biocrnpyler.components.CombinatorialConformationPromoter

class biocrnpyler.components.CombinatorialConformationPromoter(promoter_states, promoter_location, promoter_states_on=True, activating_complexes=None, inactivating_complexes=None, intermediate_states=None, final_states=None, name='CombinatorialConformationPromoter', **kwargs)

Bases: CombinatorialConformation, Promoter

Combinatorial conformation with transcriptionally active states.

A CombinatorialConformationPromoter combines CombinatorialConformation and Promoter functionality, creating a polymer with combinatorial conformations where certain conformations can transcribe/express RNA/protein products. Specific conformations can be designated as transcriptionally active (‘on’) or inactive (‘off’).

Parameters:

• promoter_states (list of PolymerConformation) – Polymer conformations used by the promoter. These states are designated as either ‘on’ or ‘off’ based on promoter_states_on.

• promoter_location (int) – Index of the monomer in the polymer conformation that represents the promoter location on the polymer.

• promoter_states_on (bool, default True) – If True, all promoter_states are transcribable. If False, all states except promoter_states are transcribable.

• activating_complexes (list of ComplexSpecies, optional) – Complexes that activate polymer conformations for transcription regardless of promoter_states.

• inactivating_complexes (list of ComplexSpecies, optional) – Complexes that inactivate polymer conformations, preventing transcription even if otherwise active.

• intermediate_states (list of PolymerConformation, optional) – Allowed intermediate conformations (see CombinatorialConformation).

• final_states (list of PolymerConformation, optional) – Final conformations (see CombinatorialConformation).

• name (str, default 'CombinatorialConformationPromoter') – Name of the component.

• **kwargs – Additional keyword arguments passed to the parent class constructors.

Attributes:

• promoter_states (list of PolymerConformation) – List of designated promoter states.

• promoter_states_on (bool) – Whether promoter_states are active or inactive.

• promoter_location (int) – Polymer position of the promoter.

• activating_complexes (list of ComplexSpecies) – Complexes that activate transcription.

• inactivating_complexes (list of ComplexSpecies) – Complexes that prevent transcription.

• conformation_species (list) – All conformation species (populated by update_species).

See also

CombinatorialConformation

Base class for conformational changes.

Promoter

Base class for transcription initiation.

PolymerConformation

Polymer with internal complexes.

Notes

A conformation is transcriptionally active if:

1. (conformation in promoter_states AND promoter_states_on=True) OR (conformation not in promoter_states AND promoter_states_on=False)

2. OR any activating_complex is present in the conformation

3. AND no inactivating_complex is present

If inactivating_complex conflicts with active_state or active_complex, a warning is issued and transcription is prevented.

The promoter location determines which DNA species from the polymer is used for transcription initiation.

Examples

Create a promoter (operon) with conformational regulation:

>>> A, B, F = (bcp.Species(s) for s in ['A', 'B', 'F'])
>>> op = bcp.PolymerConformation(polymer=[B, A, B])
>>> OF0 = bcp.Complex([op.polymers[0][0], F]).parent  # F bound at pos'n 0
>>> OF1 = bcp.Complex([op.polymers[0][2], F]).parent  # F bound at pos'n 2
>>> OF2 = tbp.Complex([OF1.polymers[0][2], F]).parent # F bound to both
>>> # Looped conformations
>>> L0 = Complex([op.polymers[0][0], op.polymers[0][1], F]).parent
>>> L1 = Complex([op.polymers[0][2], op.polymers[0][1], F]).parent
>>> # Define fully bound looped states
>>> L0F1 = bcp.Complex(
...     [OF1.polymers[0][0], OF1.polymers[0][1], F]).parent
>>> L1F0 = bcp. Complex(
...     [OF0.polymers[0][2], OF0.polymers[0][1], F]).parent
>>> # Create promoter with specific active states
>>> ccp = bcp.CombinatorialConformationPromoter(
...     name="CCP",
...     intermediate_states=[OF0, OF1],
...     final_states=[OF2, L0F1, L1F0],
...     promoter_states=[L0F1, L1F0, L0, L1],  # transcribed states
...     promoter_states_on=True,
...     promoter_location=1
... )

With repression (toggle promoter_states_on):

