biocrnpyler.components.dna.cds

Classes

CDS(name[, protein, no_stop_codons])

a CDS is a sequence of DNA that codes for a protein

class biocrnpyler.components.dna.cds.CDS(name, protein=None, no_stop_codons=None, **keywords)

a CDS is a sequence of DNA that codes for a protein

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

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)

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:

clone(position, direction, parent_dna)

this defines where the part is in what piece of DNA

property compartment

The compartment of the Component.

Returns:

Compartment

enumerate_components(**keywords) → List

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)

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_orphan()

returns a copy of this monomer, except with no parent. But it still has a position and direction

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

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()

The subclasses should implement this method!

Returns:

None

set_mixture(mixture) → None

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

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

Parameters:

• species – Species, str, Component

• material_type

• compartment

• attributes

Returns:

Species

unclone()

removes the current part from anything

update_parameters(parameter_file=None, parameters=None, parameter_database=None, overwrite_parameters=True)

Updates the ParameterDatabase inside a Component

Possible inputs:

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

update_reactions()

The subclasses should implement this method!

Returns:

empty list

update_species()

The subclasses should implement this method!

Returns:

empty list