MobsPy
Contents
Welcome
Meta-Reaction Syntax
How MobsPy works?
Following Notebooks
Reaction Inheritance
Characteristics
Restraints
For Loops
Order of Reactants and Products
Count/Concentration Assignment
Set count function
Units
Simulation Results
Reaction Rates
Models
Characteristics
List Species
Born Species
Events
Concatenated simulations
API
API
MobsPy
Index
Index
A
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B
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C
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D
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E
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F
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G
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I
|
J
|
L
|
M
|
N
|
O
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P
|
Q
|
R
|
S
|
T
|
U
|
W
A
add() (mobspy.modules.mobspy_expressions.Specific_Species_Operator method)
add_characteristic() (mobspy.modules.meta_class.Species method)
add_double_symbol() (mobspy.modules.logic_operator_objects.MetaSpeciesLogicResolver method)
add_operation_and_number() (mobspy.modules.logic_operator_objects.ReactingSpeciesComparator method)
(mobspy.modules.logic_operator_objects.SpeciesComparator method)
add_phantom_reactions() (mobspy.modules.meta_class.Compiler class method)
add_quantities() (mobspy.modules.meta_class.Species method)
add_reaction() (mobspy.modules.meta_class.Species method)
add_reference() (mobspy.modules.meta_class.Species method)
add_to_parameters_to_sbml() (mobspy.modules.meta_class.Compiler class method)
add_ts_to_data() (mobspy.data_handler.time_series_object.MobsPyList_of_TS method)
append() (mobspy.modules.meta_class.List_Species method)
Apply() (in module mobspy.modules.user_functions)
assign_values_to_model() (in module mobspy.parameter_scripts.parametric_sweeps)
average_plus_standard_deviation() (in module mobspy.plot_scripts.statistics_calculations)
B
BaseSpecies() (in module mobspy.modules.meta_class)
basic_kinetics_string() (in module mobspy.modules.function_rate_code)
Bool_Override (class in mobspy.modules.mobspy_expressions)
build() (in module mobspy.sbml_simulator.builder)
C
c() (mobspy.modules.meta_class.Reacting_Species method)
(mobspy.modules.meta_class.Species method)
characteristics_dictionary() (in module mobspy.modules.species_string_generator)
check() (in module mobspy.sbml_simulator.SBMLWriter)
check_context() (mobspy.modules.logic_operator_objects.ReactingSpeciesComparator method)
check_dimension() (in module mobspy.modules.unit_handler)
check_for_invalid_reactions() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
check_if_valid_characteristic() (mobspy.modules.meta_class.Species class method)
check_orthogonality_between_references() (in module mobspy.modules.meta_class_utils)
check_parenthesis() (mobspy.modules.logic_operator_objects.SpeciesComparator class method)
check_plot_parameters() (in module mobspy.plot_scripts.process_plot_data)
Color_cycle (class in mobspy.plot_scripts.hierarchical_plot)
combine_binary_attributes() (mobspy.modules.mobspy_expressions.ExpressionDefiner method)
combine_references() (in module mobspy.modules.meta_class_utils)
compile() (mobspy.modules.meta_class.Compiler class method)
(mobspy.simulation.Simulation method)
(mobspy.simulation.SimulationComposition method)
compile_code_line() (mobspy.modules.logic_operator_objects.SpeciesComparator class method)
compile_species_number_line() (in module mobspy.modules.meta_class)
Compiler (class in mobspy.modules.meta_class)
complete_characteristics_with_first_values() (in module mobspy.modules.meta_class_utils)
configure_parameters() (mobspy.simulation.Simulation method)
configure_plot_parameters() (mobspy.simulation.Simulation method)
construct_all_combinations() (in module mobspy.modules.species_string_generator)
construct_order_structure() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
