gillespy2 package

Subpackages

• gillespy2.core package
  • Submodules
  • gillespy2.core.assignmentrule module
    • AssignmentRule
      • AssignmentRule.sanitized_formula()
  • gillespy2.core.cleanup module
    • cleanup_tempfiles()
  • gillespy2.core.events module
    • Event
      • Event.add_assignment()
    • EventAssignment
    • EventTrigger
      • EventTrigger.sanitized_expression()
  • gillespy2.core.functiondefinition module
    • FunctionDefinition
      • FunctionDefinition.get_arg_string()
      • FunctionDefinition.sanitized_function()
  • gillespy2.core.gillespyError module
    • AssignmentRuleError
    • BuildError
    • DirectoryError
    • EventError
    • ExecutionError
    • FunctionDefinitionError
    • InvalidModelError
    • InvalidStochMLError
    • ModelError
    • ParameterError
    • RateRuleError
    • ReactionError
    • ResultsError
    • SBMLError
    • SimulationError
    • SimulationTimeoutError
    • SolverError
    • SpeciesError
    • StochMLImportError
    • TimespanError
    • ValidationError
  • gillespy2.core.gillespySolver module
    • GillesPySolver
      • GillesPySolver.get_solver_settings()
      • GillesPySolver.get_supported_features()
      • GillesPySolver.get_supported_integrator_options()
      • GillesPySolver.name
      • GillesPySolver.run()
      • GillesPySolver.validate_integrator_options()
      • GillesPySolver.validate_model()
      • GillesPySolver.validate_sbml_features()
      • GillesPySolver.validate_tspan()
  • gillespy2.core.jsonify module
    • ComplexJsonCoder
      • ComplexJsonCoder.decode()
      • ComplexJsonCoder.default()
    • Int64Coder
      • Int64Coder.from_json()
      • Int64Coder.to_dict()
    • Jsonify
      • Jsonify.from_dict()
      • Jsonify.from_json()
      • Jsonify.get_json_hash()
      • Jsonify.get_translation_table()
      • Jsonify.make_translation_table()
      • Jsonify.public_vars()
      • Jsonify.to_anon()
      • Jsonify.to_dict()
      • Jsonify.to_json()
      • Jsonify.to_named()
    • NdArrayCoder
      • NdArrayCoder.from_json()
      • NdArrayCoder.to_dict()
    • SetCoder
      • SetCoder.from_json()
      • SetCoder.to_dict()
    • TranslationTable
      • TranslationTable.obj_to_anon()
      • TranslationTable.obj_to_named()
      • TranslationTable.recursive_translate()
    • TypeCoder
      • TypeCoder.from_json()
      • TypeCoder.to_dict()
  • gillespy2.core.liveGraphing module
    • CRepeatTimer
      • CRepeatTimer.pause
      • CRepeatTimer.run()
    • LiveDisplayer
      • LiveDisplayer.display()
      • LiveDisplayer.increment_trajectory()
      • LiveDisplayer.print_text_header()
      • LiveDisplayer.trajectory_header()
    • RepeatTimer
      • RepeatTimer.pause
      • RepeatTimer.run()
    • display_types()
    • valid_graph_params()
  • gillespy2.core.model module
    • Model
      • Model.add()
      • Model.add_assignment_rule()
      • Model.add_event()
      • Model.add_function_definition()
      • Model.add_parameter()
      • Model.add_rate_rule()
      • Model.add_reaction()
      • Model.add_species()
      • Model.compile_prep()
      • Model.delete_all_assignment_rules()
      • Model.delete_all_events()
      • Model.delete_all_function_definitions()
      • Model.delete_all_parameters()
      • Model.delete_all_rate_rules()
      • Model.delete_all_reactions()
      • Model.delete_all_species()
      • Model.delete_assignment_rule()
      • Model.delete_event()
      • Model.delete_function_definition()
      • Model.delete_parameter()
      • Model.delete_rate_rule()
      • Model.delete_reaction()
      • Model.delete_species()
      • Model.get_all_assignment_rules()
      • Model.get_all_events()
      • Model.get_all_function_definitions()
      • Model.get_all_parameters()
      • Model.get_all_rate_rules()
      • Model.get_all_reactions()
      • Model.get_all_species()
      • Model.get_assignment_rule()
      • Model.get_best_solver()
      • Model.get_best_solver_algo()
      • Model.get_element()
      • Model.get_event()
      • Model.get_function_definition()
      • Model.get_model_features()
      • Model.get_parameter()
