Index

A

abstract() (funman.model.petrinet.GeneratedPetriNetModel method) add_assertion() (funman.search.box_search.FormulaStack method) (funman.search.box_search.FormulaStackFrame method) add_handler() (in module funman.utils.logging) add_log_level() (in module funman.utils.logging) add_point() (funman.representation.box.Box method) add_result() (funman.server.storage.Storage method) additional_time (funman.server.query.FunmanResultsTiming attribute) additive_bounds (funman.representation.constraint.LinearConstraint attribute)

advance() (funman.representation.box.Box method) AnalysisScenarioResult (class in funman.scenario.scenario) append_result() (funman.representation.parameter_space.ParameterSpace method) approximate() (funman.translate.simplifier.FUNMANSimplifier method) arg_magnitude() (funman.translate.simplifier.FUNMANSimplifier method) assume() (funman.translate.encoding.FlatEncoding method) (funman.translate.translate.LayeredEncoding method) at_end (funman.model.query.QueryEquals attribute) (funman.model.query.QueryGE attribute) (funman.model.query.QueryLE attribute)

B

bilayer (funman.model.bilayer.BilayerModel attribute) bound_symbols (funman.utils.sympy_utils.SympyBoundedSubstituter attribute) bounds (funman.representation.box.Box attribute) box_to_smt() (funman.translate.translate.Encoder method)

boxes() (funman.representation.parameter_space.ParameterSpace method) BoxSearch (class in funman.search.box_search) build_formula() (funman.search.simulator_check.SimulatorCheck method) (funman.search.smt_check.SMTCheck method)

C

calculate_normalization_constant() (funman.model.bilayer.BilayerModel method) (funman.model.ensemble.EnsembleModel method) (funman.model.model.FunmanModel method) (funman.model.petrinet.AbstractPetriNetModel method) can_encode() (funman.translate.bilayer.BilayerEncoder method) (funman.translate.translate.Encoder method) check_assumptions() (funman.representation.explanation.BoxExplanation method) (funman.representation.explanation.Explanation method) check_simulation() (funman.scenario.scenario.AnalysisScenario method) check_unique_names() (funman.server.query.FunmanWorkRequest class method) check_use_compartmental_constraints() (funman.config.FUNMANConfig method) claim_id() (funman.server.storage.Storage method) close() (funman.utils.handlers.NoopResultHandler method) (funman.utils.handlers.ResultCombinedHandler method) (funman.utils.handlers.ResultHandler method) closed_upper_bound (funman.representation.interval.Interval attribute) columns (funman.representation.representation.Timeseries attribute) compare() (funman.representation.parameter_space.ParameterSpace static method) compartmental_constraint_noise (funman.config.FUNMANConfig attribute) compartmental_constraints() (funman.model.model.FunmanModel method) (funman.model.petrinet.AbstractPetriNetModel method) compute_assignment() (funman.search.box_search.FormulaStack method) compute_observables() (funman.scenario.scenario.AnalysisScenario method) config (funman.search.search.SearchEpisode attribute) (funman.server.query.FunmanWorkRequest attribute) (funman.translate.bilayer.BilayerEncoder attribute) (funman.translate.decapode.DecapodeEncoder attribute) (funman.translate.encoded.EncodedEncoder attribute) (funman.translate.ensemble.EnsembleEncoder attribute) (funman.translate.regnet.RegnetEncoder attribute) (funman.translate.translate.DefaultEncoder attribute) (funman.translate.translate.Encoder attribute)

consistent (funman.scenario.consistency.ConsistencyScenarioResult attribute) consistent() (funman.representation.parameter_space.ParameterSpace method) constraint (funman.representation.assumption.Assumption attribute) constraint_noise (funman.config.FUNMANConfig attribute) constraints (funman.scenario.scenario.AnalysisScenario attribute) (funman.server.query.FunmanWorkRequest attribute) construct_all_equal() (funman.representation.parameter_space.ParameterSpace static method) construct_encoding() (funman.translate.translate.LayeredEncoding method) contains() (funman.representation.box.Box method) (funman.representation.interval.Interval method) contains_point() (funman.representation.box.Box method) contains_time() (funman.representation.constraint.TimedConstraint method) contains_value() (funman.representation.interval.Interval method) contract_model() (funman.server.query.FunmanResults method) contract_parameters() (funman.model.petrinet.GeneratedPetriNetModel method) contracted_model (funman.server.query.FunmanResults attribute) corner_points (funman.config.FUNMANConfig attribute) (funman.representation.box.Box attribute) corners() (funman.representation.box.Box method) coverage_of_representable_space (funman.server.query.FunmanProgress attribute) coverage_of_search_space (funman.server.query.FunmanProgress attribute) create_plots() (funman.api.run.Runner method) current_step() (funman.representation.box.Box method) custom_openapi() (in module funman.api.api)

D

data (funman.representation.representation.Timeseries attribute) data_path (funman.api.settings.Settings attribute) dataframe() (funman.representation.representation.Timeseries method) (funman.scenario.consistency.ConsistencyScenarioResult method) (funman.server.query.FunmanResults method) decapode (funman.model.decapode.DecapodeModel attribute) decode_labeled_object() (funman.representation.parameter_space.ParameterSpace static method) default_encoder() (funman.model.bilayer.BilayerModel method) (funman.model.decapode.DecapodeModel method) (funman.model.encoded.EncodedModel method) (funman.model.ensemble.EnsembleModel method) (funman.model.petrinet.GeneratedPetriNetModel method) (funman.model.petrinet.PetrinetModel method) (funman.model.regnet.AbstractRegnetModel method) (funman.model.simulator.SimulatorModel method) denormalize() (funman.representation.representation.Point method)

derivative (funman.representation.constraint.LinearConstraint attribute) derivative() (funman.model.petrinet.AbstractPetriNetModel method) description (funman.model.generated_models.petrinet.Header attribute) (funman.model.generated_models.petrinet.Parameter attribute) (funman.model.generated_models.petrinet.Properties attribute) (funman.model.generated_models.petrinet.State attribute) (funman.model.generated_models.regnet.Header attribute) (funman.model.generated_models.regnet.Parameter attribute) disjoint() (funman.representation.interval.Interval method) distribution (funman.model.generated_models.petrinet.Parameter attribute) (funman.model.generated_models.regnet.Parameter attribute) div() (in module funman.utils.math_utils) done (funman.server.query.FunmanResults attribute) dreal_log_level (funman.config.FUNMANConfig attribute) dreal_mcts (funman.config.FUNMANConfig attribute) dreal_precision (funman.config.FUNMANConfig attribute) dreal_prefer_parameters (funman.config.FUNMANConfig attribute)

