Index

A

abstract_sequence() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) add_context() (eBCSgen.Core.Atomic.AtomicAgent method) (eBCSgen.Core.Structure.StructureAgent method) add_rate() (eBCSgen.TS.Edge.Edge method) agent() (eBCSgen.Core.Rate.ContextReducer method) (eBCSgen.Core.Rate.DirectEvaluater method) (eBCSgen.Core.Rate.Evaluater method) (eBCSgen.Core.Rate.Extractor method) (eBCSgen.Core.Rate.SymbolicAgents method) (eBCSgen.Core.Rate.Vectorizer method) (eBCSgen.Parsing.ParseCTLformula.TreeToStrings method) (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method) align_agents() (in module eBCSgen.Core.Complex)

align_match() (eBCSgen.Core.Complex.Complex method) AND() (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method) ap() (eBCSgen.Core.Formula.APextractor method) (eBCSgen.Core.Formula.APreplacetor method) (eBCSgen.Core.Formula.ComplexReplacetor method) (eBCSgen.Parsing.ParseCTLformula.TreeToStrings method) (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method) APextractor (class in eBCSgen.Core.Formula) APreplacetor (class in eBCSgen.Core.Formula) atomic() (eBCSgen.Parsing.ParseBCSL.TreeToComplex method) atomic_complex() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) atomic_structure_complex() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) AtomicAgent (class in eBCSgen.Core.Atomic) AtomicProposition (class in eBCSgen.Core.Formula)

B

BaseRegulation (class in eBCSgen.Regulations.Base)

C

call_storm() (in module eBCSgen.Analysis.PCTL) change_hell() (eBCSgen.TS.TransitionSystem.TransitionSystem method) change_to_vector_backend() (eBCSgen.TS.TransitionSystem.TransitionSystem method) check_AP() (eBCSgen.TS.State.State method) check_intersection() (eBCSgen.Regulations.Conditional.Conditional method) (eBCSgen.Regulations.Conditional.VectorConditional method) (eBCSgen.TS.State.Multiset method) (eBCSgen.TS.State.State method) (eBCSgen.TS.State.Vector method) check_labels() (eBCSgen.Regulations.ConcurrentFree.ConcurrentFree method) (eBCSgen.Regulations.Conditional.Conditional method) (eBCSgen.Regulations.Ordered.Ordered method) (eBCSgen.Regulations.Programmed.Programmed method) (eBCSgen.Regulations.Regular.Regular method) check_rates() (eBCSgen.Core.Model.Model method) cmplx_dfn() (eBCSgen.Parsing.ParseBCSL.ExtractComplexNames method) cmplx_name() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) column() (in module eBCSgen.Core.Rule) compartment() (eBCSgen.Parsing.ParseBCSL.TreeToComplex method) compatible() (eBCSgen.Core.Atomic.AtomicAgent method) (eBCSgen.Core.Complex.Complex method) (eBCSgen.Core.Reaction.Reaction method) (eBCSgen.Core.Rule.Rule method) (eBCSgen.Core.Side.Side method) (eBCSgen.Core.Structure.StructureAgent method) Complex (class in eBCSgen.Core.Complex) complex() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) ComplexOutOfScope ComplexParsingError ComplexReplacetor (class in eBCSgen.Core.Formula) compute_bound() (eBCSgen.Core.Model.Model method) (eBCSgen.TS.VectorModel.VectorModel method) concurrent_free() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method) ConcurrentFree (class in eBCSgen.Regulations.ConcurrentFree)

