eBCSgen

• Analysis
  • CTL
    • CTL
      • CTL.model_checking()
  • PCTL
    • PCTL
      • PCTL.model_checking()
      • PCTL.parameter_synthesis()
      • PCTL.process_output()
    • call_storm()
• Core
  • Atomic
    • AtomicAgent
      • AtomicAgent.add_context()
      • AtomicAgent.compatible()
      • AtomicAgent.extend_signature()
      • AtomicAgent.reduce_context()
      • AtomicAgent.replace()
  • Complex
    • Complex
      • Complex.align_match()
      • Complex.compatible()
      • Complex.create_all_compatible()
      • Complex.extend_signature()
      • Complex.get_agent_names()
      • Complex.get_atomic_names()
      • Complex.identify_compatible()
      • Complex.is_composed()
      • Complex.reduce_context()
      • Complex.to_PRISM_code()
      • Complex.to_SBML_speciesTypes_code()
      • Complex.to_SBML_species_code()
    • align_agents()
  • Formula
    • APextractor
      • APextractor.ap()
    • APreplacetor
      • APreplacetor.ap()
    • AtomicProposition
    • ComplexReplacetor
      • ComplexReplacetor.ap()
    • Formula
      • Formula.create_complex_labels()
      • Formula.get_APs()
      • Formula.get_complexes()
      • Formula.replace_APs()
      • Formula.replace_complexes()
  • Model
    • Model
      • Model.check_rates()
      • Model.compute_bound()
      • Model.create_ordering()
      • Model.create_unique_complexes_and_params()
      • Model.eliminate_redundant()
      • Model.export_sbml()
      • Model.extract_signatures()
      • Model.generate_direct_transition_system()
      • Model.network_free_simulation()
      • Model.reduce_context()
      • Model.static_non_reachability()
      • Model.to_vector_model()
  • Rate
    • ContextReducer
      • ContextReducer.agent()
    • DirectEvaluater
      • DirectEvaluater.agent()
      • DirectEvaluater.param()
      • DirectEvaluater.rate_agent()
    • Evaluater
      • Evaluater.agent()
      • Evaluater.param()
    • Extractor
      • Extractor.agent()
      • Extractor.param()
    • MathMLtransformer
      • MathMLtransformer.fix_operator()
      • MathMLtransformer.fun()
      • MathMLtransformer.rate()
      • MathMLtransformer.rate_agent()
    • Rate
      • Rate.evaluate()
      • Rate.evaluate_direct()
      • Rate.get_formula_in_list()
      • Rate.get_params_and_agents()
      • Rate.reduce_context()
      • Rate.to_mathML()
      • Rate.to_symbolic()
      • Rate.vectorize()
    • SymbolicAgents
      • SymbolicAgents.agent()
    • Vectorizer
      • Vectorizer.agent()
      • Vectorizer.param()
      • Vectorizer.rate_agent()
  • Reaction
    • Reaction
      • Reaction.compatible()
      • Reaction.create_all_compatible()
      • Reaction.to_vector()
  • Rule
    • Rule
      • Rule.compatible()
      • Rule.create_all_compatible()
      • Rule.create_complexes()
      • Rule.create_reactions()
      • Rule.create_reversible()
      • Rule.evaluate_rate()
      • Rule.exists_compatible_agent()
      • Rule.get_unique_complexes_from_rule()
      • Rule.is_meaningful()
      • Rule.match()
      • Rule.rate_to_vector()
      • Rule.reconstruct_complexes_from_match()
      • Rule.reduce_context()
      • Rule.replace()
      • Rule.to_reaction()
    • column()
    • find_all_matches()
  • Side
    • Side
      • Side.compatible()
      • Side.create_all_compatible()
      • Side.exists_compatible_agent()
      • Side.most_frequent()
      • Side.to_counter()
      • Side.to_list_of_strings()
      • Side.to_vector()
  • Structure
    • StructureAgent