E

edges (funman.model.generated_models.regnet.Model1 attribute) elapsed_timer() (funman.api.run.Runner method) empty_volume_ok (funman.scenario.consistency.ConsistencyScenario attribute) (funman.scenario.scenario.AnalysisScenario attribute) encodable() (funman.representation.constraint.Constraint method) (funman.representation.constraint.ParameterConstraint method) encode_assumed_constraint() (funman.translate.translate.Encoder method) encode_assumption() (funman.translate.translate.Encoder method) encode_assumptions() (funman.translate.translate.Encoder method) encode_constraint() (funman.translate.translate.Encoder method) encode_init_layer() (funman.translate.translate.Encoder method) encode_linear_constraint() (funman.translate.translate.Encoder method) encode_model() (funman.translate.bilayer.BilayerEncoder method) (funman.translate.decapode.DecapodeEncoder method) (funman.translate.encoded.EncodedEncoder method) (funman.translate.ensemble.EnsembleEncoder method) (funman.translate.petrinet.PetrinetEncoder method) (funman.translate.regnet.RegnetEncoder method) encode_model_layer() (funman.translate.encoded.EncodedEncoder method) (funman.translate.translate.Encoder method) encode_model_timed() (funman.translate.encoded.EncodedEncoder method) (funman.translate.translate.Encoder method) encode_observation() (funman.translate.bilayer.BilayerEncoder method) (funman.translate.ensemble.EnsembleEncoder method) (funman.translate.petrinet.PetrinetEncoder method) encode_parameter() (funman.translate.translate.Encoder method) encode_query_layer() (funman.translate.translate.Encoder method) encode_timeseries() (funman.translate.translate.Encoder method) encode_timeseries_verification() (funman.scenario.scenario.AnalysisScenario method) encode_transition_layer() (funman.translate.translate.Encoder method)

encoding() (funman.translate.encoding.FlatEncoding method) encoding_step_activation_formula() (funman.search.box_search.BoxSearch method) encoding_time (funman.server.query.FunmanResultsTiming attribute) end_time (funman.server.query.FunmanResultsTiming attribute) enqueue_work() (funman.server.worker.FunmanWorker method) equal() (funman.representation.box.Box method) error (funman.server.query.FunmanResults attribute) error_message (funman.server.query.FunmanResults attribute) ERRORED (funman.server.worker.WorkerState attribute) eval_point() (funman.search.simulator_check.SimulatorCheck method) exception (funman.scenario.scenario.AnalysisScenarioResultException attribute) exit_gracefully() (funman.api.run.GracefulKiller method) expand() (funman.search.simulator_check.SimulatorCheck method) (funman.search.smt_check.SMTCheck method) explain() (funman.representation.box.Box method) (funman.representation.explanation.BoxExplanation method) (funman.representation.explanation.Explanation method) (funman.representation.parameter_space.ParameterSpace method) (funman.server.query.FunmanResults method) explanation (funman.representation.box.Box attribute) expression (funman.model.generated_models.petrinet.Initial attribute) (funman.model.generated_models.petrinet.Observable attribute) (funman.model.generated_models.petrinet.Rate attribute) (funman.model.generated_models.petrinet.Unit attribute) (funman.representation.explanation.Explanation attribute) (funman.representation.explanation.TimeoutExplanation attribute) expression_mathml (funman.model.generated_models.petrinet.Initial attribute) (funman.model.generated_models.petrinet.Observable attribute) (funman.model.generated_models.petrinet.Rate attribute) (funman.model.generated_models.petrinet.Unit attribute)

F

false_boxes (funman.representation.parameter_space.ParameterSpace attribute) false_explanations (funman.representation.explanation.ParameterSpaceExplanation attribute) false_points() (funman.representation.box.Box method) (funman.representation.parameter_space.ParameterSpace method) finalize() (funman.server.query.FunmanResultsTiming method) finalize_result() (funman.server.query.FunmanResults method) finalize_result_as_error() (funman.server.query.FunmanResults method) finite() (funman.representation.box.Box method) (funman.representation.interval.Interval method) flux (funman.model.bilayer.BilayerMeasurement attribute) formula_stack (funman.search.box_search.FormulaStack attribute) formulate_bounds() (funman.model.petrinet.GeneratedPetriNetModel method) from_point() (funman.representation.box.Box static method) from_steps() (funman.representation.encoding_schedule.EncodingSchedule static method) from_value() (funman.representation.interval.Interval static method) function (funman.model.query.QueryFunction attribute) funman module Funman (class in funman.funman) funman.api module funman.api.api module funman.api.client module funman.api.run module funman.api.server module funman.api.settings module funman.config module funman.constants module funman.funman module funman.model module funman.model.bilayer module funman.model.decapode module funman.model.encoded module funman.model.ensemble module funman.model.generated_models module funman.model.generated_models.petrinet module funman.model.generated_models.regnet module funman.model.model module funman.model.petrinet module funman.model.query module funman.model.regnet module funman.model.simulator module funman.representation module funman.representation.assumption module funman.representation.box module funman.representation.constraint module funman.representation.encoding_schedule module funman.representation.explanation module funman.representation.interval module funman.representation.parameter module funman.representation.parameter_space module