      • Model.get_rate_rule()
      • Model.get_reaction()
      • Model.get_species()
      • Model.make_translation_table()
      • Model.problem_with_name()
      • Model.reserved_names
      • Model.run()
      • Model.sanitized_parameter_names()
      • Model.sanitized_species_names()
      • Model.serialize()
      • Model.set_parameter()
      • Model.set_units()
      • Model.special_characters
      • Model.timespan()
      • Model.update_namespace()
      • Model.validate_reactants_and_products()
    • StochMLDocument
      • StochMLDocument.from_file()
      • StochMLDocument.from_model()
      • StochMLDocument.from_string()
      • StochMLDocument.to_model()
      • StochMLDocument.to_string()
    • export_SBML()
    • export_StochSS()
    • import_SBML()
  • gillespy2.core.parameter module
    • Parameter
      • Parameter.sanitized_expression()
      • Parameter.validate()
  • gillespy2.core.raterule module
    • RateRule
      • RateRule.sanitized_formula()
  • gillespy2.core.reaction module
    • Reaction
      • Reaction.Annotate()
      • Reaction.addProduct()
      • Reaction.addReactant()
      • Reaction.add_product()
      • Reaction.add_reactant()
      • Reaction.create_mass_action()
      • Reaction.from_json()
      • Reaction.sanitized_propensity_function()
      • Reaction.setType()
      • Reaction.set_annotation()
      • Reaction.set_propensities()
      • Reaction.set_rate()
      • Reaction.to_dict()
      • Reaction.validate()
      • Reaction.verify()
  • gillespy2.core.results module
    • Results
      • Results.average_ensemble()
      • Results.build_from_solver_results()
      • Results.plot()
      • Results.plot_mean_stdev()
      • Results.plot_std_dev_range()
      • Results.plotplotly()
      • Results.plotplotly_mean_stdev()
      • Results.plotplotly_std_dev_range()
      • Results.stddev_ensemble()
      • Results.to_array()
      • Results.to_csv()
    • Trajectory
    • common_rgb_values()
  • gillespy2.core.sortableobject module
    • SortableObject
  • gillespy2.core.species module
    • Species
      • Species.set_initial_value()
      • Species.validate()
  • gillespy2.core.timespan module
    • TimeSpan
      • TimeSpan.arange()
      • TimeSpan.linspace()
      • TimeSpan.validate()
  • Module contents
    • AssignmentRule
      • AssignmentRule.sanitized_formula()
    • AssignmentRuleError
    • BuildError
    • ChainMap
      • ChainMap.clear()
      • ChainMap.copy()
      • ChainMap.fromkeys()
      • ChainMap.get()
      • ChainMap.new_child()
      • ChainMap.parents
      • ChainMap.pop()
      • ChainMap.popitem()
    • DirectoryError
    • Event
      • Event.add_assignment()
    • EventAssignment
    • EventError
    • EventTrigger
      • EventTrigger.sanitized_expression()
    • ExecutionError
    • FunctionDefinition
      • FunctionDefinition.get_arg_string()
      • FunctionDefinition.sanitized_function()
    • FunctionDefinitionError
    • GillesPySolver
      • GillesPySolver.get_solver_settings()
      • GillesPySolver.get_supported_features()
      • GillesPySolver.get_supported_integrator_options()
      • GillesPySolver.name
      • GillesPySolver.run()
      • GillesPySolver.validate_integrator_options()
      • GillesPySolver.validate_model()
      • GillesPySolver.validate_sbml_features()
      • GillesPySolver.validate_tspan()
    • InvalidModelError
    • InvalidStochMLError
    • Jsonify
      • Jsonify.from_dict()
      • Jsonify.from_json()
      • Jsonify.get_json_hash()
      • Jsonify.get_translation_table()
      • Jsonify.make_translation_table()
      • Jsonify.public_vars()
      • Jsonify.to_anon()
      • Jsonify.to_dict()
      • Jsonify.to_json()
      • Jsonify.to_named()
    • Model
      • Model.add()
      • Model.add_assignment_rule()
      • Model.add_event()
      • Model.add_function_definition()
      • Model.add_parameter()
      • Model.add_rate_rule()
      • Model.add_reaction()
      • Model.add_species()
      • Model.compile_prep()
      • Model.delete_all_assignment_rules()
      • Model.delete_all_events()
      • Model.delete_all_function_definitions()
      • Model.delete_all_parameters()