Conditional (class in eBCSgen.Regulations.Conditional) conditional() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method) const() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) context() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method) ContextReducer (class in eBCSgen.Core.Rate) create_all_compatible() (eBCSgen.Core.Complex.Complex method) (eBCSgen.Core.Reaction.Reaction method) (eBCSgen.Core.Rule.Rule method) (eBCSgen.Core.Side.Side method) create_all_reactions() (eBCSgen.Export.ModelSBML.ModelSBML method) create_all_species_compartments_and_complex_species_types() (eBCSgen.Export.ModelSBML.ModelSBML method) create_AP_labels() (eBCSgen.TS.TransitionSystem.TransitionSystem method) create_basic_species_types() (eBCSgen.Export.ModelSBML.ModelSBML method) create_compartment() (eBCSgen.Export.ModelSBML.ModelSBML method) create_complex_labels() (eBCSgen.Core.Formula.Formula method) create_complexes() (eBCSgen.Core.Rule.Rule method) create_indices() (in module eBCSgen.TS.TransitionSystem) create_kinetic_law_and_modifiers() (eBCSgen.Export.ModelSBML.ModelSBML method) create_ordering() (eBCSgen.Core.Model.Model method) create_parameters() (eBCSgen.Export.ModelSBML.ModelSBML method) create_products() (eBCSgen.Export.ModelSBML.ModelSBML method) create_reactants() (eBCSgen.Export.ModelSBML.ModelSBML method) create_reaction_for_isomorphisms() (eBCSgen.Export.ModelSBML.ModelSBML method) create_reactions() (eBCSgen.Core.Rule.Rule method) create_reversible() (eBCSgen.Core.Rule.Rule method) create_species() (eBCSgen.Export.ModelSBML.ModelSBML method) create_species_feature_type() (eBCSgen.Export.ModelSBML.ModelSBML method) create_species_features() (eBCSgen.Export.ModelSBML.ModelSBML method) create_species_type_from_complex() (eBCSgen.Export.ModelSBML.ModelSBML method) create_species_types_from_atomic() (eBCSgen.Export.ModelSBML.ModelSBML method) create_species_types_from_structure() (eBCSgen.Export.ModelSBML.ModelSBML method) create_unique_complexes_and_params() (eBCSgen.Core.Model.Model method) CTL (class in eBCSgen.Analysis.CTL) CTLparser (class in eBCSgen.Parsing.ParseCTLformula)

D

decode() (eBCSgen.TS.TransitionSystem.TransitionSystem method) def_param() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method)

definitions() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) deterministic_simulation() (eBCSgen.TS.VectorModel.VectorModel method) DirectEvaluater (class in eBCSgen.Core.Rate)

E

eBCSgen.Analysis.CTL module eBCSgen.Analysis.PCTL module eBCSgen.Core.Atomic module eBCSgen.Core.Complex module eBCSgen.Core.Formula module eBCSgen.Core.Model module eBCSgen.Core.Rate module eBCSgen.Core.Reaction module eBCSgen.Core.Rule module eBCSgen.Core.Side module eBCSgen.Core.Structure module eBCSgen.Errors.ComplexOutOfScope module eBCSgen.Errors.ComplexParsingError module eBCSgen.Errors.FormulaParsingError module eBCSgen.Errors.InvalidInputError module eBCSgen.Errors.ModelParsingError module eBCSgen.Errors.RatesNotSpecifiedError module eBCSgen.Errors.StormNotAvailable module eBCSgen.Errors.UnspecifiedParsingError module eBCSgen.Export.ModelSBML module eBCSgen.Parsing.ParseBCSL module eBCSgen.Parsing.ParseCTLformula module eBCSgen.Parsing.ParsePCTLformula module

eBCSgen.Regulations.Base module eBCSgen.Regulations.ConcurrentFree module eBCSgen.Regulations.Conditional module eBCSgen.Regulations.Ordered module eBCSgen.Regulations.Programmed module eBCSgen.Regulations.Regular module eBCSgen.TS.Edge module eBCSgen.TS.State module eBCSgen.TS.TransitionSystem module eBCSgen.TS.TSworker module eBCSgen.TS.VectorModel module eBCSgen.TS.VectorReaction module Edge (class in eBCSgen.TS.Edge) edge_from_dict() (in module eBCSgen.TS.Edge) edges_to_PRISM() (eBCSgen.TS.TransitionSystem.TransitionSystem method) eliminate_redundant() (eBCSgen.Core.Model.Model method) encode() (eBCSgen.TS.Edge.Edge method) (eBCSgen.TS.TransitionSystem.TransitionSystem method) encode_edges() (eBCSgen.TS.TransitionSystem.TransitionSystem method) evaluate() (eBCSgen.Core.Rate.Rate method) evaluate_direct() (eBCSgen.Core.Rate.Rate method) evaluate_rate() (eBCSgen.Core.Rule.Rule method) (eBCSgen.TS.VectorReaction.VectorReaction method) Evaluater (class in eBCSgen.Core.Rate) exists_compatible_agent() (eBCSgen.Core.Rule.Rule method) (eBCSgen.Core.Side.Side method) export_sbml() (eBCSgen.Core.Model.Model method) extend_signature() (eBCSgen.Core.Atomic.AtomicAgent method) (eBCSgen.Core.Complex.Complex method) (eBCSgen.Core.Structure.StructureAgent method) extract_signatures() (eBCSgen.Core.Model.Model method) ExtractComplexNames (class in eBCSgen.Parsing.ParseBCSL) Extractor (class in eBCSgen.Core.Rate)