      • StructureAgent.add_context()
      • StructureAgent.compatible()
      • StructureAgent.extend_signature()
      • StructureAgent.reduce_context()
      • StructureAgent.replace()
• Errors
  • ComplexOutOfScope
    • ComplexOutOfScope
  • ComplexParsingError
    • ComplexParsingError
  • FormulaParsingError
    • FormulaParsingError
  • InvalidInputError
    • InvalidInputError
  • ModelParsingError
    • ModelParsingError
  • RatesNotSpecifiedError
    • RatesNotSpecifiedError
  • StormNotAvailable
    • StormNotAvailable
  • UnspecifiedParsingError
    • UnspecifiedParsingError
• Export
  • ModelSBML
    • ModelSBML
      • ModelSBML.create_all_reactions()
      • ModelSBML.create_all_species_compartments_and_complex_species_types()
      • ModelSBML.create_basic_species_types()
      • ModelSBML.create_compartment()
      • ModelSBML.create_kinetic_law_and_modifiers()
      • ModelSBML.create_parameters()
      • ModelSBML.create_products()
      • ModelSBML.create_reactants()
      • ModelSBML.create_reaction_for_isomorphisms()
      • ModelSBML.create_species()
      • ModelSBML.create_species_feature_type()
      • ModelSBML.create_species_features()
      • ModelSBML.create_species_type_from_complex()
      • ModelSBML.create_species_types_from_atomic()
      • ModelSBML.create_species_types_from_structure()
      • ModelSBML.set_initial_amounts()
      • ModelSBML.set_species_feature()
• Parsing
  • ParseBCSL
    • ExtractComplexNames
      • ExtractComplexNames.cmplx_dfn()
      • ExtractComplexNames.rules()
    • Parser
      • Parser.parse()
      • Parser.replace()
      • Parser.syntax_check()
      • Parser.transform()
    • ReplaceVariables
      • ReplaceVariables.VAR()
    • Result
    • SideHelper
      • SideHelper.to_side()
    • TransformAbstractSyntax
      • TransformAbstractSyntax.abstract_sequence()
      • TransformAbstractSyntax.atomic_complex()
      • TransformAbstractSyntax.atomic_structure_complex()
      • TransformAbstractSyntax.cmplx_name()
      • TransformAbstractSyntax.complex()
      • TransformAbstractSyntax.get_name()
      • TransformAbstractSyntax.insert_atomic_to_complex()
      • TransformAbstractSyntax.insert_atomic_to_struct()
      • TransformAbstractSyntax.insert_struct_to_complex()
      • TransformAbstractSyntax.is_empty()
      • TransformAbstractSyntax.structure_complex()
    • TransformRegulations
      • TransformRegulations.concurrent_free()
      • TransformRegulations.conditional()
      • TransformRegulations.context()
      • TransformRegulations.order()
      • TransformRegulations.ordered()
      • TransformRegulations.programmed()
      • TransformRegulations.regular()
      • TransformRegulations.regulation()
      • TransformRegulations.regulation_def()
      • TransformRegulations.successors()
    • TreeToComplex
      • TreeToComplex.atomic()
      • TreeToComplex.compartment()
      • TreeToComplex.rate_complex()
      • TreeToComplex.state()
      • TreeToComplex.structure()
    • TreeToObjects
      • TreeToObjects.const()
      • TreeToObjects.def_param()
      • TreeToObjects.definitions()
      • TreeToObjects.init()
      • TreeToObjects.inits()
      • TreeToObjects.label()
      • TreeToObjects.model()
      • TreeToObjects.number()
      • TreeToObjects.observable()
      • TreeToObjects.observables()
      • TreeToObjects.param()
      • TreeToObjects.rule()
      • TreeToObjects.rules()
      • TreeToObjects.side()
    • load_TS_from_json()
    • remove_nested_complex_aliases()
  • ParseCTLformula