funman.representation.representation module funman.representation.symbol module funman.scenario module funman.scenario.consistency module funman.scenario.parameter_synthesis module funman.scenario.scenario module funman.scenario.simulation module funman.search module funman.search.box_search module funman.search.search module funman.search.simulate module funman.search.simulator_check module funman.search.smt_check module funman.server module funman.server.exception module funman.server.query module funman.server.storage module funman.server.worker module funman.translate module funman.translate.bilayer module funman.translate.decapode module funman.translate.encoded module funman.translate.encoding module funman.translate.ensemble module funman.translate.petrinet module funman.translate.regnet module funman.translate.simplifier module funman.translate.translate module funman.utils module funman.utils.handlers module funman.utils.logging module funman.utils.math_utils module funman.utils.smtlib_utils module funman.utils.sympy_utils module funman_admin_token (funman.api.settings.Settings attribute) funman_api_token (funman.api.settings.Settings attribute) funman_base_url (funman.api.settings.Settings attribute) FunmanException FUNMANFormulaManager (class in funman.utils.sympy_utils) FUNMANSimplifier (class in funman.translate.simplifier) FUNMANSmtDagPrinter (class in funman.utils.smtlib_utils) FUNMANSmtLibScript (class in funman.utils.smtlib_utils) FUNMANSmtPrinter (class in funman.utils.smtlib_utils) FunmanWorker (class in funman.server.worker) FunmanWorkerException

G

get_args() (in module funman.api.run) get_box_corners() (funman.search.box_search.BoxSearch method) get_candiate_point() (funman.search.box_search.BoxSearchEpisode method) get_candidate_boxes_for_point() (funman.search.box_search.BoxSearchEpisode method) get_current() (funman.server.worker.FunmanWorker method) (in module funman.api.api) get_kind() (funman.scenario.consistency.ConsistencyScenario class method) (funman.scenario.parameter_synthesis.ParameterSynthesisScenario class method) (funman.scenario.scenario.AnalysisScenario class method) (funman.scenario.simulation.SimulationScenario class method) get_model() (funman.api.run.Runner method) get_patched_schema() (in module funman.api.client) get_queries() (in module funman.api.api) get_result() (funman.server.storage.Storage method) get_results() (funman.server.worker.FunmanWorker method) get_search() (funman.scenario.consistency.ConsistencyScenario method) (funman.scenario.parameter_synthesis.ParameterSynthesisScenario method) (funman.scenario.scenario.AnalysisScenario method)

get_state() (funman.server.worker.FunmanWorker method) get_storage() (in module funman.api.api) get_worker() (in module funman.api.api) GracefulKiller (class in funman.api.run) gradient() (funman.model.ensemble.EnsembleModel method) (funman.model.petrinet.AbstractPetriNetModel method) grounding (funman.model.generated_models.petrinet.Parameter attribute) (funman.model.generated_models.petrinet.Properties attribute) (funman.model.generated_models.petrinet.State attribute) (funman.model.generated_models.petrinet.Transition attribute) (funman.model.generated_models.regnet.BaseProperties attribute) (funman.model.generated_models.regnet.Parameter attribute) gt() (in module funman.utils.math_utils) gte() (in module funman.utils.math_utils)

H

halt() (funman.server.worker.FunmanWorker method) (in module funman.api.api)

has_reserved() (in module funman.utils.sympy_utils) header (funman.model.generated_models.petrinet.Model attribute) (funman.model.generated_models.regnet.Model attribute)

I

id (funman.model.generated_models.petrinet.Observable attribute) (funman.model.generated_models.petrinet.Parameter attribute) (funman.model.generated_models.petrinet.State attribute) (funman.model.generated_models.petrinet.Time attribute) (funman.model.generated_models.petrinet.Transition attribute) (funman.model.generated_models.regnet.Parameter attribute) (funman.model.generated_models.regnet.SignedGraphElement attribute) (funman.server.query.FunmanResults attribute) (funman.server.query.FunmanWorkUnit attribute) identical_parameters (funman.model.bilayer.BilayerModel attribute) identifiers (funman.model.generated_models.petrinet.Grounding attribute) (funman.model.generated_models.regnet.Grounding attribute) import_dreal() (funman.config.FUNMANConfig class method) in_state() (funman.server.worker.FunmanWorker method) index (funman.model.bilayer.BilayerFluxNode attribute) (funman.model.bilayer.BilayerNode attribute) (funman.model.bilayer.BilayerStateNode attribute) inherit_level() (in module funman.utils.logging) init (funman.search.simulate.Simulator attribute) init_values (funman.model.model.FunmanModel attribute) (funman.model.regnet.AbstractRegnetModel attribute) initial (funman.model.generated_models.regnet.Vertice attribute) initial_state() (funman.search.simulate.Simulator method) initial_state_tolerance (funman.config.FUNMANConfig attribute) initial_value (funman.model.bilayer.BilayerMetadata attribute) initialize() (funman.scenario.scenario.AnalysisScenario method)

initialize_encodings() (funman.translate.translate.Encoder method) initials (funman.model.generated_models.petrinet.OdeSemantics attribute) input (funman.model.generated_models.petrinet.Transition attribute) input_edges (funman.model.bilayer.BilayerMeasurement attribute) internal_error_handler() (in module funman.api.api) intersection() (funman.representation.box.Box method) (funman.representation.interval.Interval method) (funman.representation.parameter_space.ParameterSpace method) intersects() (funman.representation.box.Box method) (funman.representation.interval.Interval method) interval (funman.representation.constraint.StateVariableConstraint attribute) (funman.representation.parameter.NumSteps attribute) (funman.representation.parameter.Parameter attribute) (funman.representation.parameter.StepSize attribute) (funman.representation.parameter.StructureParameter attribute) interval_to_smt() (funman.translate.translate.Encoder method) invoke_solver() (funman.search.search.Search method) is_final() (funman.server.query.FunmanResults method) is_observable() (in module funman.model.model) is_point() (funman.representation.interval.Interval method) is_processing_id() (funman.server.worker.FunmanWorker method) is_state_variable() (in module funman.model.model) is_synthesized() (funman.representation.parameter.LabeledParameter method) (funman.representation.parameter.StructureParameter method) is_timed_observable() (funman.model.petrinet.GeneratedPetriNetModel method) is_unbound() (funman.representation.interval.Interval method) (funman.representation.parameter.Parameter method)