construct_product_structure() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
construct_rate_function_arguments() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
construct_reactant_structures() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
construct_single_reaction_for_sbml() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
construct_species_char_list() (in module mobspy.modules.species_string_generator)
context_finish_for_meta_specie_named_any() (mobspy.modules.class_of_meta_specie_named_any.Context_specie_named_any method)
context_finish_for_reacting_specie() (mobspy.modules.meta_class.Reacting_Species method)
context_initiator_for_meta_specie_named_any() (mobspy.modules.class_of_meta_specie_named_any.Context_specie_named_any method)
context_initiator_for_reacting_specie() (mobspy.modules.meta_class.Reacting_Species method)
Context_specie_named_any (class in mobspy.modules.class_of_meta_specie_named_any)
convert() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
convert_counts() (in module mobspy.modules.unit_handler)
convert_data_to_desired_unit() (in module mobspy.data_handler.process_result_data)
convert_into() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
convert_rate() (in module mobspy.modules.unit_handler)
convert_received_unit() (mobspy.modules.mobspy_expressions.QuantityConverter class method)
convert_time() (in module mobspy.modules.unit_handler)
convert_volume() (in module mobspy.modules.unit_handler)
copy_reaction() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
count_string_dictionary() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
create_all_reactions() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
create_from_new_operation() (mobspy.modules.mobspy_expressions.ExpressionDefiner method)
create_model() (in module mobspy.sbml_simulator.SBMLWriter)
create_orthogonal_vector_structure() (in module mobspy.modules.meta_class_utils)
D
debug() (in module mobspy.simulation_logging.log_scripts)
deterministic_plot() (in module mobspy.plot_scripts.default_plots)
deterministic_string() (in module mobspy.modules.function_rate_code)
E
entity_counter (mobspy.modules.meta_class.Compiler attribute)
error() (in module mobspy.simulation_logging.log_scripts)
event_compilation_error() (mobspy.simulation.Simulation class method)
event_condition() (mobspy.simulation.Simulation method)
event_context_add() (mobspy.simulation.Simulation method)
event_context_finish() (mobspy.simulation.Simulation method)
event_context_initiator() (mobspy.simulation.Simulation method)
event_time() (mobspy.simulation.Simulation method)
execute_op() (mobspy.modules.mobspy_expressions.ExpressionDefiner class method)
execute_quantity_op() (mobspy.modules.mobspy_expressions.ExpressionDefiner method)
expression_compilation_finish() (in module mobspy.modules.reaction_construction_nb)
expression_compilation_initiation() (in module mobspy.modules.reaction_construction_nb)
ExpressionDefiner (class in mobspy.modules.mobspy_expressions)
extend() (mobspy.modules.meta_class.List_Species method)
extract_length_dimension() (in module mobspy.modules.unit_handler)
extract_plot_essentials() (mobspy.simulation.Simulation method)
extract_reaction_rate() (in module mobspy.modules.function_rate_code)
F
figure_hash() (in module mobspy.plot_scripts.hierarchical_plot)
figure_hash_creation() (in module mobspy.plot_scripts.hierarchical_plot)
find_all_species_strings() (mobspy.modules.logic_operator_objects.MetaSpeciesLogicResolver class method)
find_parameter() (in module mobspy.plot_scripts.hierarchical_plot)
find_species_time_series() (in module mobspy.plot_scripts.hierarchical_plot)
for_local_use
module
format_event_dictionary_for_sbml() (in module mobspy.modules.event_functions)
G
generate_all_sbml_models() (in module mobspy.parameter_scripts.parametric_sweeps)
generate_sbml() (mobspy.simulation.Simulation method)
(mobspy.simulation.SimulationComposition method)
