mobspy package

Subpackages

• mobspy.data_handler package
  • Submodules
  • mobspy.data_handler.process_result_data module
    • convert_data_to_desired_unit()
  • mobspy.data_handler.time_series_object module
    • MobsPyList_of_TS
      • MobsPyList_of_TS.add_ts_to_data()
      • MobsPyList_of_TS.get_max_time_for_species()
      • MobsPyList_of_TS.return_pandas()
      • MobsPyList_of_TS.to_dict()
    • MobsPyTimeSeries
  • Module contents
• mobspy.modules package
  • Submodules
  • mobspy.modules.class_of_meta_specie_named_any module
    • Context_specie_named_any
      • Context_specie_named_any.context_finish_for_meta_specie_named_any()
      • Context_specie_named_any.context_initiator_for_meta_specie_named_any()
  • mobspy.modules.event_functions module
    • format_event_dictionary_for_sbml()
  • mobspy.modules.function_rate_code module
    • basic_kinetics_string()
    • deterministic_string()
    • extract_reaction_rate()
    • prepare_arguments_for_callable()
    • search_for_parameters_in_str()
    • stochastic_string()
  • mobspy.modules.logic_operator_objects module
    • MetaSpeciesLogicResolver
      • MetaSpeciesLogicResolver.add_double_symbol()
      • MetaSpeciesLogicResolver.find_all_species_strings()
      • MetaSpeciesLogicResolver.generate_string()
    • ReactingSpeciesComparator
      • ReactingSpeciesComparator.add_operation_and_number()
      • ReactingSpeciesComparator.check_context()
    • SpeciesComparator
      • SpeciesComparator.add_operation_and_number()
      • SpeciesComparator.check_parenthesis()
      • SpeciesComparator.compile_code_line()
      • SpeciesComparator.logical_add_reacting_species()
      • SpeciesComparator.logical_add_species()
      • SpeciesComparator.reformat_number_and_species()
  • mobspy.modules.meta_class module
    • BaseSpecies()
    • Compiler
      • Compiler.add_phantom_reactions()
      • Compiler.add_to_parameters_to_sbml()
      • Compiler.compile()
      • Compiler.entity_counter
      • Compiler.last_rate
      • Compiler.override_get_item()
      • Compiler.ref_characteristics_to_object
    • ListSpecies()
    • List_Species
      • List_Species.append()
      • List_Species.extend()
      • List_Species.insert()
      • List_Species.is_in()
      • List_Species.remove()
      • List_Species.remove_repeated_elements()
    • New()
    • Reacting_Species
      • Reacting_Species.c()
      • Reacting_Species.context_finish_for_reacting_specie()
      • Reacting_Species.context_initiator_for_reacting_specie()
      • Reacting_Species.is_spe_or_reac()
      • Reacting_Species.is_species()
      • Reacting_Species.label()
      • Reacting_Species.old_context
    • Reactions
      • Reactions.set_rate()
    • Species
      • Species.add_characteristic()
      • Species.add_quantities()
      • Species.add_reaction()
      • Species.add_reference()
      • Species.c()
      • Species.check_if_valid_characteristic()
      • Species.get_all_characteristics()
      • Species.get_characteristics()
      • Species.get_index_from_reference_dict()
      • Species.get_name()
      • Species.get_ordered_references()
      • Species.get_quantities()
      • Species.get_reactions()
      • Species.get_references()
      • Species.get_simulation_context()
      • Species.is_spe_or_reac()
      • Species.is_species()
      • Species.label()
      • Species.meta_specie_named_any_context
      • Species.name()
      • Species.order_references()
      • Species.print_characteristics()
      • Species.remove_characteristic()
      • Species.remove_repeated_elements()
      • Species.reset_counts()
      • Species.reset_quantities()
      • Species.reset_reactions()
      • Species.reset_references()
      • Species.reset_simulation_context()
      • Species.set_reactions()
      • Species.set_references()
      • Species.set_simulation_context()
      • Species.show_characteristics()
      • Species.show_quantities()
      • Species.show_reactions()
      • Species.show_references()
      • Species.str_under_context()
      • Species.unit()
      • Species.update_meta_specie_named_any_context()
    • compile_species_number_line()
  • mobspy.modules.meta_class_utils module
    • check_orthogonality_between_references()
    • combine_references()
    • complete_characteristics_with_first_values()
    • create_orthogonal_vector_structure()
    • unite_characteristics()
  • mobspy.modules.mobspy_expressions module
    • Bool_Override
    • ExpressionDefiner
      • ExpressionDefiner.combine_binary_attributes()
      • ExpressionDefiner.create_from_new_operation()
      • ExpressionDefiner.execute_op()
      • ExpressionDefiner.execute_quantity_op()