    • CTLparser
      • CTLparser.grammar
      • CTLparser.parse()
      • CTLparser.replace()
    • TreeToStrings
      • TreeToStrings.agent()
      • TreeToStrings.ap()
      • TreeToStrings.number()
      • TreeToStrings.sign()
      • TreeToStrings.sign_ap()
  • ParsePCTLformula
    • PCTLparser
      • PCTLparser.parse()
      • PCTLparser.replace()
    • TreeToStrings
      • TreeToStrings.AND()
      • TreeToStrings.FUTURE()
      • TreeToStrings.LB()
      • TreeToStrings.NEXT()
      • TreeToStrings.OR()
      • TreeToStrings.UNTIL()
      • TreeToStrings.agent()
      • TreeToStrings.ap()
      • TreeToStrings.number()
      • TreeToStrings.sign()
      • TreeToStrings.sign_ap()
• Regulations
  • Base
    • BaseRegulation
      • BaseRegulation.filter()
  • ConcurrentFree
    • ConcurrentFree
      • ConcurrentFree.check_labels()
      • ConcurrentFree.filter()
  • Conditional
    • Conditional
      • Conditional.check_intersection()
      • Conditional.check_labels()
      • Conditional.filter()
    • VectorConditional
      • VectorConditional.check_intersection()
      • VectorConditional.filter()
  • Ordered
    • Ordered
      • Ordered.check_labels()
      • Ordered.filter()
      • Ordered.transitive_closure()
  • Programmed
    • Programmed
      • Programmed.check_labels()
      • Programmed.filter()
  • Regular
    • Regular
      • Regular.check_labels()
      • Regular.filter()
• TS
  • Edge
    • Edge
      • Edge.add_rate()
      • Edge.encode()
      • Edge.normalise()
      • Edge.recode()
      • Edge.to_PRISM_string()
      • Edge.to_dict()
      • Edge.to_vector()
    • edge_from_dict()
    • truncate()
  • State
    • Memory
      • Memory.update_memory()
    • Multiset
      • Multiset.check_intersection()
      • Multiset.reorder()
      • Multiset.set_hell()
      • Multiset.to_vector()
      • Multiset.validate_bound()
    • State
      • State.check_AP()
      • State.check_intersection()
      • State.reorder()
      • State.to_PRISM_string()
      • State.to_vector()
      • State.update_state()
    • Vector
      • Vector.check_intersection()
      • Vector.filter_values()
      • Vector.reorder()
      • Vector.set_hell()
      • Vector.to_ODE_string()
      • Vector.to_multiset()
      • Vector.validate_bound()
  • TSworker
    • TSworker
      • TSworker.join()
      • TSworker.run()
  • TransitionSystem
    • TransitionSystem
      • TransitionSystem.change_hell()
      • TransitionSystem.change_to_vector_backend()
      • TransitionSystem.create_AP_labels()
      • TransitionSystem.decode()
      • TransitionSystem.edges_to_PRISM()
      • TransitionSystem.encode()
      • TransitionSystem.encode_edges()
      • TransitionSystem.filter_unused_agents()
      • TransitionSystem.recode()
      • TransitionSystem.revert_encoding()
      • TransitionSystem.save_to_STORM_explicit()
      • TransitionSystem.save_to_json()
      • TransitionSystem.save_to_prism()
      • TransitionSystem.to_kripke()
    • create_indices()
  • VectorModel
    • VectorModel
      • VectorModel.compute_bound()
      • VectorModel.deterministic_simulation()
      • VectorModel.generate_transition_system()
      • VectorModel.stochastic_simulation()
    • fake_expovariate()
    • handle_number_of_threads()
  • VectorReaction
    • VectorReaction
      • VectorReaction.evaluate_rate()
      • VectorReaction.match()
      • VectorReaction.reconstruct_complexes_from_match()
      • VectorReaction.replace()
      • VectorReaction.to_symbolic()