      • Model.delete_all_rate_rules()
      • Model.delete_all_reactions()
      • Model.delete_all_species()
      • Model.delete_assignment_rule()
      • Model.delete_event()
      • Model.delete_function_definition()
      • Model.delete_parameter()
      • Model.delete_rate_rule()
      • Model.delete_reaction()
      • Model.delete_species()
      • Model.get_all_assignment_rules()
      • Model.get_all_events()
      • Model.get_all_function_definitions()
      • Model.get_all_parameters()
      • Model.get_all_rate_rules()
      • Model.get_all_reactions()
      • Model.get_all_species()
      • Model.get_assignment_rule()
      • Model.get_best_solver()
      • Model.get_best_solver_algo()
      • Model.get_element()
      • Model.get_event()
      • Model.get_function_definition()
      • Model.get_model_features()
      • Model.get_parameter()
      • Model.get_rate_rule()
      • Model.get_reaction()
      • Model.get_species()
      • Model.make_translation_table()
      • Model.problem_with_name()
      • Model.reserved_names
      • Model.run()
      • Model.sanitized_parameter_names()
      • Model.sanitized_species_names()
      • Model.serialize()
      • Model.set_parameter()
      • Model.set_units()
      • Model.special_characters
      • Model.timespan()
      • Model.update_namespace()
      • Model.validate_reactants_and_products()
    • ModelError
    • OrderedDict
      • OrderedDict.clear()
      • OrderedDict.copy()
      • OrderedDict.fromkeys()
      • OrderedDict.items()
      • OrderedDict.keys()
      • OrderedDict.move_to_end()
      • OrderedDict.pop()
      • OrderedDict.popitem()
      • OrderedDict.setdefault()
      • OrderedDict.update()
      • OrderedDict.values()
    • Parameter
      • Parameter.sanitized_expression()
      • Parameter.validate()
    • ParameterError
    • RateRule
      • RateRule.sanitized_formula()
    • RateRuleError
    • Reaction
      • Reaction.Annotate()
      • Reaction.addProduct()
      • Reaction.addReactant()
      • Reaction.add_product()
      • Reaction.add_reactant()
      • Reaction.create_mass_action()
      • Reaction.from_json()
      • Reaction.sanitized_propensity_function()
      • Reaction.setType()
      • Reaction.set_annotation()
      • Reaction.set_propensities()
      • Reaction.set_rate()
      • Reaction.to_dict()
      • Reaction.validate()
      • Reaction.verify()
    • ReactionError
    • Results
      • Results.average_ensemble()
      • Results.build_from_solver_results()
      • Results.plot()
      • Results.plot_mean_stdev()
      • Results.plot_std_dev_range()
      • Results.plotplotly()
      • Results.plotplotly_mean_stdev()
      • Results.plotplotly_std_dev_range()
      • Results.stddev_ensemble()
      • Results.to_array()
      • Results.to_csv()
    • ResultsError
    • SBMLError
    • SimulationError
    • SimulationTimeoutError
    • SolverError
    • SortableObject
    • Species
      • Species.set_initial_value()
      • Species.validate()
    • SpeciesError
    • StochMLDocument
      • StochMLDocument.from_file()
      • StochMLDocument.from_model()
      • StochMLDocument.from_string()
      • StochMLDocument.to_model()
      • StochMLDocument.to_string()
    • StochMLImportError
    • TimeSpan
      • TimeSpan.arange()
      • TimeSpan.linspace()
      • TimeSpan.validate()
    • TimespanError
    • Trajectory
    • TranslationTable
      • TranslationTable.obj_to_anon()
      • TranslationTable.obj_to_named()
      • TranslationTable.recursive_translate()
    • UserDict
      • UserDict.copy()
      • UserDict.fromkeys()
    • UserList
      • UserList.append()
      • UserList.clear()
      • UserList.copy()
      • UserList.count()
      • UserList.extend()
      • UserList.index()
      • UserList.insert()
      • UserList.pop()
      • UserList.remove()
      • UserList.reverse()
      • UserList.sort()
    • ValidationError
    • cleanup_tempfiles()
    • common_rgb_values()
    • datetime
      • datetime.astimezone()
      • datetime.combine()
      • datetime.ctime()
      • datetime.date()
      • datetime.dst()
      • datetime.fold