J

json_graph (funman.model.bilayer.BilayerGraph attribute) (funman.model.decapode.DecapodeDynamics attribute) (funman.model.petrinet.PetrinetDynamics attribute) (funman.model.regnet.RegnetDynamics attribute)

K

kill_now (funman.api.run.GracefulKiller attribute)

L

label (funman.representation.box.Box attribute) (funman.representation.parameter.LabeledParameter attribute) (funman.representation.parameter.NumSteps attribute) (funman.representation.parameter.StepSize attribute) (funman.representation.parameter.StructureParameter attribute) (funman.representation.representation.Point attribute) labeled_volume() (funman.representation.parameter_space.ParameterSpace method)

last_boxes() (funman.representation.parameter_space.ParameterSpace method) lb (funman.model.bilayer.BilayerMetadata attribute) (funman.model.query.QueryGE attribute) (funman.representation.interval.Interval attribute) lifespan() (in module funman.api.api) lt() (in module funman.utils.math_utils) lte() (in module funman.utils.math_utils)

M

main() (in module funman.api.run) main_fn (funman.model.simulator.SimulatorModel attribute) make_client() (in module funman.api.client) map (funman.model.generated_models.petrinet.TypingSemantics attribute) max_true_volume() (funman.representation.parameter_space.ParameterSpace method) maximize() (funman.utils.sympy_utils.SympyBoundedSubstituter method) measurements (funman.model.bilayer.BilayerModel attribute) meets() (funman.representation.interval.Interval method) metadata (funman.model.bilayer.BilayerFluxNode attribute) (funman.model.bilayer.BilayerNode attribute) (funman.model.bilayer.BilayerStateNode attribute) (funman.model.generated_models.petrinet.Model attribute) (funman.model.generated_models.regnet.Model attribute) midpoint() (funman.representation.interval.Interval method) minimize() (funman.utils.sympy_utils.SympyBoundedSubstituter method) minus() (in module funman.utils.math_utils) mode (funman.config.FUNMANConfig attribute) model (funman.model.generated_models.petrinet.Model attribute) (funman.model.generated_models.regnet.Model attribute) (funman.model.query.Query attribute) (funman.model.query.QueryTrue attribute) (funman.representation.constraint.ModelConstraint attribute) (funman.representation.symbol.ModelSymbol attribute) (funman.scenario.scenario.AnalysisScenario attribute) (funman.scenario.simulation.SimulationScenario attribute) (funman.search.simulate.Simulator attribute) (funman.server.query.FunmanResults attribute) (funman.server.query.FunmanWorkUnit attribute) model_args() (funman.search.simulate.Simulator method) model_parameters() (funman.scenario.scenario.AnalysisScenario method) model_post_init() (funman.config.FUNMANConfig method) (funman.model.bilayer.BilayerDynamics method) (funman.model.bilayer.BilayerGraph method) (funman.model.bilayer.BilayerMeasurement method) (funman.model.bilayer.BilayerModel method) (funman.model.decapode.DecapodeModel method) (funman.model.encoded.EncodedModel method) (funman.model.ensemble.EnsembleModel method) (funman.model.model.FunmanModel method) (funman.model.petrinet.AbstractPetriNetModel method) (funman.model.petrinet.GeneratedPetriNetModel method) (funman.model.petrinet.PetrinetModel method) (funman.model.query.QueryEncoded method) (funman.model.regnet.AbstractRegnetModel method) (funman.model.regnet.GeneratedRegnetModel method) (funman.model.regnet.RegnetModel method) (funman.model.simulator.SimulatorModel method) (funman.representation.box.Box method) (funman.representation.constraint.Constraint method) (funman.representation.constraint.LinearConstraint method) (funman.representation.constraint.ModelConstraint method) (funman.representation.constraint.ParameterConstraint method) (funman.representation.constraint.QueryConstraint method) (funman.representation.constraint.StateVariableConstraint method) (funman.representation.constraint.TimedConstraint method) (funman.representation.constraint.TimeseriesConstraint method) (funman.representation.parameter.LabeledParameter method) (funman.representation.parameter.ModelParameter method) (funman.representation.parameter.NumSteps method) (funman.representation.parameter.Parameter method) (funman.representation.parameter.Schedules method) (funman.representation.parameter.StepSize method) (funman.representation.parameter.StructureParameter method) (funman.scenario.consistency.ConsistencyScenario method) (funman.scenario.consistency.ConsistencyScenarioResult method) (funman.scenario.parameter_synthesis.ParameterSynthesisScenario method) (funman.scenario.scenario.AnalysisScenario method) (funman.scenario.simulation.SimulationScenario method) (funman.search.box_search.BoxSearchEpisode method) (funman.search.box_search.BoxSearchEpisodeMP method) (funman.search.box_search.FormulaStack method) (funman.search.box_search.FormulaStackFrame method) (funman.search.search.SearchEpisode method) (funman.search.search.SearchStaticsMP method) (funman.search.search.SearchStatistics method) (funman.server.query.FunmanResults method) (funman.translate.bilayer.BilayerEncoder method) (funman.translate.decapode.DecapodeEncoder method) (funman.translate.encoded.EncodedEncoder method) (funman.translate.encoding.Encoding method) (funman.translate.encoding.FlatEncoding method) (funman.translate.ensemble.EnsembleEncoder method) (funman.translate.petrinet.PetrinetEncoder method) (funman.translate.regnet.RegnetEncoder method) (funman.translate.translate.DefaultEncoder method) (funman.translate.translate.Encoder method) (funman.translate.translate.LayeredEncoding method)

