biocrnpyler.components.ChemicalComplex

class biocrnpyler.components.ChemicalComplex(species: List[Species], name: str = None, material_type='complex', attributes=None, **kwargs)[source]

Bases: Component

Complex formed by binding of two or more molecular species.

A ChemicalComplex component represents a molecular complex formed when two or more species bind together. The complex automatically inherits attributes from its constituent species. The component uses a ‘binding’ mechanism to generate binding and unbinding reactions.

Parameters:

species (list of Species, str, or Component) – List of species that form the complex. Must contain at least two elements. Each element can be a Species object, string name, or Component with an associated species.
name (str, optional) – Name of the complex. If None, a name is automatically generated from the constituent species names.
material_type (str, default 'complex') – Material type identifier for the complex species. Can be customized for specific complex types.
attributes (list of str, optional) – List of attribute tags to associate with the complex species. The complex also inherits attributes from its constituent species.
**kwargs – Additional keyword arguments passed to the Component base class constructor.

Attributes:

species (Complex) – The complex species object created from the constituent species.
internal_species (list of Species) – List of individual species that make up the complex.

See also

Component: Base class for biomolecular components.
Species: Chemical species representation.
Complex: Species subclass for molecular complexes.

Notes

The ChemicalComplex component uses a ‘binding’ mechanism which must be provided by the containing mixture. The binding mechanism generates:

Forward binding reactions (species \(\rightarrow\) complex)
Reverse unbinding reactions (complex \(\rightarrow\) species)

The first species in the list is treated as the ‘bindee’ and remaining species are treated as ‘binders’ in the binding mechanism.

Examples

Create a simple protein-DNA complex:

>>> complex = bcp.ChemicalComplex(
...     species=['TF_protein', 'DNA_promoter'],
...     name='TF_bound'
... )

Create an enzyme-substrate complex:

>>> complex = bcp.ChemicalComplex(
...     species=['protein_E', 'S'],
...     name='ES_complex'
... )

Use with a mixture and binding mechanism:

>>> from biocrnpyler.mechanisms import One_Step_Binding
>>> mixture = bcp.Mixture(
...     components=[complex],
...     mechanisms={'binding': One_Step_Binding()},
...     parameters={'kb': 1.0, 'ku': 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 complex 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 'binding' mechanism to generate binding/unbinding reactions.
`update_species`	Use 'binding' mechanism to generate species for binding reactions.

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() → List[Species][source]

Get the complex species.

Returns:: The complex species object containing all constituent species.
Return type:: Complex

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[Reaction][source]

Use ‘binding’ mechanism to generate binding/unbinding reactions.

Uses the ‘binding’ mechanism to generate reactions for complex formation (binding) and dissociation (unbinding).

Returns:: List of reactions generated by the binding mechanism, typically including forward binding and reverse unbinding reactions.
Return type:: list of Reaction

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

Use ‘binding’ mechanism to generate species for binding reactions.

Uses the ‘binding’ mechanism to generate all species needed for binding and unbinding reactions, including the individual species and the complex.

Returns:: List of all species generated by the binding mechanism, typically including the constituent species and the complex species.
Return type:: list of Species