biocrnpyler.components.CombinatorialComplex

class biocrnpyler.components.CombinatorialComplex(final_states, initial_states=None, intermediate_states=None, excluded_states=None, name=None, **kwargs)[source]

Bases: Component

Complex formed through combinatorial binding of multiple species.

A CombinatorialComplex component represents a complex that can form through multiple combinatorial binding pathways. The component enumerates all possible intermediate complexes and generates binding reactions between initial states and final states, optionally constrained by intermediate states and excluded states. Uses a ‘binding’ mechanism to generate combinatorial binding reactions.

Parameters:

final_states (ComplexSpecies or list of ComplexSpecies) – The final complex(es) to be formed. All binding reactions ultimately lead to these states.
initial_states (list of Species or ComplexSpecies, optional) – Starting species that bind together to form final_states. If None, defaults to all individual species contained within final_states.
intermediate_states (list of ComplexSpecies, optional) – Allowed intermediate complexes formed during binding. Restricts the binding pathway. If None, all possible intermediates are enumerated.
excluded_states (list of Species or ComplexSpecies, optional) – Species or complexes that are NOT allowed to form. If None, no complexes are excluded.
name (str, optional) – Name of the component. If None, automatically generated from final_states names.
**kwargs – Additional keyword arguments passed to the Component base class constructor.

Attributes:

final_states (list of ComplexSpecies) – List of final complex states.
initial_states (list of Species or ComplexSpecies) – List of initial binding species.
intermediate_states (list of ComplexSpecies or None) – List of allowed intermediate complexes, or None if unrestricted.
excluded_states (list) – List of excluded species/complexes.
sub_species (list of Species) – All individual species contained in final_states.
combination_dict (dict) – Dictionary storing computed binding combinations.

See also

ChemicalComplex: Simple complex of two or more molecules.
Component: Base class for biomolecular components.
ComplexSpecies: Species subclass for molecular complexes.

Notes

The combinatorial binding process generates reactions based on the provided constraints:

Case 1 - only final_states given: all species in final_states bind combinatorially:

\[{\text{individual species}} \rightleftharpoons {\text{all intermediates}} \rightleftharpoons {\text{final states}}\]

Case 2 - final_states + initial_states: binding starts from specified initial states directly to final states:

\[{\text{initial_states}} \rightleftharpoons {\text{final_states}}\]

Case 3 - final_states + intermediate_states: binding restricted to specified intermediates:

\[{\text{individual species}} \rightleftharpoons {\text{intermediate states}} \rightleftharpoons {\text{final states}}\]

Case 4 - final_states + initial_states + intermediate_states: both initial and intermediate constraints applied:

\[{\text{initial states}} \rightleftharpoons {\text{intermediate states}} \rightleftharpoons {\text{final states}}\]

The component name is automatically generated as a concatenation of final_states names separated by underscores if not provided.

Examples

Example 1: Full combinatorial binding

>>> A = bcp.Species('A')
>>> B = bcp.Species('B')
>>> C = bcp.Species('C')
>>> final = bcp.Complex([A, B, C])
>>> cc = bcp.CombinatorialComplex(
...     final_states=final,
...     mechanisms={'binding': bcp.One_Step_Binding()},
...     parameters={'kb': 1e-1, 'ku': 1e-1})

Initial states default to [A, B, C]. All intermediates [A, B], [A, C], [B, C] are enumerated, resulting in 6 reversible reactions:

A + B \(\rightleftharpoons\) Complex([A, B])
A + C \(\rightleftharpoons\) Complex([A, C])
B + C \(\rightleftharpoons\) Complex([B, C])
Complex([A, B]) + C \(\rightleftharpoons\) Complex([A, B, C])
Complex([A, C]) + B \(\rightleftharpoons\) Complex([A, B, C])
Complex([B, C]) + A \(\rightleftharpoons\) Complex([A, B, C])

Example 2: Constrained initial states

>>> initial = [bcp.Complex([A, B]), bcp.Complex([A, C])]
>>> cc = bcp.CombinatorialComplex(
...     final_states=final, initial_states=initial,
...     mechanisms={'binding': bcp.One_Step_Binding()},
...     parameters={'kb': 1e-1, 'ku': 1e-1})

Results in 2 reactions:

Complex([A, B]) + C \(\rightleftharpoons\) Complex([A, B, C])
Complex([A, C]) + B \(\rightleftharpoons\) Complex([A, B, C])

Example 3: Restricted intermediate states

>>> inter = [bcp.Complex([A, B]), bcp.Complex([A, C])]
>>> cc = bcp.CombinatorialComplex(
...     final_states=final, intermediate_states=inter,
...     mechanisms={'binding': bcp.One_Step_Binding()},
...     parameters={'kb': 1e-1, 'ku': 1e-1})

Results in 4 reactions:

A + B \(\rightleftharpoons\) Complex([A, B])
A + C \(\rightleftharpoons\) Complex([A, C])
Complex([A, B]) + C \(\rightleftharpoons\) Complex([A, B, C])
Complex([A, C]) + B \(\rightleftharpoons\) Complex([A, B, C])