model_to_dict() (in module funman.utils.smtlib_utils) model_version (funman.model.generated_models.petrinet.Header attribute) (funman.model.generated_models.regnet.Header attribute) models (funman.model.ensemble.EnsembleModel attribute) modifiers (funman.model.generated_models.petrinet.Grounding attribute) (funman.model.generated_models.regnet.Grounding attribute) module funman funman.api funman.api.api funman.api.client funman.api.run funman.api.server funman.api.settings funman.config funman.constants funman.funman funman.model funman.model.bilayer funman.model.decapode funman.model.encoded funman.model.ensemble funman.model.generated_models funman.model.generated_models.petrinet funman.model.generated_models.regnet funman.model.model funman.model.petrinet funman.model.query funman.model.regnet funman.model.simulator funman.representation funman.representation.assumption funman.representation.box funman.representation.constraint funman.representation.encoding_schedule funman.representation.explanation funman.representation.interval funman.representation.parameter funman.representation.parameter_space funman.representation.representation funman.representation.symbol funman.scenario funman.scenario.consistency funman.scenario.parameter_synthesis funman.scenario.scenario funman.scenario.simulation funman.search funman.search.box_search funman.search.search funman.search.simulate funman.search.simulator_check funman.search.smt_check funman.server funman.server.exception funman.server.query funman.server.storage funman.server.worker funman.translate funman.translate.bilayer funman.translate.decapode funman.translate.encoded funman.translate.encoding funman.translate.ensemble funman.translate.petrinet funman.translate.regnet funman.translate.simplifier funman.translate.translate funman.utils funman.utils.handlers funman.utils.logging funman.utils.math_utils funman.utils.smtlib_utils funman.utils.sympy_utils

N

name (funman.model.generated_models.petrinet.Header attribute) (funman.model.generated_models.petrinet.Observable attribute) (funman.model.generated_models.petrinet.Parameter attribute) (funman.model.generated_models.petrinet.Properties attribute) (funman.model.generated_models.petrinet.State attribute) (funman.model.generated_models.regnet.BaseProperties attribute) (funman.model.generated_models.regnet.Header attribute) (funman.model.model.FunmanModel attribute) (funman.model.regnet.AbstractRegnetModel attribute) (funman.representation.constraint.Constraint attribute) (funman.representation.parameter.NumSteps attribute) (funman.representation.parameter.Parameter attribute) (funman.representation.parameter.StepSize attribute) (funman.representation.parameter.StructureParameter attribute) (funman.representation.symbol.ModelSymbol attribute) next_timestep() (funman.representation.constraint.LinearConstraint method) NoopResultHandler (class in funman.utils.handlers) normalization_constant (funman.config.FUNMANConfig attribute) (funman.scenario.scenario.AnalysisScenario attribute) (funman.translate.encoding.EncodingOptions attribute)

normalize (funman.config.FUNMANConfig attribute) (funman.translate.encoding.EncodingOptions attribute) normalize() (funman.representation.interval.Interval method) normalize_bounds() (funman.representation.interval.Interval method) (funman.representation.parameter.Parameter method) normalized (funman.representation.interval.Interval attribute) normalized_values (funman.representation.representation.Point attribute) normalized_volume() (funman.representation.box.Box method) normalized_width() (funman.representation.box.Box method) (funman.representation.interval.Interval method) NotFoundFunmanException num_dimensions (funman.representation.parameter_space.ParameterSpace attribute) num_dimensions() (funman.scenario.scenario.AnalysisScenario method) num_initial_boxes (funman.config.FUNMANConfig attribute) num_parameters() (funman.search.search.SearchEpisode method) num_steps (funman.config.FUNMANConfig attribute) num_timepoints() (funman.scenario.scenario.AnalysisScenario method) number_of_processes (funman.config.FUNMANConfig attribute)

O

observable (funman.model.bilayer.BilayerMeasurement attribute) observable_expression() (funman.model.petrinet.GeneratedPetriNetModel method) observables (funman.model.generated_models.petrinet.OdeSemantics attribute) observables() (funman.model.model.FunmanModel method) (funman.model.petrinet.GeneratedPetriNetModel method) ode (funman.model.generated_models.petrinet.Semantics attribute)

open() (funman.utils.handlers.NoopResultHandler method) (funman.utils.handlers.ResultCombinedHandler method) (funman.utils.handlers.ResultHandler method) original_width (funman.representation.interval.Interval attribute) outer_interval() (funman.representation.parameter_space.ParameterSpace method) output (funman.model.generated_models.petrinet.Transition attribute) output_edges (funman.model.bilayer.BilayerMeasurement attribute)

P

parameter (funman.model.bilayer.BilayerFluxNode attribute) (funman.model.bilayer.BilayerNode attribute) (funman.model.bilayer.BilayerStateNode attribute) (funman.representation.constraint.ParameterConstraint attribute) parameter() (funman.server.query.FunmanWorkRequest method) parameter_bounds (funman.model.model.FunmanModel attribute) (funman.model.regnet.AbstractRegnetModel attribute) parameter_space (funman.scenario.consistency.ConsistencyScenarioResult attribute) (funman.scenario.parameter_synthesis.ParameterSynthesisScenarioResult attribute) (funman.server.query.FunmanResults attribute) parameter_values() (funman.translate.translate.Encoder method) parameters (funman.model.encoded.EncodedModel attribute) (funman.model.generated_models.petrinet.Distribution attribute) (funman.model.generated_models.petrinet.OdeSemantics attribute) (funman.model.generated_models.regnet.Distribution attribute) (funman.model.generated_models.regnet.Model1 attribute) (funman.scenario.scenario.AnalysisScenario attribute) (funman.search.simulate.Simulator attribute) (funman.server.query.FunmanWorkRequest attribute) parameters_of_type() (funman.scenario.scenario.AnalysisScenario method) petrinet (funman.model.petrinet.GeneratedPetriNetModel attribute) (funman.model.petrinet.PetrinetModel attribute) plot() (funman.representation.parameter_space.ParameterSpace method) (funman.representation.representation.Timeseries method) (funman.scenario.consistency.ConsistencyScenarioResult method) (funman.scenario.parameter_synthesis.ParameterSynthesisScenarioResult method) (funman.scenario.scenario.AnalysisScenarioResult method) (funman.scenario.scenario.AnalysisScenarioResultException method) (funman.scenario.simulation.SimulationScenarioResult method) (funman.server.query.FunmanResults method)