    • MobsPyExpression
      • MobsPyExpression.generate_string_operation()
    • OverrideQuantity
      • OverrideQuantity.convert()
      • OverrideQuantity.convert_into()
      • OverrideQuantity.non_expression_add()
      • OverrideQuantity.non_expression_mul()
      • OverrideQuantity.non_expression_pow()
      • OverrideQuantity.non_expression_radd()
      • OverrideQuantity.non_expression_rmul()
      • OverrideQuantity.non_expression_rsub()
      • OverrideQuantity.non_expression_rtruediv()
      • OverrideQuantity.non_expression_sub()
      • OverrideQuantity.non_expression_truediv()
      • OverrideQuantity.set_ms_active()
    • OverrideUnitRegistry
    • QuantityConverter
      • QuantityConverter.convert_received_unit()
    • Specific_Species_Operator
      • Specific_Species_Operator.add()
      • Specific_Species_Operator.get_characteristics()
      • Specific_Species_Operator.get_name()
      • Specific_Species_Operator.is_a()
  • mobspy.modules.mobspy_parameters module
    • Mobspy_Parameter
      • Mobspy_Parameter.parameter_stack
      • Mobspy_Parameter.rename()
    • ModelParameters()
  • mobspy.modules.order_operators module
  • mobspy.modules.reaction_construction_nb module
    • check_for_invalid_reactions()
    • construct_order_structure()
    • construct_product_structure()
    • construct_rate_function_arguments()
    • construct_reactant_structures()
    • construct_single_reaction_for_sbml()
    • copy_reaction()
    • count_string_dictionary()
    • create_all_reactions()
    • expression_compilation_finish()
    • expression_compilation_initiation()
    • get_involved_species()
    • iterator_for_combinations()
  • mobspy.modules.reaction_construction_nb_parallel module
    • check_for_invalid_reactions()
    • construct_order_structure()
    • construct_product_structure()
    • construct_rate_function_arguments()
    • construct_reactant_structures()
    • construct_single_reaction_for_sbml()
    • copy_reaction()
    • count_string_dictionary()
    • create_all_reactions()
    • get_involved_species()
    • iterator_for_combinations()
  • mobspy.modules.set_counts_module module
    • set_counts()
  • mobspy.modules.species_string_generator module
    • characteristics_dictionary()
    • construct_all_combinations()
    • construct_species_char_list()
  • mobspy.modules.unit_handler module
    • check_dimension()
    • convert_counts()
    • convert_rate()
    • convert_time()
    • convert_volume()
    • extract_length_dimension()
  • mobspy.modules.user_functions module
    • Apply()
  • Module contents
• mobspy.parameter_scripts package
  • Submodules
  • mobspy.parameter_scripts.parameter_reader module
    • parameter_process()
    • read_json()
  • mobspy.parameter_scripts.parametric_sweeps module
    • assign_values_to_model()
    • generate_all_sbml_models()
    • unite_parameter_dictionaries()
  • Module contents
• mobspy.parameters package
  • Submodules
  • mobspy.parameters.default_reader module
    • get_default_parameters()
  • mobspy.parameters.example_reader module
    • get_example_parameters()
  • Module contents
• mobspy.plot_params package
  • Submodules
  • mobspy.plot_params.default_plot_reader module
    • get_default_plot_parameters()
  • mobspy.plot_params.example_plot_reader module
    • get_example_plot_parameters()
  • Module contents
• mobspy.plot_scripts package
  • Submodules
  • mobspy.plot_scripts.default_plots module
    • deterministic_plot()
    • parametric_plot()
    • raw_plot()
    • read_plot_json()
    • set_plot_units()
    • stochastic_plot()
  • mobspy.plot_scripts.hierarchical_plot module
    • Color_cycle
    • figure_hash()
    • figure_hash_creation()
    • find_parameter()
    • find_species_time_series()
    • get_total_figure_number()
    • plot_curves()
    • plot_data()
    • set_figure_characteristics()
    • set_global_parameters()
  • mobspy.plot_scripts.process_plot_data module
    • check_plot_parameters()
    • query_plot_data()
    • time_filter_operation()
  • mobspy.plot_scripts.statistics_calculations module
    • average_plus_standard_deviation()
    • standard_deviation()
    • time_series_average()
  • Module contents
• mobspy.sbml_simulator package
  • Submodules
  • mobspy.sbml_simulator.SBMLWriter module
    • check()
    • create_model()
  • mobspy.sbml_simulator.builder module
    • build()
  • mobspy.sbml_simulator.run module
    • job_execution()
    • reformat_time_series()
    • simulate()
  • Module contents
• mobspy.simulation_logging package
  • Submodules
  • mobspy.simulation_logging.log_scripts module
    • debug()
    • error()
    • warning()
  • Module contents

