biocrnpyler.components.Metabolite

class biocrnpyler.components.Metabolite(name: str, attributes=None, precursors=None, products=None, **kwargs)[source]

Bases: Component

Metabolic compound that can be produced, utilized, or degraded.

A Metabolite component represents a metabolic compound that participates in biochemical pathways. It can have precursors (species that are converted into this metabolite) and products (species that this metabolite is converted into). The component uses a ‘metabolic_pathway’ mechanism to generate production and degradation reactions.

Parameters:

name (str) – Name of the metabolite.
attributes (list of str, optional) – List of attribute tags to associate with the metabolite species.
precursors (list of Species, str, Component, or None, optional) – List of chemical species that are directly transformed into this metabolite via the production mechanism. None represents constitutive production (production from nothing).
products (list of Species, str, Component, or None, optional) – List of chemical species produced from this metabolite via the degradation mechanism. None represents total degradation (degradation to nothing).
**kwargs – Additional keyword arguments passed to the Component base class constructor.

Attributes:

species (Species) – The metabolite species object with material_type=’metabolite’.
precursors (list of Species or None) – List of precursor species. None values represent constitutive production.
products (list of Species or None) – List of product species. None values represent total degradation.

See also

Enzyme: Enzymatic component for catalysis.
Component: Base class for biomolecular components.

Notes

The Metabolite component looks for a ‘metabolic_pathway’ mechanism but will not throw an error if it is not found. If the mechanism is present:

Production reactions are generated from precursors to the metabolite
Degradation reactions are generated from the metabolite to products

None is a valid precursor/product representing constitutive production/degradation.

Examples

Create a metabolite with constitutive production and degradation:

>>> atp = bcp.Metabolite(
...     name='ATP',
...     precursors=[None],
...     products=[None]
... )

Create a metabolite with specific precursor and product:

>>> adp = bcp.Metabolite(
...     name='ADP',
...     precursors=['ATP'],
...     products=['AMP']
... )

Use with a mixture and metabolic pathway mechanism:

>>> from biocrnpyler.mechanisms import OneStepPathway
>>> mixture = bcp.Mixture(
...     components=[atp],
...     mechanisms={'metabolic_pathway': OneStepPathway()},
...     parameters={'k': 0.1}
... )
>>> crn = mixture.compile_crn()

Methods

`add_attribute`	Add a single attribute to the component.
`add_mechanism`	Add a mechanism to this component's mechanism dictionary.
`add_mechanisms`	Add multiple mechanisms to this component.
`enumerate_components`	Enumerate derived components created from this component.
`get_mechanism`	Retrieve a mechanism by type from the component or its mixture.
`get_parameter`	Retrieve parameter from component or mixture parameter database.
`get_species`	Get the metabolite species.
`set_attributes`	Set multiple attributes for the component.
`set_mixture`	Set the mixture containing this component.
`set_species`	Convert various inputs into Species objects.
`update_parameters`	Update the parameter database with new parameters.
`update_reactions`	Use 'metabolic_pathway' mechanism to generate reactions.
`update_species`	Use 'metabolic_pathway' mechanism to generate species.

add_attribute(attribute: str)[source]

Add a single attribute to the component.

Adds an attribute tag to the component’s attribute list and to its associated species object, if one exists. Attributes can be used for mechanism selection, species filtering, and tracking special properties.

Parameters:

attribute (str) – Attribute string to add to the component. Must be a non-None string value.

Raises:

AssertionError – If attribute is not a string or is None.
Warning – If the component has no internal species to which the attribute can be added.

Notes

Attributes are commonly used to tag components with properties such as:

Degradation tags (e.g., ‘degtagged’, ‘ssrAtagged’, )
Functional properties (e.g., ‘fluorescent’, ‘membranebound’)
Regulatory elements (e.g., ‘inducible’, ‘repressible’)

Examples

Add attributes to tag a protein with special properties:

>>> protein = bcp.Protein('GFP')
>>> protein.add_attribute('fluorescent')
>>> protein.add_attribute('ssrAtagged')
>>> protein.attributes
['fluorescent', 'ssrAtagged']

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

Add a mechanism to this component’s mechanism dictionary.

Parameters:

mechanism (Mechanism) – The mechanism object to add.
mech_type (str, optional) – The type key under which to store the mechanism. If None, uses the mechanism’s mechanism_type attribute.
overwrite (bool, default False) – If True, replaces any existing mechanism with the same key. If False, raises ValueError when key already exists.
optional_mechanism (bool, default False) – If True, suppresses the ValueError when a mechanism key conflict occurs and overwrite is False.

Raises:

TypeError – If mechanism is not a Mechanism object, or if mech_type is not a string.
ValueError – If mechanism key already exists, overwrite is False, and optional_mechanism is False.

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

Add multiple mechanisms to this component.

Accepts mechanisms as a single object, list, or dictionary and adds them to the component’s mechanism dictionary.

Parameters:

mechanisms (Mechanism, GlobalMechanism, dict, or list) – The mechanism(s) to add. Can be a single mechanism, a dict with mechanism types as keys and mechanisms as values, or a list of mechanisms.
overwrite (bool, default False) – If True, replaces any existing mechanisms with the same keys. If False, raises ValueError when keys already exist.
optional_mechanism (bool, default False) – If True, suppresses ValueError when mechanism key conflicts occur and overwrite is False.