plot_trajectories() (funman.server.query.FunmanResults method) plus() (in module funman.utils.math_utils) point_based_evaluation (funman.config.FUNMANConfig attribute) point_entropy() (funman.representation.box.Box method) point_parameters() (funman.server.query.FunmanResults method) point_to_smt() (funman.translate.translate.Encoder method) points (funman.representation.box.Box attribute) points() (funman.representation.parameter_space.ParameterSpace method) (funman.server.query.FunmanResults method) pop() (funman.search.box_search.FormulaStack method) post_queries() (in module funman.api.api) Pow() (funman.utils.sympy_utils.FUNMANFormulaManager method) prioritize_box_entropy (funman.config.FUNMANConfig attribute) problem (funman.search.search.SearchEpisode attribute) process() (funman.utils.handlers.NoopResultHandler method) (funman.utils.handlers.ResultCombinedHandler method) (funman.utils.handlers.ResultHandler method) profile (funman.config.FUNMANConfig attribute) progress (funman.server.query.FunmanProgress attribute) (funman.server.query.FunmanResults attribute) (funman.server.query.FunmanWorkUnit attribute) progress_timeseries (funman.server.query.FunmanResultsTiming attribute) project() (funman.representation.box.Box method) (funman.representation.parameter_space.ParameterSpace static method) properties (funman.model.generated_models.petrinet.Model attribute) (funman.model.generated_models.petrinet.Transition attribute) (funman.model.generated_models.regnet.Edge attribute) (funman.model.generated_models.regnet.Model attribute) ps() (funman.search.simulator_check.SimulatorCheck method) push() (funman.search.box_search.FormulaStack method)

Q

queries (funman.model.query.QueryAnd attribute) query (funman.representation.constraint.QueryConstraint attribute) (funman.scenario.scenario.AnalysisScenario attribute) (funman.scenario.simulation.SimulationScenario attribute) (funman.server.query.FunmanWorkRequest attribute)

query_satisfied (funman.scenario.simulation.SimulationScenarioResult attribute) queue_timeout (funman.config.FUNMANConfig attribute)

R

random_seed (funman.config.FUNMANConfig attribute) rate_constant (funman.model.generated_models.regnet.BaseProperties attribute) rate_expr_to_pysmt() (in module funman.utils.sympy_utils) rates (funman.model.generated_models.petrinet.OdeSemantics attribute) read_root() (in module funman.api.api) ref (funman.model.bilayer.BilayerMetadata attribute) regnet (funman.model.regnet.GeneratedRegnetModel attribute) (funman.model.regnet.RegnetModel attribute) relevant_assumptions (funman.representation.explanation.BoxExplanation attribute) relevant_at_time() (funman.representation.assumption.Assumption method) (funman.representation.constraint.Constraint method) (funman.representation.constraint.LinearConstraint method) (funman.representation.constraint.ParameterConstraint method) (funman.representation.constraint.TimedConstraint method) relevant_timepoints() (funman.representation.representation.Point method) relevant_timesteps() (funman.representation.representation.Point method) remove_irrelevant_steps() (funman.representation.representation.Point method) replace_reserved() (in module funman.utils.sympy_utils)

representable_space_volume() (funman.scenario.scenario.AnalysisScenario method) request (funman.server.query.FunmanResults attribute) (funman.server.query.FunmanWorkUnit attribute) ResultCombinedHandler (class in funman.utils.handlers) ResultHandler (class in funman.utils.handlers) results (funman.scenario.simulation.SimulationScenarioResult attribute) root (funman.model.generated_models.petrinet.States attribute) (funman.model.generated_models.petrinet.Transitions attribute) (funman.model.generated_models.regnet.ParamOrNumber attribute) run() (funman.api.run.Runner method) (funman.utils.handlers.WaitAction method) run_in_thread() (funman.api.server.Server method) run_instance() (funman.api.run.Runner method) run_point_simulation() (funman.scenario.scenario.AnalysisScenario method) run_scenario_simulation() (funman.scenario.scenario.AnalysisScenario method) run_test_case() (funman.api.run.Runner method) run_with_limited_time() (in module funman.search.search) Runner (class in funman.api.run) RUNNING (funman.server.worker.WorkerState attribute)