Submodules

mobspy.simulation module

Main MobsPy module. It stocks the Simulation class which is responsible for simulating a Model

class mobspy.simulation.Simulation(model, names=None, parameters=None, plot_parameters=None)

Bases: object

compile(verbose=True)

Compiler method that calls the Compiler class in the modules directory

Parameters:

verbose – (bool) = print or not the results of the compilation

configure_parameters(config)

Configure simulation parameters from json file or dictionary

Parameters:

file_name – (str) name of the json file

configure_plot_parameters(config)

Configure plot parameters from json file or dictionary

Parameters:

file_name – (str) name of the json file

classmethod event_compilation_error()

event_condition(trigger, delay=0)

Context manager for condition events. Called in “with Simulation.event_condition(trigger) :” format.

Parameters:

• trigger – () condition that triggers the event when fulfilled

• delay – (int, float, Quantity) time to wait before triggering the event once the trigger condition has been fulfilled

event_context_add(time, trigger)

Adds an event to the event context

Parameters:

• trigger – () condition that triggers the event when fulfilled

• time – (int, float, Quantity) time to wait before triggering the event once the trigger condition has been fulfilled

event_context_finish()

Removes the context in all meta-species and resets some varaiables. Called each time an event context is finished.

event_context_initiator()

Sets the context in all meta-species. Called each time an event context is initiated.

event_time(time)

Context manager for time events. Called in “with Simulation.event_time(time) :” format.

Parameters:

time – (int, float, Quantity) any time used

extract_plot_essentials(*species)

Extract essential information for plotting

Parameters:

species – (meta-species objects) meta-species objects to plot

Returns:

species_strings (str) = species strings to be plotted, self.results = data resulting from the

simulation, self.plot_parameters (dict) = parameters for plotting

generate_sbml()

Generates sbmls strings from the current stored models in the simulation

“return: to_return (list of str) list of sbml files from all the simulations stored

classmethod is_simulation()

plot(*species)

Another way of calling plot_deterministic for simplicity

Parameters:

species – (str or meta-species objects) list of species to be plotted

plot_deterministic(*species)

Calls deterministic plot. See default_plots module in the plot_scripts directory

Parameters:

species – (str or meta-species objects) list of species to be plotted

plot_parametric(*species)

plot_raw(parameters_or_file)

Calls raw plot. See default_plots module in the plot_scripts directory

Parameters:

parameters_or_file – json file name with plot parameter configuration or dictionary with plot

parameter configuration

plot_stochastic(*species)

Calls stochastic plot. See default_plots module in the plot_scripts directory

Parameters:

species – (str or meta-species objects) list of species to be plotted

run()

Runs the simulation by colling the models in the sbml_simulator directory. Compiles the model if it was not yet compiled

save_data(file=None)

Saves the simulation result data to a file in json format

Parameters:

file – (str) name of the file to save the data to. If none a default name is provided

set_from_json(file_name)

Set simulation parameters from json file

Parameters:

file_name – (str) name of the json file

classmethod set_job_number(params)

class mobspy.simulation.SimulationComposition(S1, S2)

Bases: object

compile(verbose=True)

generate_sbml()

classmethod is_simulation()

plot(*species)

plot_deterministic(*species)

plot_raw(parameters_or_file)

plot_stochastic(*species)

run()

Module contents

MobsPy: A Query-Based Language for Chemical Reaction Networks