Example 4: Multiple final states with homodimers

>>> final = [bcp.Complex([A, A, B]), bcp.Complex([A, B, B])]
>>> cc = bcp.CombinatorialComplex(
...     final_states=final,
...     mechanisms={'binding': bcp.One_Step_Binding()},
...     parameters={'kb': 1e-1, 'ku': 1e-1})

Results in 7 reactions including homodimer formation:

A + A \(\rightleftharpoons\) Complex([A, A])
Complex([A, A]) + B \(\rightleftharpoons\) Complex([A, A, B])
B + B \(\rightleftharpoons\) Complex([B, B])
Complex([B, B]) + A \(\rightleftharpoons\) Complex([A, B, B])
A + B \(\rightleftharpoons\) Complex([A, B])
Complex([A, B]) + A \(\rightleftharpoons\) Complex([A, A, B])
Complex([A, B]) + B \(\rightleftharpoons\) Complex([A, B, B])

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.
`compute_species_to_add`	Compute species needed to convert s0 into complex sf.
`enumerate_components`	Enumerate derived components created from this component.
`get_combinations_between`	Get all binding combinations to form complex sf from s0.
`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 primary species associated with this component.
`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 combinatorial reactions.
`update_species`	Use 'binding' mechanism to generate combinatorial 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

compute_species_to_add(s0, sf)[source]

Compute species needed to convert s0 into complex sf.

Parameters:

s0 (Species or ComplexSpecies) – Starting species or complex.
sf (ComplexSpecies) – Target final complex.

Returns:

List of species that need to be added to s0 to form sf. Returns None if s0 contains species not in sf or more copies of any species than sf contains.

Return type:

list of Species or None

Raises:

ValueError – If sf is not a ComplexSpecies.

Notes

This method compares the stoichiometry of species in s0 and sf to determine what needs to be added. If s0 contains more of any species than sf, or contains species not in sf, None is returned.

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.

property excluded_states

Species or complexes excluded from enumeration.

Type:: list

property final_states

List of final complex states to be formed.

Return type:: list of ComplexSpecies

get_combinations_between(s0, sf)[source]

Get all binding combinations to form complex sf from s0.

Enumerates all possible binding orders (permutations) to construct the final complex sf starting from s0, generating tuples of (binder, bindee, complex_species) for each binding step.

Parameters:

s0 (Species or ComplexSpecies) – Starting species or complex.
sf (ComplexSpecies) – Target final complex.

Returns:

List of (binder, bindee, complex_species) tuples representing all possible binding combinations. Each tuple represents one binding step. Returns empty list if no combinations are possible.

Return type:

list of tuple

Notes

The method:

Computes which species need to be added to s0 to form sf
Generates all permutations of these species (different binding orders)
For each permutation, creates binding steps: binder + bindee \(\rightarrow\) complex
Filters out any combinations involving excluded_states

Examples

If s0 = A and sf = Complex([A, B, C]), and no exclusions:

Returns combinations for different binding orders:

Order 1: (B, A, [A,B]), (C, [A,B], [A,B,C])
Order 2: (C, A, [A,C]), (B, [A,C], [A,B,C])

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() → None[source]

Get the primary species associated with this component.

Returns:: Subclasses should override this method to return their primary Species object.
Return type:: None

Notes

This is a placeholder that should be implemented by subclasses.

property initial_states

List of initial states for binding.

Return type:: list of Species or ComplexSpecies

property intermediate_states

List of allowed intermediate complexes.

Return type:: list of ComplexSpecies or None

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()[source]

Use ‘binding’ mechanism to generate combinatorial reactions.

Uses the ‘binding’ mechanism to generate reactions for all possible binding combinations between initial_states and final_states, optionally constrained by intermediate_states and excluding excluded_states.

Returns:: List of all binding reactions (forward and reverse) along all enumerated pathways.
Return type:: list of Reaction

Notes

The method handles two cases:

With intermediate_states:

Generate reactions: initial_states \(\rightleftharpoons\) intermediate_states

Generate reactions: intermediate_states \(\rightleftharpoons\) final_states

Without intermediate_states:

Generate reactions: initial_states \(\rightleftharpoons\) final_states directly

Duplicate reactions are automatically filtered out. The method uses combination_dict computed by update_species() or computes it if needed. Reactions are symmetric, so (binder, bindee, complex) and (bindee, binder, complex) are treated as duplicates.

update_species()[source]

Use ‘binding’ mechanism to generate combinatorial species.

Uses the ‘binding’ mechanism to generate species for all possible binding combinations between initial_states and final_states, optionally constrained by intermediate_states and excluding excluded_states.

Returns:: List of all unique species generated, including initial states, final states, and all intermediate complexes along binding pathways.
Return type:: list of Species

Notes

The method handles two cases:

With intermediate_states:

Generate combinations: initial_states \(\rightarrow\) intermediate_states

Generate combinations: intermediate_states \(\rightarrow\) final_states

Without intermediate_states:

Generate combinations: initial_states \(\rightarrow\) final_states directly

Duplicate species are automatically removed from the final list. The combination_dict is populated during this process for use by update_reactions.