S

save_smtlib (funman.config.FUNMANConfig attribute) scenario (funman.scenario.consistency.ConsistencyScenarioResult attribute) (funman.scenario.parameter_synthesis.ParameterSynthesisScenarioResult attribute) (funman.scenario.simulation.SimulationScenarioResult attribute) schedule (funman.representation.box.Box attribute) (funman.representation.representation.Point attribute) (funman.search.box_search.BoxSearchEpisode attribute) (funman.search.search.SearchEpisode attribute) (funman.translate.encoding.EncodingOptions attribute) schedules (funman.representation.parameter.Schedules attribute) schema_ (funman.model.generated_models.petrinet.Header attribute) (funman.model.generated_models.regnet.Header attribute) schema_name (funman.model.generated_models.petrinet.Header attribute) (funman.model.generated_models.regnet.Header attribute) Search (class in funman.search.search) search() (funman.search.box_search.BoxSearch method) (funman.search.search.Search method) (funman.search.simulator_check.SimulatorCheck method) (funman.search.smt_check.SMTCheck method) search_space_volume() (funman.scenario.scenario.AnalysisScenario method) semantics (funman.model.generated_models.petrinet.Model attribute) ser_wrap() (funman.representation.interval.Interval method) serialize() (funman.utils.smtlib_utils.FUNMANSmtLibScript method) series_approx() (in module funman.utils.sympy_utils) series_approximation_threshold (funman.config.FUNMANConfig attribute) Server (class in funman.api.server) ServerConfig (class in funman.api.server) set_expression() (funman.representation.explanation.Explanation method) set_level() (in module funman.utils.logging) set_step_substitutions() (funman.translate.translate.Encoder method) set_time_step_constraints() (funman.translate.translate.Encoder method) setup_logging() (in module funman.utils.logging) sign (funman.model.generated_models.regnet.SignedGraphElement attribute) sim() (funman.search.simulate.Simulator method) simplify() (funman.translate.translate.LayeredEncoding method) simplify_query (funman.config.FUNMANConfig attribute) simulate_scenario() (funman.scenario.scenario.AnalysisScenario method) simulation (funman.representation.representation.Point attribute) simulation_tvects() (funman.scenario.scenario.AnalysisScenario method) SimulatorCheck (class in funman.search.simulator_check) SMTCheck (class in funman.search.smt_check) smtlibscript_from_formula() (in module funman.utils.smtlib_utils) smtlibscript_from_formula_list() (in module funman.utils.smtlib_utils) soft (funman.representation.constraint.Constraint attribute) (funman.representation.constraint.LinearConstraint attribute) (funman.representation.constraint.ModelConstraint attribute) (funman.representation.constraint.ParameterConstraint attribute) (funman.representation.constraint.QueryConstraint attribute) (funman.representation.constraint.TimeseriesConstraint attribute) solve() (funman.funman.Funman method) (funman.scenario.consistency.ConsistencyScenario method) (funman.scenario.parameter_synthesis.ParameterSynthesisScenario method) (funman.scenario.scenario.AnalysisScenario method) (funman.scenario.simulation.SimulationScenario method) solve_formula() (funman.search.simulator_check.SimulatorCheck method) (funman.search.smt_check.SMTCheck method) solver (funman.config.FUNMANConfig attribute) solver_time (funman.server.query.FunmanResultsTiming attribute) solver_timeout (funman.config.FUNMANConfig attribute) source (funman.model.generated_models.regnet.Edge attribute) span (funman.model.generated_models.petrinet.Semantics attribute) split() (funman.representation.box.Box method) src (funman.model.bilayer.BilayerEdge attribute) (funman.model.bilayer.BilayerNegativeEdge attribute) (funman.model.bilayer.BilayerPositiveEdge attribute)

start() (funman.server.query.FunmanResults method) (funman.server.storage.Storage method) (funman.server.worker.FunmanWorker method) start_in_thread() (funman.api.server.Server method) start_time (funman.server.query.FunmanResultsTiming attribute) STARTING (funman.server.worker.WorkerState attribute) state (funman.model.bilayer.BilayerMeasurement attribute) state_timepoint() (funman.translate.translate.Encoder method) state_values() (funman.representation.representation.Point method) states (funman.model.generated_models.petrinet.Model1 attribute) statistics (funman.search.box_search.BoxSearchEpisode attribute) (funman.search.box_search.BoxSearchEpisodeMP attribute) (funman.search.search.SearchEpisode attribute) step_size (funman.config.FUNMANConfig attribute) step_size_index() (funman.translate.translate.Encoder method) stepsize_at_step() (funman.representation.encoding_schedule.EncodingSchedule method) stop() (funman.server.query.FunmanResults method) (funman.server.storage.Storage method) (funman.server.worker.FunmanWorker method) STOPPED (funman.server.worker.WorkerState attribute) STOPPING (funman.server.worker.WorkerState attribute) Storage (class in funman.server.storage) store_smtlib() (funman.search.box_search.BoxSearch method) (funman.search.simulator_check.SimulatorCheck method) (funman.search.smt_check.SMTCheck method) str_to_symbol (funman.utils.sympy_utils.SympyBoundedSubstituter attribute) stratified_parameter_id() (funman.model.petrinet.GeneratedPetriNetModel method) stratified_state_id() (funman.model.petrinet.GeneratedPetriNetModel method) stratified_trans_id() (funman.model.petrinet.GeneratedPetriNetModel method) stratify() (funman.model.petrinet.GeneratedPetriNetModel method) stratify_transition() (funman.model.petrinet.GeneratedPetriNetModel method) structure_parameter() (funman.scenario.scenario.AnalysisScenario method) structure_parameters (funman.server.query.FunmanWorkRequest attribute) structure_parameters() (funman.scenario.scenario.AnalysisScenario method) substitute() (funman.translate.translate.LayeredEncoding method) (in module funman.utils.sympy_utils) substitute_subformulas (funman.config.FUNMANConfig attribute) substitutions() (funman.translate.translate.Encoder method) subtract() (funman.representation.interval.Interval method) symbol() (funman.representation.parameter.ModelParameter method) symbol_timeseries() (funman.server.query.FunmanResults method) (funman.translate.translate.Encoder method) symbol_values() (funman.server.query.FunmanResults method) (funman.translate.ensemble.EnsembleEncoder method) (funman.translate.translate.Encoder method) symbols (funman.representation.explanation.Explanation attribute) (funman.representation.explanation.TimeoutExplanation attribute) symbols() (funman.translate.encoding.FlatEncoding method) (funman.translate.translate.LayeredEncoding method) symm_diff() (funman.representation.box.Box method) symmetric_difference() (funman.representation.parameter_space.ParameterSpace static method) sympy_simplify() (funman.translate.simplifier.FUNMANSimplifier method) sympy_subs() (in module funman.utils.sympy_utils) sympy_to_pysmt() (in module funman.utils.sympy_utils) sympy_to_pysmt_abs() (in module funman.utils.sympy_utils) sympy_to_pysmt_op() (in module funman.utils.sympy_utils) sympy_to_pysmt_piecewise() (in module funman.utils.sympy_utils) sympy_to_pysmt_pow() (in module funman.utils.sympy_utils) sympy_to_pysmt_real() (in module funman.utils.sympy_utils) sympy_to_pysmt_symbol() (in module funman.utils.sympy_utils) SympySerializer (class in funman.utils.sympy_utils) SympyToPysmt (class in funman.translate.simplifier) sympyToPysmt() (funman.translate.simplifier.SympyToPysmt method) synthesized_model_parameters() (funman.scenario.scenario.AnalysisScenario method) synthesized_parameters() (funman.scenario.scenario.AnalysisScenario method) system (funman.model.generated_models.petrinet.TypingSemantics attribute)