Raises:

ValueError – If mechanisms is not a valid type, or if mechanism key conflicts occur with overwrite=False and optional_mechanism=False.

property compartment

The compartment containing this component.

Type:: Compartment or None

enumerate_components(previously_enumerated=None) → List[source]

Enumerate derived components created from this component.

This method generates new components based on the current component, typically used during CRN compilation to expand higher-level components into their constituent parts and products.

Parameters:: previously_enumerated (set or list, optional) – Collection of components that have already been enumerated, used to prevent infinite recursion in component enumeration.
Returns:: List of new components created from this component. This base implementation returns an empty list.
Return type:: list

Notes

Subclasses override this method to implement specific enumeration behavior. For example:

A DNA_construct returns copies of its parts and RNA_construct objects representing transcripts.
An RNA_construct returns copies of its parts and Protein components representing translation products.

get_mechanism(mechanism_type, optional_mechanism=False)[source]

Retrieve a mechanism by type from the component or its mixture.

Searches first in the component’s mechanism dictionary, then falls back to the mixture’s mechanisms if not found.

Parameters:

mechanism_type (str) – The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).
optional_mechanism (bool, default False) – If True, returns None when mechanism not found. If False, raises KeyError when mechanism not found.

Returns:

The requested mechanism object, or None if not found and optional_mechanism is True.

Return type:

Mechanism or None

Raises:

TypeError – If mechanism_type is not a string.
KeyError – If mechanism not found and optional_mechanism is False.

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

Retrieve parameter from component or mixture parameter database.

Searches first in the component’s parameter database, then falls back to the mixture’s parameter database if not found.

Parameters:

param_name (str) – Name of the parameter to retrieve.
part_id (str, optional) – Part identifier for the parameter lookup key.
mechanism (str, optional) – Mechanism identifier for the parameter lookup key.
return_numerical (bool, default False) – If True, returns the numerical value. If False, returns the Parameter object.
return_none (bool, default False) – If True, returns None when parameter not found. If False, raises ValueError when parameter not found.
check_mixture (bool, default True) – If True, searches the mixture’s parameter database if not found in the component’s database.

Returns:

The parameter object or its numerical value, or None if not found and return_none is True.

Return type:

Parameter, Real, or None

Raises:

ValueError – If parameter not found and return_none is False.

Notes

Parameter lookup follows the hierarchy:

Component.parameter_database
Component.mixture.parameter_database (if check_mixture is True)

get_species() → Species[source]

Get the metabolite species.

Returns:: The metabolite species object with material_type=’metabolite’.
Return type:: Species

set_attributes(attributes: List[str])[source]

Set multiple attributes for the component.

Adds a list of attribute tags to the component and its associated species by calling add_attribute for each attribute in the list.

Parameters:: attributes (list of str or None) – List of attribute strings to add to the component. If None, no action is taken.

See also

add_attribute: Add a single attribute to the component.

Examples

>>> comp = bcp.Protein(name="MyProtein")
>>> comp.set_attributes(["degtagged", "fluorescent"])
>>> comp.attributes
['degtagged', 'fluorescent']

set_mixture(mixture) → None[source]

Set the mixture containing this component.

Parameters:: mixture (Mixture or None) – The mixture object that contains this component and provides default mechanisms and parameters.

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

Convert various inputs into Species objects.

Parameters:

species (Species, str, Component, or list) – The species to convert. Can be a Species object (returned as-is), a string (creates new Species), a Component (extracts its species), or a list of any of these types.
material_type (str, optional) – Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). Only used when creating new Species from strings.
compartment (Compartment, optional) – Compartment to assign to the species. Only used when creating new Species from strings.
attributes (list of str, optional) – Attributes to assign to the species. Only used when creating new Species from strings.

Returns:

The converted Species object(s). Returns a list if input was a list.

Return type:

Species or list of Species

Raises:

ValueError – If the input cannot be converted to a valid Species.

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

Update the parameter database with new parameters.

Parameters:

parameter_file (str, optional) – Path to a CSV or TSV file containing parameters to load.
parameters (dict, optional) – Dictionary of parameters to add. Keys follow the format (mechanism, part_id, param_name).
parameter_database (ParameterDatabase, optional) – Another parameter database to merge into component’s database.
overwrite_parameters (bool, default True) – If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

update_reactions() → List[source]

Use ‘metabolic_pathway’ mechanism to generate reactions.

Uses the ‘metabolic_pathway’ mechanism (if present) to generate production reactions (from precursors to metabolite) and degradation reactions (from metabolite to products).

Returns:: List of reactions including production and degradation pathways. If no mechanism is present, returns an empty list.
Return type:: list of Reaction

update_species() → List[Species][source]

Use ‘metabolic_pathway’ mechanism to generate species.

Uses the ‘metabolic_pathway’ mechanism (if present) to generate species for production reactions (from precursors to metabolite) and degradation reactions (from metabolite to products).

Returns:: List of species including the metabolite itself and any additional species generated by the ‘metabolic_pathway’ mechanism. If no mechanism is present, returns only the metabolite species.
Return type:: list of Species