      • datetime.fromisoformat()
      • datetime.fromtimestamp()
      • datetime.hour
      • datetime.isoformat()
      • datetime.max
      • datetime.microsecond
      • datetime.min
      • datetime.minute
      • datetime.now()
      • datetime.replace()
      • datetime.resolution
      • datetime.second
      • datetime.strptime()
      • datetime.time()
      • datetime.timestamp()
      • datetime.timetuple()
      • datetime.timetz()
      • datetime.tzinfo
      • datetime.tzname()
      • datetime.utcfromtimestamp()
      • datetime.utcnow()
      • datetime.utcoffset()
      • datetime.utctimetuple()
    • export_SBML()
    • export_StochSS()
    • import_SBML()
• gillespy2.sbml package
  • Submodules
  • gillespy2.sbml.SBMLexport module
  • gillespy2.sbml.SBMLimport module
  • Module contents
• gillespy2.solvers package
  • Subpackages
    • gillespy2.solvers.cpp package
      • Subpackages
      • Submodules
      • gillespy2.solvers.cpp.c_decoder module
      • gillespy2.solvers.cpp.c_solver module
      • gillespy2.solvers.cpp.ode_c_solver module
      • gillespy2.solvers.cpp.ssa_c_solver module
      • gillespy2.solvers.cpp.tau_hybrid_c_solver module
      • gillespy2.solvers.cpp.tau_leaping_c_solver module
      • Module contents
    • gillespy2.solvers.numpy package
      • Submodules
      • gillespy2.solvers.numpy.CLE_solver module
      • gillespy2.solvers.numpy.ode_solver module
      • gillespy2.solvers.numpy.ssa_solver module
      • gillespy2.solvers.numpy.tau_hybrid_solver module
      • gillespy2.solvers.numpy.tau_leaping_solver module
      • Module contents
    • gillespy2.solvers.stochkit package
      • Submodules
      • gillespy2.solvers.stochkit.stochkit_solvers module
      • Module contents
    • gillespy2.solvers.utilities package
      • Submodules
      • gillespy2.solvers.utilities.Tau module
      • gillespy2.solvers.utilities.cpp_support_test module
      • gillespy2.solvers.utilities.solverutils module
      • Module contents
  • Module contents
    • CLESolver
      • CLESolver.get_solver_settings()
      • CLESolver.name
      • CLESolver.pause_event
      • CLESolver.rc
      • CLESolver.result
      • CLESolver.run()
      • CLESolver.stop_event
    • NumPySSASolver
      • NumPySSASolver.get_solver_settings()
      • NumPySSASolver.name
      • NumPySSASolver.pause_event
      • NumPySSASolver.rc
      • NumPySSASolver.result
      • NumPySSASolver.run()
      • NumPySSASolver.stop_event
    • ODECSolver
      • ODECSolver.get_solver_settings()
      • ODECSolver.get_supported_integrator_options()
      • ODECSolver.name
      • ODECSolver.run()
      • ODECSolver.target
    • ODESolver
      • ODESolver.get_solver_settings()
      • ODESolver.name
      • ODESolver.pause_event
      • ODESolver.rc
      • ODESolver.result
      • ODESolver.run()
      • ODESolver.stop_event
    • SSACSolver
      • SSACSolver.get_solver_settings()
      • SSACSolver.name
      • SSACSolver.run()
      • SSACSolver.target
    • TauHybridCSolver
      • TauHybridCSolver.ErrorStatus
      • TauHybridCSolver.get_solver_settings()
      • TauHybridCSolver.get_supported_features()
      • TauHybridCSolver.get_supported_integrator_options()
      • TauHybridCSolver.name
      • TauHybridCSolver.run()
      • TauHybridCSolver.target
    • TauHybridSolver
      • TauHybridSolver.get_solver_settings()
      • TauHybridSolver.get_supported_features()
      • TauHybridSolver.name
      • TauHybridSolver.rc
      • TauHybridSolver.result
      • TauHybridSolver.run()
      • TauHybridSolver.stop_event
    • TauLeapingCSolver
      • TauLeapingCSolver.get_solver_settings()
      • TauLeapingCSolver.name
      • TauLeapingCSolver.run()
      • TauLeapingCSolver.target
    • TauLeapingSolver
      • TauLeapingSolver.get_solver_settings()
      • TauLeapingSolver.name
      • TauLeapingSolver.pause_event
      • TauLeapingSolver.rc
      • TauLeapingSolver.result
      • TauLeapingSolver.run()
      • TauLeapingSolver.stop_event
• gillespy2.stochss package
  • Submodules
  • gillespy2.stochss.StochSSexport module
    • export()
  • Module contents

Module contents