eBCSgen
- Analysis
- Core
- Atomic
- 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
- 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
- Reaction
- 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
- Structure
- Errors
- 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()
- ModelSBML
- Parsing
- ParseBCSL
ExtractComplexNames
Parser
ReplaceVariables
Result
SideHelper
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
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
- ParsePCTLformula
- ParseBCSL
- Regulations
- TS
- Edge
- State
- TSworker
- 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
- VectorReaction