T

target (funman.model.generated_models.petrinet.Initial attribute) (funman.model.generated_models.petrinet.Rate attribute) (funman.model.generated_models.regnet.Edge attribute) taylor_series_order (funman.config.FUNMANConfig attribute) tgt (funman.model.bilayer.BilayerEdge attribute) (funman.model.bilayer.BilayerNegativeEdge attribute) (funman.model.bilayer.BilayerPositiveEdge attribute) time (funman.model.generated_models.petrinet.OdeSemantics attribute) (funman.search.box_search.FormulaStack attribute) time_at_step() (funman.representation.encoding_schedule.EncodingSchedule method) time_dependent() (funman.representation.constraint.Constraint method) (funman.representation.constraint.LinearConstraint method) (funman.representation.constraint.TimedConstraint method) time_step_constraints() (funman.translate.translate.Encoder method) timed_copy() (funman.representation.parameter.ModelParameter method) timepoints (funman.representation.constraint.TimedConstraint attribute) (funman.representation.encoding_schedule.EncodingSchedule attribute) timeseries (funman.representation.constraint.TimeseriesConstraint attribute) timestep() (funman.representation.box.Box method) (funman.representation.representation.Point method) timing (funman.server.query.FunmanResults attribute) to_dot() (funman.model.bilayer.BilayerDynamics method) (funman.model.bilayer.BilayerEdge method) (funman.model.bilayer.BilayerMeasurement method) (funman.model.bilayer.BilayerNegativeEdge method) (funman.model.bilayer.BilayerNode method) (funman.model.ensemble.EnsembleModel method) (funman.model.petrinet.AbstractPetriNetModel method) (funman.model.regnet.RegnetModel method)

to_list() (funman.search.box_search.FormulaStack method) to_scenario() (funman.server.query.FunmanWorkUnit method) to_sympy() (funman.utils.sympy_utils.SympySerializer method) (in module funman.utils.sympy_utils) tolerance (funman.config.FUNMANConfig attribute) total_time (funman.server.query.FunmanResultsTiming attribute) transitions (funman.model.generated_models.petrinet.Model1 attribute) true_boxes (funman.representation.parameter_space.ParameterSpace attribute) true_explanations (funman.representation.explanation.ParameterSpaceExplanation attribute) true_point_timeseries() (funman.scenario.parameter_synthesis.ParameterSynthesisScenarioResult method) true_points() (funman.representation.box.Box method) (funman.representation.parameter_space.ParameterSpace method) tvect (funman.search.simulate.Simulator attribute) type (funman.model.bilayer.BilayerMetadata attribute) (funman.model.generated_models.petrinet.Distribution attribute) (funman.model.generated_models.regnet.Distribution attribute) (funman.representation.box.Box attribute) (funman.representation.representation.Point attribute) typing (funman.model.generated_models.petrinet.Semantics attribute)

U

ub (funman.model.bilayer.BilayerMetadata attribute) (funman.model.query.QueryLE attribute) (funman.representation.interval.Interval attribute) uniform_box_splits (funman.config.FUNMANConfig attribute) UNINITIALIZED (funman.server.worker.WorkerState attribute) union() (funman.representation.interval.Interval method) units (funman.model.generated_models.petrinet.Parameter attribute) (funman.model.generated_models.petrinet.State attribute) (funman.model.generated_models.petrinet.Time attribute)

unknown_points (funman.representation.parameter_space.ParameterSpace attribute) unnormalized_lb (funman.representation.interval.Interval attribute) unnormalized_ub (funman.representation.interval.Interval attribute) update_parameter_space() (funman.server.query.FunmanResults method) update_progress() (funman.server.query.FunmanResultsTiming method) use_compartmental_constraints (funman.config.FUNMANConfig attribute) use_transition_symbols (funman.config.FUNMANConfig attribute)

V

value (funman.model.generated_models.petrinet.Parameter attribute) (funman.model.generated_models.regnet.Parameter attribute) (funman.model.query.QueryEquals attribute) value_of() (funman.representation.representation.Point method) (funman.translate.simplifier.FUNMANSimplifier method) values (funman.representation.representation.Point attribute) values_at() (funman.representation.representation.Point method) variable (funman.model.query.QueryEquals attribute) (funman.model.query.QueryGE attribute) (funman.model.query.QueryLE attribute) (funman.representation.constraint.StateVariableConstraint attribute)

variables (funman.representation.constraint.LinearConstraint attribute) variables() (funman.model.model.FunmanModel method) variance() (funman.representation.box.Box method) verbosity (funman.config.FUNMANConfig attribute) vertices (funman.model.generated_models.regnet.Model1 attribute) volume() (funman.representation.box.Box method)

W

wait_action_timeout (funman.config.FUNMANConfig attribute) wait_timeout (funman.config.FUNMANConfig attribute) WaitAction (class in funman.utils.handlers) walk_div() (funman.utils.sympy_utils.SympySerializer method) walk_minus() (funman.utils.sympy_utils.SympySerializer method) walk_plus() (funman.utils.sympy_utils.SympySerializer method) walk_pow() (funman.translate.simplifier.FUNMANSimplifier method) (funman.utils.sympy_utils.SympySerializer method) walk_real_constant() (funman.utils.smtlib_utils.FUNMANSmtDagPrinter method) (funman.utils.smtlib_utils.FUNMANSmtPrinter method) (funman.utils.sympy_utils.SympySerializer method)

walk_symbol() (funman.utils.sympy_utils.SympySerializer method) walk_times() (funman.utils.sympy_utils.SympySerializer method) weights (funman.representation.constraint.LinearConstraint attribute) width() (funman.representation.box.Box method) (funman.representation.interval.Interval method) (funman.representation.parameter.Parameter method) WorkerState (class in funman.server.worker)