F

fake_expovariate() (in module eBCSgen.TS.VectorModel) filter() (eBCSgen.Regulations.Base.BaseRegulation method) (eBCSgen.Regulations.ConcurrentFree.ConcurrentFree method) (eBCSgen.Regulations.Conditional.Conditional method) (eBCSgen.Regulations.Conditional.VectorConditional method) (eBCSgen.Regulations.Ordered.Ordered method) (eBCSgen.Regulations.Programmed.Programmed method) (eBCSgen.Regulations.Regular.Regular method)

filter_unused_agents() (eBCSgen.TS.TransitionSystem.TransitionSystem method) filter_values() (eBCSgen.TS.State.Vector method) find_all_matches() (in module eBCSgen.Core.Rule) fix_operator() (eBCSgen.Core.Rate.MathMLtransformer method) Formula (class in eBCSgen.Core.Formula) FormulaParsingError fun() (eBCSgen.Core.Rate.MathMLtransformer method) FUTURE() (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method)

G

generate_direct_transition_system() (eBCSgen.Core.Model.Model method) generate_transition_system() (eBCSgen.TS.VectorModel.VectorModel method) get_agent_names() (eBCSgen.Core.Complex.Complex method) get_APs() (eBCSgen.Core.Formula.Formula method) get_atomic_names() (eBCSgen.Core.Complex.Complex method)

get_complexes() (eBCSgen.Core.Formula.Formula method) get_formula_in_list() (eBCSgen.Core.Rate.Rate method) get_name() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) get_params_and_agents() (eBCSgen.Core.Rate.Rate method) get_unique_complexes_from_rule() (eBCSgen.Core.Rule.Rule method) grammar (eBCSgen.Parsing.ParseCTLformula.CTLparser attribute)

H

handle_number_of_threads() (in module eBCSgen.TS.VectorModel)

I

identify_compatible() (eBCSgen.Core.Complex.Complex method) init() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) inits() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) insert_atomic_to_complex() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) insert_atomic_to_struct() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method)

insert_struct_to_complex() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) InvalidInputError is_composed() (eBCSgen.Core.Complex.Complex method) is_empty() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) is_meaningful() (eBCSgen.Core.Rule.Rule method)

J

join() (eBCSgen.TS.TSworker.TSworker method)

L

label() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method)

LB() (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method) load_TS_from_json() (in module eBCSgen.Parsing.ParseBCSL)

M

match() (eBCSgen.Core.Rule.Rule method) (eBCSgen.TS.VectorReaction.VectorReaction method) MathMLtransformer (class in eBCSgen.Core.Rate) Memory (class in eBCSgen.TS.State) Model (class in eBCSgen.Core.Model) model() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) model_checking() (eBCSgen.Analysis.CTL.CTL static method) (eBCSgen.Analysis.PCTL.PCTL static method) ModelParsingError ModelSBML (class in eBCSgen.Export.ModelSBML) module eBCSgen.Analysis.CTL eBCSgen.Analysis.PCTL eBCSgen.Core.Atomic eBCSgen.Core.Complex eBCSgen.Core.Formula eBCSgen.Core.Model eBCSgen.Core.Rate eBCSgen.Core.Reaction eBCSgen.Core.Rule eBCSgen.Core.Side eBCSgen.Core.Structure eBCSgen.Errors.ComplexOutOfScope eBCSgen.Errors.ComplexParsingError eBCSgen.Errors.FormulaParsingError eBCSgen.Errors.InvalidInputError eBCSgen.Errors.ModelParsingError eBCSgen.Errors.RatesNotSpecifiedError eBCSgen.Errors.StormNotAvailable eBCSgen.Errors.UnspecifiedParsingError eBCSgen.Export.ModelSBML eBCSgen.Parsing.ParseBCSL eBCSgen.Parsing.ParseCTLformula eBCSgen.Parsing.ParsePCTLformula eBCSgen.Regulations.Base eBCSgen.Regulations.ConcurrentFree eBCSgen.Regulations.Conditional eBCSgen.Regulations.Ordered eBCSgen.Regulations.Programmed eBCSgen.Regulations.Regular eBCSgen.TS.Edge eBCSgen.TS.State eBCSgen.TS.TransitionSystem eBCSgen.TS.TSworker eBCSgen.TS.VectorModel eBCSgen.TS.VectorReaction

most_frequent() (eBCSgen.Core.Side.Side method) Multiset (class in eBCSgen.TS.State)