generate_string() (mobspy.modules.logic_operator_objects.MetaSpeciesLogicResolver method)
generate_string_operation() (mobspy.modules.mobspy_expressions.MobsPyExpression method)
get_all_characteristics() (mobspy.modules.meta_class.Species method)
get_characteristics() (mobspy.modules.meta_class.Species method)
(mobspy.modules.mobspy_expressions.Specific_Species_Operator method)
get_default_parameters() (in module mobspy.parameters.default_reader)
get_default_plot_parameters() (in module mobspy.plot_params.default_plot_reader)
get_example_parameters() (in module mobspy.parameters.example_reader)
get_example_plot_parameters() (in module mobspy.plot_params.example_plot_reader)
get_index_from_reference_dict() (mobspy.modules.meta_class.Species method)
get_involved_species() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
get_max_time_for_species() (mobspy.data_handler.time_series_object.MobsPyList_of_TS method)
get_name() (mobspy.modules.meta_class.Species method)
(mobspy.modules.mobspy_expressions.Specific_Species_Operator method)
get_ordered_references() (mobspy.modules.meta_class.Species method)
get_quantities() (mobspy.modules.meta_class.Species method)
get_reactions() (mobspy.modules.meta_class.Species method)
get_references() (mobspy.modules.meta_class.Species method)
get_simulation_context() (mobspy.modules.meta_class.Species class method)
get_total_figure_number() (in module mobspy.plot_scripts.hierarchical_plot)
I
insert() (mobspy.modules.meta_class.List_Species method)
is_a() (mobspy.modules.mobspy_expressions.Specific_Species_Operator method)
is_in() (mobspy.modules.meta_class.List_Species method)
is_simulation() (mobspy.simulation.Simulation class method)
(mobspy.simulation.SimulationComposition class method)
is_spe_or_reac() (mobspy.modules.meta_class.Reacting_Species class method)
(mobspy.modules.meta_class.Species class method)
is_species() (mobspy.modules.meta_class.Reacting_Species class method)
(mobspy.modules.meta_class.Species class method)
iterator_for_combinations() (in module mobspy.modules.reaction_construction_nb)
(in module mobspy.modules.reaction_construction_nb_parallel)
J
job_execution() (in module mobspy.sbml_simulator.run)
L
label() (mobspy.modules.meta_class.Reacting_Species method)
(mobspy.modules.meta_class.Species method)
last_rate (mobspy.modules.meta_class.Compiler attribute)
List_Species (class in mobspy.modules.meta_class)
ListSpecies() (in module mobspy.modules.meta_class)
logical_add_reacting_species() (mobspy.modules.logic_operator_objects.SpeciesComparator class method)
logical_add_species() (mobspy.modules.logic_operator_objects.SpeciesComparator class method)
M
meta_specie_named_any_context (mobspy.modules.meta_class.Species attribute)
MetaSpeciesLogicResolver (class in mobspy.modules.logic_operator_objects)
mobspy
module
,
[1]
mobspy.data_handler
module
mobspy.data_handler.process_result_data
module
mobspy.data_handler.time_series_object
module
mobspy.modules
module
mobspy.modules.class_of_meta_specie_named_any
module
mobspy.modules.event_functions
module
mobspy.modules.function_rate_code
module
mobspy.modules.logic_operator_objects
module
mobspy.modules.meta_class
module
mobspy.modules.meta_class_utils
module
mobspy.modules.mobspy_expressions
module
mobspy.modules.mobspy_parameters
module
mobspy.modules.order_operators
module
mobspy.modules.reaction_construction_nb
module
mobspy.modules.reaction_construction_nb_parallel
module
mobspy.modules.set_counts_module
module
mobspy.modules.species_string_generator
module
mobspy.modules.unit_handler
module
mobspy.modules.user_functions
module
mobspy.parameter_scripts
module
mobspy.parameter_scripts.parameter_reader
module
mobspy.parameter_scripts.parametric_sweeps
module
mobspy.parameters
module
mobspy.parameters.default_reader
module
mobspy.parameters.example_reader
module
mobspy.plot_params
module
mobspy.plot_params.default_plot_reader
module
mobspy.plot_params.example_plot_reader
