara.pattern.Site property) kappa_state_str (kappybara.pattern.Site property) kappa_str (kappybara.algebra.Expression property) (kappybara.mixture.Mixture property) (kappybara.pattern.Agent property) (kappybara.pattern.Component property) (kappybara.pattern.Pattern property) (kappybara.pattern.Site property) (kappybara.rule.KappaRule property) (kappybara.rule.KappaRuleBimolecular property) (kappybara.rule.KappaRuleUnimolecular property) (kappybara.system.System property) KappaParser (class in kappybara.grammar) KappaRule (class in kappybara.rule) KappaRuleBimolecular (class in kappybara.rule) KappaRuleUnimolecular (class in kappybara.rule) kappybara.algebra module kappybara.grammar module kappybara.mixture module kappybara.pattern module kappybara.rule module kappybara.system module kappybara.utils module kinetic_to_stochastic_on_rate() (in module kappybara.rule) L label (kappybara.pattern.Site attribute) LarkTreetoExpression (class in kappybara.grammar) left (kappybara.rule.KappaRule attribute), [1] left_agents (kappybara.grammar.RuleBuilder attribute), [1] list_from_kappa() (kappybara.rule.KappaRule class method) list_op_expression() (kappybara.grammar.LarkTreetoExpression method) logical_and() (kappybara.grammar.LarkTreetoExpression method) logical_not() (kappybara.grammar.LarkTreetoExpression method) logical_or() (kappybara.grammar.LarkTreetoExpression method) lookup() (kappybara.utils.IndexedSet method) M measure() (kappybara.system.Monitor method) Mixture (class in kappybara.mixture) mixture (kappybara.system.System attribute), [1] MixtureUpdate (class in kappybara.mixture) module kappybara.algebra kappybara.grammar kappybara.mixture kappybara.pattern kappybara.rule kappybara.system kappybara.utils Monitor (class in kappybara.system) monitor (kappybara.system.System attribute), [1] N n_automorphisms (kappybara.pattern.Component property) n_copies (kappybara.pattern.Component attribute), [1] n_embeddings() (kappybara.rule.KappaRule method) (kappybara.rule.KappaRuleBimolecular method) (kappybara.rule.KappaRuleUnimolecular method) (kappybara.rule.Rule method) n_isomorphisms() (kappybara.pattern.Pattern method) n_symmetries (kappybara.rule.KappaRule property) names (kappybara.system.System property) neighborhood() (in module kappybara.mixture) neighbors (kappybara.pattern.Agent property) O object (kappybara.grammar.AgentBuilder property) (kappybara.grammar.PatternBuilder property) (kappybara.grammar.SiteBuilder property) objects (kappybara.grammar.RuleBuilder property) observables (kappybara.system.System attribute), [1] OrderedSet (class in kappybara.utils) P parentheses() (kappybara.grammar.LarkTreetoExpression method) parse() (kappybara.grammar.KappaParser method) parse_file() (kappybara.grammar.KappaParser method) parse_operator() (in module kappybara.algebra) parse_tree_to_expression() (in module kappybara.grammar) parsed_agents (kappybara.grammar.PatternBuilder attribute), [1] parsed_interface (kappybara.grammar.AgentBuilder attribute), [1] parsed_label (kappybara.grammar.RuleBuilder attribute), [1] parsed_partner (kappybara.grammar.SiteBuilder attribute), [1] parsed_rates (kappybara.grammar.RuleBuilder attribute), [1] parsed_site_name (kappybara.grammar.SiteBuilder attribute), [1] parsed_state (kappybara.grammar.SiteBuilder attribute), [1] parsed_type (kappybara.grammar.AgentBuilder attribute), [1] partner (kappybara.pattern.Site attribute) partner() (kappybara.grammar.SiteBuilder method) Pattern (class in kappybara.pattern) pattern() (kappybara.grammar.LarkTreetoExpression method) PatternBuilder (class in kappybara.grammar) plot() (kappybara.system.Monitor method) properties (kappybara.utils.IndexedSet attribute) Property (class in kappybara.utils) R rate() (kappybara.grammar.RuleBuilder method) (kappybara.rule.KappaRule method) (kappybara.rule.Rule method) reactivity (kappybara.system.System property) reactivity() (kappybara.rule.KappaRule method) (kappybara.rule.Rule method) read_ka() (kappybara.system.System class method) register_changed_agent() (kappybara.mixture.MixtureUpdate method) rejection_sample() (in module kappybara.utils) remove() (kappybara.mixture.Mixture method) (kappybara.utils.IndexedSet method) (kappybara.utils.OrderedSet method) remove_agent() (kappybara.mixture.MixtureUpdate method) remove_by() (kappybara.utils.IndexedSet method) remove_rule() (kappybara.system.System method) reserved_variable_name() (kappybara.grammar.LarkTreetoExpression method) rev_rule_expression() (kappybara.grammar.RuleBuilder method) right (kappybara.rule.KappaRule attribute), [1] right_agents (kappybara.grammar.RuleBuilder attribute), [1] Rule (class in kappybara.rule) rule_expression() (kappybara.grammar.RuleBuilder method) rule_reactivities (kappybara.system.System property) RuleBuilder (class in kappybara.grammar) rules (kappybara.system.System attribute), [1] S select() (kappybara.rule.KappaRule method) (kappybara.rule.KappaRuleBimolecular method) (kappybara.rule.KappaRuleUnimolecular method) (kappybara.rule.Rule method) set_mixture() (kappybara.system.System method) SetProperty (class in kappybara.utils) SIGNED_FLOAT() (kappybara.grammar.LarkTreetoExpression method) SIGNED_INT() (kappybara.grammar.LarkTreetoExpression method) Site (class in kappybara.pattern) site() (kappybara.grammar.AgentBuilder method) site1 (kappybara.mixture.Edge attribute), [1] site2 (kappybara.mixture.Edge attribute), [1] site_name (kappybara.pattern.SiteType attribute) site_name() (kappybara.grammar.SiteBuilder method) SiteBuilder (class in kappybara.grammar) sites (kappybara.pattern.Agent property) SiteType (class in kappybara.pattern) state (kappybara.pattern.Site attribute) state() (kappybara.grammar.SiteBuilder method) stated (kappybara.pattern.Site property) stochastic_rate (kappybara.rule.KappaRule attribute), [1] System (class in kappybara.system) system (kappybara.system.Monitor attribute), [1] T tallies (kappybara.system.System attribute), [1] tallies_str (kappybara.system.System property) time (kappybara.system.System attribute), [1] to_ka() (kappybara.system.System method) touched_after (kappybara.mixture.MixtureUpdate property) touched_before (kappybara.mixture.MixtureUpdate property) track_component() (kappybara.mixture.ComponentMixture method) (kappybara.mixture.Mixture method) tree_data (kappybara.grammar.RuleBuilder attribute), [1] TRUE() (kappybara.grammar.LarkTreetoExpression method) type (kappybara.algebra.Expression attribute) (kappybara.pattern.Agent attribute) U unary_op() (kappybara.grammar.LarkTreetoExpression method) unary_op_expression() (kappybara.grammar.LarkTreetoExpression method) underspecified (kappybara.pattern.Agent property) (kappybara.pattern.Pattern property) (kappybara.pattern.Site property) undetermined (kappybara.pattern.Site property) update() (kappybara.system.Monitor method) (kappybara.system.System method) update_via_kasim() (kappybara.system.System method) V variables (kappybara.system.System attribute), [1] W wait() (kappybara.system.System method)