N

network_free_simulation() (eBCSgen.Core.Model.Model method) NEXT() (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method) normalise() (eBCSgen.TS.Edge.Edge method)

number() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) (eBCSgen.Parsing.ParseCTLformula.TreeToStrings method) (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method)

O

observable() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) observables() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) OR() (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method)

order() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method) Ordered (class in eBCSgen.Regulations.Ordered) ordered() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method)

P

param() (eBCSgen.Core.Rate.DirectEvaluater method) (eBCSgen.Core.Rate.Evaluater method) (eBCSgen.Core.Rate.Extractor method) (eBCSgen.Core.Rate.Vectorizer method) (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) parameter_synthesis() (eBCSgen.Analysis.PCTL.PCTL static method) parse() (eBCSgen.Parsing.ParseBCSL.Parser method) (eBCSgen.Parsing.ParseCTLformula.CTLparser method) (eBCSgen.Parsing.ParsePCTLformula.PCTLparser method)

Parser (class in eBCSgen.Parsing.ParseBCSL) PCTL (class in eBCSgen.Analysis.PCTL) PCTLparser (class in eBCSgen.Parsing.ParsePCTLformula) process_output() (eBCSgen.Analysis.PCTL.PCTL static method) Programmed (class in eBCSgen.Regulations.Programmed) programmed() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method)

R

Rate (class in eBCSgen.Core.Rate) rate() (eBCSgen.Core.Rate.MathMLtransformer method) rate_agent() (eBCSgen.Core.Rate.DirectEvaluater method) (eBCSgen.Core.Rate.MathMLtransformer method) (eBCSgen.Core.Rate.Vectorizer method) rate_complex() (eBCSgen.Parsing.ParseBCSL.TreeToComplex method) rate_to_vector() (eBCSgen.Core.Rule.Rule method) RatesNotSpecifiedError Reaction (class in eBCSgen.Core.Reaction) recode() (eBCSgen.TS.Edge.Edge method) (eBCSgen.TS.TransitionSystem.TransitionSystem method) reconstruct_complexes_from_match() (eBCSgen.Core.Rule.Rule method) (eBCSgen.TS.VectorReaction.VectorReaction method) reduce_context() (eBCSgen.Core.Atomic.AtomicAgent method) (eBCSgen.Core.Complex.Complex method) (eBCSgen.Core.Model.Model method) (eBCSgen.Core.Rate.Rate method) (eBCSgen.Core.Rule.Rule method) (eBCSgen.Core.Structure.StructureAgent method) Regular (class in eBCSgen.Regulations.Regular) regular() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method) regulation() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method)

regulation_def() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method) remove_nested_complex_aliases() (in module eBCSgen.Parsing.ParseBCSL) reorder() (eBCSgen.TS.State.Multiset method) (eBCSgen.TS.State.State method) (eBCSgen.TS.State.Vector method) replace() (eBCSgen.Core.Atomic.AtomicAgent method) (eBCSgen.Core.Rule.Rule method) (eBCSgen.Core.Structure.StructureAgent method) (eBCSgen.Parsing.ParseBCSL.Parser method) (eBCSgen.Parsing.ParseCTLformula.CTLparser method) (eBCSgen.Parsing.ParsePCTLformula.PCTLparser method) (eBCSgen.TS.VectorReaction.VectorReaction method) replace_APs() (eBCSgen.Core.Formula.Formula method) replace_complexes() (eBCSgen.Core.Formula.Formula method) ReplaceVariables (class in eBCSgen.Parsing.ParseBCSL) Result (class in eBCSgen.Parsing.ParseBCSL) revert_encoding() (eBCSgen.TS.TransitionSystem.TransitionSystem method) Rule (class in eBCSgen.Core.Rule) rule() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) rules() (eBCSgen.Parsing.ParseBCSL.ExtractComplexNames method) (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) run() (eBCSgen.TS.TSworker.TSworker method)