module
mobspy.plot_scripts
module
mobspy.plot_scripts.default_plots
module
mobspy.plot_scripts.hierarchical_plot
module
mobspy.plot_scripts.process_plot_data
module
mobspy.plot_scripts.statistics_calculations
module
mobspy.sbml_simulator
module
mobspy.sbml_simulator.builder
module
mobspy.sbml_simulator.run
module
mobspy.sbml_simulator.SBMLWriter
module
mobspy.simulation
module
mobspy.simulation_logging
module
mobspy.simulation_logging.log_scripts
module
Mobspy_Parameter (class in mobspy.modules.mobspy_parameters)
MobsPyExpression (class in mobspy.modules.mobspy_expressions)
MobsPyList_of_TS (class in mobspy.data_handler.time_series_object)
MobsPyTimeSeries (class in mobspy.data_handler.time_series_object)
ModelParameters() (in module mobspy.modules.mobspy_parameters)
module
for_local_use
mobspy
,
[1]
mobspy.data_handler
mobspy.data_handler.process_result_data
mobspy.data_handler.time_series_object
mobspy.modules
mobspy.modules.class_of_meta_specie_named_any
mobspy.modules.event_functions
mobspy.modules.function_rate_code
mobspy.modules.logic_operator_objects
mobspy.modules.meta_class
mobspy.modules.meta_class_utils
mobspy.modules.mobspy_expressions
mobspy.modules.mobspy_parameters
mobspy.modules.order_operators
mobspy.modules.reaction_construction_nb
mobspy.modules.reaction_construction_nb_parallel
mobspy.modules.set_counts_module
mobspy.modules.species_string_generator
mobspy.modules.unit_handler
mobspy.modules.user_functions
mobspy.parameter_scripts
mobspy.parameter_scripts.parameter_reader
mobspy.parameter_scripts.parametric_sweeps
mobspy.parameters
mobspy.parameters.default_reader
mobspy.parameters.example_reader
mobspy.plot_params
mobspy.plot_params.default_plot_reader
mobspy.plot_params.example_plot_reader
mobspy.plot_scripts
mobspy.plot_scripts.default_plots
mobspy.plot_scripts.hierarchical_plot
mobspy.plot_scripts.process_plot_data
mobspy.plot_scripts.statistics_calculations
mobspy.sbml_simulator
mobspy.sbml_simulator.builder
mobspy.sbml_simulator.run
mobspy.sbml_simulator.SBMLWriter
mobspy.simulation
mobspy.simulation_logging
mobspy.simulation_logging.log_scripts
N
name() (mobspy.modules.meta_class.Species method)
New() (in module mobspy.modules.meta_class)
non_expression_add() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_mul() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_pow() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_radd() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_rmul() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_rsub() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_rtruediv() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_sub() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
non_expression_truediv() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
O
old_context (mobspy.modules.meta_class.Reacting_Species attribute)
order_references() (mobspy.modules.meta_class.Species method)
override_get_item() (mobspy.modules.meta_class.Compiler class method)
OverrideQuantity (class in mobspy.modules.mobspy_expressions)
OverrideUnitRegistry (class in mobspy.modules.mobspy_expressions)
P
parameter_process() (in module mobspy.parameter_scripts.parameter_reader)
parameter_stack (mobspy.modules.mobspy_parameters.Mobspy_Parameter attribute)
parametric_plot() (in module mobspy.plot_scripts.default_plots)
plot() (mobspy.simulation.Simulation method)
(mobspy.simulation.SimulationComposition method)
plot_curves() (in module mobspy.plot_scripts.hierarchical_plot)
plot_data() (in module mobspy.plot_scripts.hierarchical_plot)
plot_deterministic() (mobspy.simulation.Simulation method)
(mobspy.simulation.SimulationComposition method)
plot_parametric() (mobspy.simulation.Simulation method)
plot_raw() (mobspy.simulation.Simulation method)
(mobspy.simulation.SimulationComposition method)
plot_stochastic() (mobspy.simulation.Simulation method)
(mobspy.simulation.SimulationComposition method)