>>> # Same setup as above, but with promoter_states_on=False
>>> # Now only states NOT in promoter_states will transcribe
>>> ccp = bcp.CombinatorialConformationPromoter(
...     name="CCP",
...     intermediate_states=[OF0, OF1],
...     final_states=[OF2, L0F1, L1F0],
...     promoter_states=[L0F1, L1F0, L0, L1],
...     promoter_states_on=False,
...     promoter_location=1
... )
>>> # Use in a DNAassembly for transcription
>>> assy = bcp.DNAassembly(
...     name="X", dna=op, promoter=ccp, rbs="rbs", protein="X")
>>> mixture = bcp.Mixture(
...     components=[assy],
...     mechanisms=[bcp.SimpleTranscription(), bcp.SimpleTranslation()],
...     parameters={'kf': 1, 'kr': 0.01, 'ktx': 1, 'ktl': 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.
clone	Attach this part to a specific position in a DNA construct.
compute_species_changes	Compute changes needed to convert conformation s0 into sf.
enumerate_components	Enumerate derived components created from this component.
find_polymer_component	Find the polymer component within this monomer or its species.
from_promoter	Create a promoter instance from another promoter or string.
get_combinations_between	Get all conformation change combinations from s0 to sf.
get_mechanism	Retrieve a mechanism by type from the component or its mixture.
get_orphan	Create a copy of this monomer without a parent reference.
get_parameter	Retrieve parameter from component or mixture parameter database.
get_protein_for_expression	Get protein product for expression mixtures.
get_removed	Create a fully detached copy of this monomer.
get_species	Get the bare polymer conformation.
monomer_insert	Insert this monomer into a polymer at a specific position.
remove	Remove this monomer from its parent polymer.
reverse	Reverse the orientation of this DNA part.
set_attributes	Set multiple attributes for the component.
set_dir	Set the direction of the monomer and return self.
set_mixture	Set the mixture containing this component.
set_species	Convert various inputs into Species objects.
subhash	Compute hash contribution from monomer properties.
unclone	Remove this part from its parent construct.
update_component	Create a copy of the promoter with updated DNA binding target.
update_parameters	Update the parameter database with new parameters.
update_reactions	Generate reactions for conformation changes and transcription.
update_species	Generate species for conformation changes and transcription.

__eq__(other)

Test equality between two DNA_parts.

Parts are equal if they have the same type, name, parent assembly/ construct, direction, and position.

Parameters:

other (DNA_part) – The other part to compare with.

Returns:

True if parts are equal, False otherwise.

Return type:

bool

Notes

Equality requires matching:

1. Type (both must be the same DNA_part subclass)

2. Name (identical names)

3. Assembly/parent (same parent construct or both have None)

4. Direction (both forward or both reverse)

5. Position (same position in parent construct)

Parts are considered equal even if their parent constructs are different objects, as long as the string representations of the parents match.

add_attribute(attribute: str)

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)

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)

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.

clone(position, direction, parent_dna)

Attach this part to a specific position in a DNA construct.

Parameters:

• position (int) – Position in the parent DNA where this part should be placed.

• direction (str) – Orientation of the part: ‘forward’ or ‘reverse’.

• parent_dna (DNA_construct or OrderedPolymer) – The DNA construct that will contain this part.

Returns:

Returns self after setting position and parent.

Return type:

DNA_part

Notes

This method establishes the relationship between a part and its containing construct, setting the part’s position and orientation.

property compartment

The compartment containing this component.

Type:

Compartment or None

compute_species_changes(s0, sf)

Compute changes needed to convert conformation s0 into sf.

Analyzes what species need to be added and which complexes need to be merged to transform the initial conformation s0 into the final conformation sf. Assumes both conformations share the same underlying polymer.

Parameters:

• s0 (PolymerConformation) – Starting conformation.

• sf (PolymerConformation) – Target final conformation.

Returns:

Returns False if s0 cannot be additively transformed into sf. Otherwise returns (species_changes, merged_complexes) where:

• species_changes: dict mapping (complex, positions) to list of external species to add

• merged_complexes: dict mapping (complex, positions) to list of complexes from s0 that merge to form sf

Return type:

tuple of (dict, dict) or False

Notes

Returns False if:

• s0 has more complexes at any position than sf

• Any complex in sf cannot be formed additively from s0

property dna_species

The chemical species representation of this DNA part.

Returns a Species object with material_type=’part’ representing this DNA_part as a chemical species in the CRN.

Type:

Species

property dna_to_bind

DNA species used as transcription template.

If not explicitly set, defaults to the assembly’s DNA species.

Type:

Species or None

enumerate_components(previously_enumerated=None) → List

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

List of excluded conformations.

Return type:

list of PolymerConformation

property final_states

List of final conformation states.

Return type:

list of PolymerConformation

find_polymer_component()

Find the polymer component within this monomer or its species.

Searches this monomer and, if it is a ComplexSpecies, its constituent species to find which one is marked as a polymer component.

Returns:

The monomer that is part of a polymer structure, or None if no polymer component is found.

Return type:

OrderedMonomer or None

Raises:

ValueError – If multiple species are marked as polymer components in the same location.

