biocrnpyler.core.component

Classes

Component(name[, mechanisms, parameters, ...])

Component class for core components.
class biocrnpyler.core.component.Component(name: str | Species, mechanisms=None, parameters=None, parameter_file=None, mixture=None, compartment=None, attributes=None, initial_concentration=None, initial_condition_dictionary=None, **keywords)[source]

Component class for core components.

These subclasses of Component represent different kinds of biomolecules.

This class must be Subclassed to provide functionality with the functions get_species and get_reactions overwritten.

Initializes a Component object.

Parameters:

  • name

  • mechanisms

  • parameters

  • parameter_file

  • mixture

  • compartment

  • attributes

  • initial_concentration

  • initial_condition_dictionary

  • keywords

add_mechanism(mechanism: Mechanism, mech_type=None, overwrite=False, optional_mechanism=False)[source]

adds a mechanism of type mech_type to the Component Mechanism dictionary.

Parameters:

  • mechanism

  • mech_type

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

add_mechanisms(mechanisms: Mechanism | GlobalMechanism, overwrite=False, optional_mechanism=False)[source]

This function adds a list or dictionary of mechanisms to the mixture.

Parameters:

  • mechanisms – Can take both GlobalMechanisms and Mechanisms

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

property compartment

The compartment of the Component.

Returns:

Compartment

enumerate_components(**keywords) → List[source]

this is for component enumeration. Usually you will return a list of components that are copies of existing ones (first list) and new components (second list). For example, A DNA_construct makes a list of copies of its parts as the first output, and a list of RNA_constructs as the second output. An RNA_construct will make a list of copies of its parts as the first output, and a list of Protein components as its second output (if it makes any proteins)

get_mechanism(mechanism_type, optional_mechanism=False)[source]

Searches the Component for a Mechanism of the correct type.

If the Component does not have the mechanism, searches the Components’ Mixture for the Mechanism.

Parameters:

  • mechanism_type

  • optional_mechanism – toggles whether an error is thrown if no mechanism is found

Returns:

get_parameter(param_name: str, part_id=None, mechanism=None, return_numerical=False, return_none=False, check_mixture=True) → Parameter | Real[source]

Get a parameter from different objects that hold parameters.

Hierarchy:

  1. tries to find the Parameter in Component.parameter_database

  2. tries to find the parameter in Component.mixture.parameter_database

Parameters:

  • param_name

  • part_id

  • mechanism

  • return_numerical – numerical value or the parameter object is returned

  • return_none – returns None instead of throwing an error if a parameter isn’t found

  • check_mixture – toggle whether or not to check the Component’s Mixture as well

Returns:

Parameter object or a Real number

get_species() → None[source]

The subclasses should implement this method!

Returns:

None

set_mixture(mixture) → None[source]

Set the mixture the Component is in.

Parameters:

mixture

Returns:

None

classmethod set_species(species: Species | str, material_type=None, compartment=None, attributes=None) → Species[source]

Helper function that allows species to be set from strings, species, or Components

Parameters:

  • species – Species, str, Component

  • material_type

  • compartment

  • attributes

Returns:

Species

update_parameters(parameter_file=None, parameters=None, parameter_database=None, overwrite_parameters=True)[source]

Updates the ParameterDatabase inside a Component

Possible inputs:

parameter_file (string) parameters (dict) parameter_database (ParameterDatabase)

update_reactions() → List[Species][source]

The subclasses should implement this method!

Returns:

empty list

update_species() → List[Species][source]

The subclasses should implement this method!

Returns:

empty list