S

save_to_json() (eBCSgen.TS.TransitionSystem.TransitionSystem method) save_to_prism() (eBCSgen.TS.TransitionSystem.TransitionSystem method) save_to_STORM_explicit() (eBCSgen.TS.TransitionSystem.TransitionSystem method) set_hell() (eBCSgen.TS.State.Multiset method) (eBCSgen.TS.State.Vector method) set_initial_amounts() (eBCSgen.Export.ModelSBML.ModelSBML method) set_species_feature() (eBCSgen.Export.ModelSBML.ModelSBML method) Side (class in eBCSgen.Core.Side) side() (eBCSgen.Parsing.ParseBCSL.TreeToObjects method) SideHelper (class in eBCSgen.Parsing.ParseBCSL) sign() (eBCSgen.Parsing.ParseCTLformula.TreeToStrings method) (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method)

sign_ap() (eBCSgen.Parsing.ParseCTLformula.TreeToStrings method) (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method) State (class in eBCSgen.TS.State) state() (eBCSgen.Parsing.ParseBCSL.TreeToComplex method) static_non_reachability() (eBCSgen.Core.Model.Model method) stochastic_simulation() (eBCSgen.TS.VectorModel.VectorModel method) StormNotAvailable structure() (eBCSgen.Parsing.ParseBCSL.TreeToComplex method) structure_complex() (eBCSgen.Parsing.ParseBCSL.TransformAbstractSyntax method) StructureAgent (class in eBCSgen.Core.Structure) successors() (eBCSgen.Parsing.ParseBCSL.TransformRegulations method) SymbolicAgents (class in eBCSgen.Core.Rate) syntax_check() (eBCSgen.Parsing.ParseBCSL.Parser method)

T

to_counter() (eBCSgen.Core.Side.Side method) to_dict() (eBCSgen.TS.Edge.Edge method) to_kripke() (eBCSgen.TS.TransitionSystem.TransitionSystem method) to_list_of_strings() (eBCSgen.Core.Side.Side method) to_mathML() (eBCSgen.Core.Rate.Rate method) to_multiset() (eBCSgen.TS.State.Vector method) to_ODE_string() (eBCSgen.TS.State.Vector method) to_PRISM_code() (eBCSgen.Core.Complex.Complex method) to_PRISM_string() (eBCSgen.TS.Edge.Edge method) (eBCSgen.TS.State.State method) to_reaction() (eBCSgen.Core.Rule.Rule method) to_SBML_species_code() (eBCSgen.Core.Complex.Complex method) to_SBML_speciesTypes_code() (eBCSgen.Core.Complex.Complex method) to_side() (eBCSgen.Parsing.ParseBCSL.SideHelper method) to_symbolic() (eBCSgen.Core.Rate.Rate method) (eBCSgen.TS.VectorReaction.VectorReaction method)

to_vector() (eBCSgen.Core.Reaction.Reaction method) (eBCSgen.Core.Side.Side method) (eBCSgen.TS.Edge.Edge method) (eBCSgen.TS.State.Multiset method) (eBCSgen.TS.State.State method) to_vector_model() (eBCSgen.Core.Model.Model method) transform() (eBCSgen.Parsing.ParseBCSL.Parser method) TransformAbstractSyntax (class in eBCSgen.Parsing.ParseBCSL) TransformRegulations (class in eBCSgen.Parsing.ParseBCSL) TransitionSystem (class in eBCSgen.TS.TransitionSystem) transitive_closure() (eBCSgen.Regulations.Ordered.Ordered method) TreeToComplex (class in eBCSgen.Parsing.ParseBCSL) TreeToObjects (class in eBCSgen.Parsing.ParseBCSL) TreeToStrings (class in eBCSgen.Parsing.ParseCTLformula) (class in eBCSgen.Parsing.ParsePCTLformula) truncate() (in module eBCSgen.TS.Edge) TSworker (class in eBCSgen.TS.TSworker)

U

UnspecifiedParsingError UNTIL() (eBCSgen.Parsing.ParsePCTLformula.TreeToStrings method)

update_memory() (eBCSgen.TS.State.Memory method) update_state() (eBCSgen.TS.State.State method)

V

validate_bound() (eBCSgen.TS.State.Multiset method) (eBCSgen.TS.State.Vector method) VAR() (eBCSgen.Parsing.ParseBCSL.ReplaceVariables method) Vector (class in eBCSgen.TS.State)

VectorConditional (class in eBCSgen.Regulations.Conditional) vectorize() (eBCSgen.Core.Rate.Rate method) Vectorizer (class in eBCSgen.Core.Rate) VectorModel (class in eBCSgen.TS.VectorModel) VectorReaction (class in eBCSgen.TS.VectorReaction)