Export

ModelSBML

class eBCSgen.Export.ModelSBML.ModelSBML(level, version)

Bases: object

create_all_reactions(rules: set)

This function creates all reactions from rules At first, it translates to RHS/LHS

Then it creates kinetic law for all reactions and at the same time it creates modifiers for those Complexes that were not used either as reactant or product.

Parameters:

rules – set of BCSL rules used in a model

create_all_species_compartments_and_complex_species_types(unique_complexes: dict, structure_signature: dict)

Creates all compartments

Creates species for every unique Complex agent in values Creates SpeciesType for Complex agent if there is new one - no isomorphisms here

Parameters:

unique_complexes – dict() of representative Complexes[Keys] & tuple() of pairs (Core.Complex,str. SBML_species_code()) Encapsulates all used Complexes and theirs isomorphisms in the model

create_basic_species_types(atomics: dict, structs: dict)

Function creates SBML speciesTypes from signatures. speciesTypes do not have compartments by default. compartment is added in specific species later and they are cereated using map compartments -> outside agents

Parameters:

  • atomics – signature of atomic agents

  • structs – signature of structure agents

create_compartment(compartment: str)

Function creates SBML-compartment using string name of compartment

Parameters:

compartment – string name of compartment

create_kinetic_law_and_modifiers(ordered_rules, reaction_objects)

Creates kinetic law for all reactions and at the same time it creates modifiers for those Complexes that were not used either as reactant or product.

Parameters:

  • ordered_rules – BCSL rules

  • reaction_objects – list of all libSBML reaction objects

create_parameters(definitions: dict, unique_params: set)

Sets up parameters from definitions and parameters in rates

Parameters:

  • definitions – parameters in BCSL definition

  • unique_params – parameters in BCSL rates

create_products(items: list, reaction)

Creates all products from Complexes in list of tuples

Parameters:

  • items – list of RHS complexes in reaction

  • reaction – given reaction

create_reactants(items: list, reaction)

Creates all reactants from Complexes in list of tuples

Parameters:

  • items – list of LHS complexes in reaction

  • reaction – given reaction

create_reaction_for_isomorphisms(unique_complexes)

Function creates all reactions between isomorphism in order to ensure that given Complexes are interchangeable but specific rule applies only to that exact isomorphism

Parameters:

unique_complexes – given possible unique complexes

create_species(comp_agent: Complex)

Creates all species in the model

Parameters:

comp_agent – BCSL Complex agent to be translated to SBML Species

create_species_feature_type(new_species_type, atomic: str, atomics: dict)

Function creates species feature Type inside Atomic agent.

Add all possible feature values to ListOfPossibleFeatureValues of given speciesFeatureType. If feature value is ‘_’, ignore itte

Parameters:

  • new_species_type – libsbml object of new speciesType

  • atomic – name of given atomic agent

  • atomics – atomic signature of the model

create_species_features(comp_agent: Complex, new_species_multi_plugin)

Creates all species features for given species

Parameters:

  • comp_agent – BCSL complex agent to create SBML species features for

  • new_species_multi_plugin – libsbml plugin for manipulating SBML-multi species

create_species_type_from_complex(comp_agent: Complex, structure_signature: dict)

All complex agents are translated to SpeciesTypes Here

Parameters:

comp_agent – BCSL agent to be translated to SBML-multi species type

create_species_types_from_atomic(atomics: dict)

Function creates speciesTypes from Atomic agents

Parameters:

atomics – atomic signature of the model in <dict>

create_species_types_from_structure(structs: dict)

Function creates speciesTypes from Structure agents

Parameters:

structs – structure signature of the model in <dict>

set_initial_amounts(init)

Sets up initial Amount of Complex agents from inits

Parameters:

init – Complex agents at the beginning of the running of the model

set_species_feature(agent, plugin, component_ref, is_component: bool)

Creates and sets up species feature

If there are 2 or more agents in complex with the same name, reference can distinguish between them by mentioning their parent structure agent too.

If SpeciesFeature should be ‘_’, ignore it. This corresponds to any value.

Parameters:

  • agent – agent of given feature

  • plugin – multi plugin to manipulate with species features

  • component_ref – reference to agent where this feature belongs.

  • is_component – says about if setting the component atr. is necessary