prepare_arguments_for_callable() (in module mobspy.modules.function_rate_code)
print_characteristics() (mobspy.modules.meta_class.Species method)
Q
QuantityConverter (class in mobspy.modules.mobspy_expressions)
query_plot_data() (in module mobspy.plot_scripts.process_plot_data)
R
raw_plot() (in module mobspy.plot_scripts.default_plots)
Reacting_Species (class in mobspy.modules.meta_class)
ReactingSpeciesComparator (class in mobspy.modules.logic_operator_objects)
Reactions (class in mobspy.modules.meta_class)
read_json() (in module mobspy.parameter_scripts.parameter_reader)
read_plot_json() (in module mobspy.plot_scripts.default_plots)
ref_characteristics_to_object (mobspy.modules.meta_class.Compiler attribute)
reformat_number_and_species() (mobspy.modules.logic_operator_objects.SpeciesComparator method)
reformat_time_series() (in module mobspy.sbml_simulator.run)
remove() (mobspy.modules.meta_class.List_Species method)
remove_characteristic() (mobspy.modules.meta_class.Species method)
remove_repeated_elements() (mobspy.modules.meta_class.List_Species method)
(mobspy.modules.meta_class.Species method)
rename() (mobspy.modules.mobspy_parameters.Mobspy_Parameter method)
reset_counts() (mobspy.modules.meta_class.Species method)
reset_quantities() (mobspy.modules.meta_class.Species method)
reset_reactions() (mobspy.modules.meta_class.Species method)
reset_references() (mobspy.modules.meta_class.Species method)
reset_simulation_context() (mobspy.modules.meta_class.Species class method)
return_pandas() (mobspy.data_handler.time_series_object.MobsPyList_of_TS method)
run() (mobspy.simulation.Simulation method)
(mobspy.simulation.SimulationComposition method)
S
save_data() (mobspy.simulation.Simulation method)
search_for_parameters_in_str() (in module mobspy.modules.function_rate_code)
set_counts() (in module mobspy.modules.set_counts_module)
set_figure_characteristics() (in module mobspy.plot_scripts.hierarchical_plot)
set_from_json() (mobspy.simulation.Simulation method)
set_global_parameters() (in module mobspy.plot_scripts.hierarchical_plot)
set_job_number() (mobspy.simulation.Simulation class method)
set_ms_active() (mobspy.modules.mobspy_expressions.OverrideQuantity method)
set_plot_units() (in module mobspy.plot_scripts.default_plots)
set_rate() (mobspy.modules.meta_class.Reactions method)
set_reactions() (mobspy.modules.meta_class.Species method)
set_references() (mobspy.modules.meta_class.Species method)
set_simulation_context() (mobspy.modules.meta_class.Species class method)
show_characteristics() (mobspy.modules.meta_class.Species method)
show_quantities() (mobspy.modules.meta_class.Species method)
show_reactions() (mobspy.modules.meta_class.Species method)
show_references() (mobspy.modules.meta_class.Species method)
simulate() (in module mobspy.sbml_simulator.run)
Simulation (class in mobspy.simulation)
SimulationComposition (class in mobspy.simulation)
Species (class in mobspy.modules.meta_class)
SpeciesComparator (class in mobspy.modules.logic_operator_objects)
Specific_Species_Operator (class in mobspy.modules.mobspy_expressions)
standard_deviation() (in module mobspy.plot_scripts.statistics_calculations)
stochastic_plot() (in module mobspy.plot_scripts.default_plots)
stochastic_string() (in module mobspy.modules.function_rate_code)
str_under_context() (mobspy.modules.meta_class.Species class method)
T
time_filter_operation() (in module mobspy.plot_scripts.process_plot_data)
time_series_average() (in module mobspy.plot_scripts.statistics_calculations)
to_dict() (mobspy.data_handler.time_series_object.MobsPyList_of_TS method)
U
unit() (mobspy.modules.meta_class.Species method)
unite_characteristics() (in module mobspy.modules.meta_class_utils)
unite_parameter_dictionaries() (in module mobspy.parameter_scripts.parametric_sweeps)
update_meta_specie_named_any_context() (mobspy.modules.meta_class.Species class method)
W
warning() (in module mobspy.simulation_logging.log_scripts)