Notes

This method is primarily used internally to handle complex species that may contain monomers as part of larger structures.

classmethod from_promoter(name, assembly, transcript, protein)

Create a promoter instance from another promoter or string.

Factory method for creating promoters from various input types.

Parameters:

• name (Promoter or str) – Either a string name for a new promoter, or an existing Promoter object to copy.

• assembly (DNAassembly) – The assembly containing this promoter.

• transcript (RNA or str) – The RNA transcript produced by this promoter.

• protein (Protein, str, or list) – The protein product(s) for expression mixtures.

Returns:

A new Promoter instance. If name is a Promoter, returns a deep copy with updated assembly, transcript, and protein attributes.

Return type:

Promoter

Raises:

TypeError – If name is neither a string nor a Promoter.

get_combinations_between(s0, sf)

Get all conformation change combinations from s0 to sf.

Enumerates all possible orders of complex formation to transform conformation s0 into sf, generating tuples representing each step.

Parameters:

• s0 (PolymerConformation) – Starting conformation.

• sf (PolymerConformation) – Target final conformation.

Returns:

List of (old_state, species_to_add, new_state) tuples representing all possible transformation pathways. Each tuple represents one conformation change step. Returns empty list if no valid pathways exist.

Return type:

list of tuple

Notes

The method:

1. Computes which species/complexes change between s0 and sf

2. Generates all permutations (different formation orders)

3. For each permutation, creates conformational change steps

4. Filters out any combinations involving excluded_states

Unlike CombinatorialComplex, this method adds groups of species simultaneously to form complete complexes at polymer positions.

get_mechanism(mechanism_type, optional_mechanism=False)

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_orphan()

Create a copy of this monomer without a parent reference.

Returns a copy that retains position and direction but has no parent polymer. Useful for temporarily working with monomers outside their polymer context.

Returns:

A copy of this monomer with parent set to None but position and direction preserved.

Return type:

OrderedMonomer

See also

get_removed

Create a fully detached copy.

remove

Remove this monomer from its parent in place.

Notes

This is a shallow copy of the monomer object itself, though the parent reference is explicitly cleared.

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

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:

1. Component.parameter_database

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

get_protein_for_expression()

Get protein product for expression mixtures.

In expression mixtures, transcription may be bypassed and translation may occur directly from DNA. This method returns the protein product when the gene is expressed.

Returns:

The protein product(s) if transcript is None, otherwise None.

Return type:

list of Species or None

Notes

This is used by expression mixtures where the transcript species is omitted and translation occurs directly.

get_removed()

Create a fully detached copy of this monomer.

Returns a copy with all polymer-related attributes (parent, position, direction) cleared. Also removes ‘forward’ and ‘reverse’ attributes if present.

Returns:

A copy of this monomer with no parent, position, or direction, and with directional attributes removed.

Return type:

OrderedMonomer

See also

get_orphan

Create a copy without parent but with position and direction.

remove

Remove this monomer from its parent in place.

Notes

This method is useful for creating completely independent copies of monomers that can be reused in different contexts without any polymer associations.

get_species()

Get the bare polymer conformation.

Returns:

The internal polymer without any complexes.

Return type:

PolymerConformation

property initial_states

List of initial conformation states.

Return type:

list of PolymerConformation

property intermediate_states

List of allowed intermediates.

Return type:

list of PolymerConformation or None

monomer_insert(parent: OrderedPolymer, position: int, direction=None)

Insert this monomer into a polymer at a specific position.

Sets the monomer’s parent, position, and direction attributes to reflect its insertion into the polymer. Marks the monomer (or its polymer component if it is a complex species) as a polymer component.

Parameters:

• parent (OrderedPolymer) – The polymer to insert this monomer into.

• position (int) – The position index where this monomer is being inserted.

• direction (str, int, or None, optional) – The direction for this monomer. If None, uses the monomer’s existing direction.

Raises:

ValueError – If position is None, or if parent is None.

property promoter_states

List of designated promoter states.

Return type:

list of PolymerConformation

remove()

Remove this monomer from its parent polymer.

Clears the monomer’s parent, position, and direction attributes, effectively detaching it from any polymer structure.

Returns:

Returns self for method chaining.

Return type:

OrderedMonomer

See also

get_removed

Create a fully detached copy of the monomer.

get_orphan

Create a copy with parent removed but position and direction preserved.

reverse()

Reverse the orientation of this DNA part.

Flips the direction of the part between ‘forward’ and ‘reverse’.

Returns:

Returns self after reversing direction.

Return type:

DNA_part

Notes

This method is typically called when a containing construct is reversed, ensuring all parts maintain proper relative orientation.

set_attributes(attributes: List[str])

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_dir(direction)

Set the direction of the monomer and return self.

Convenience method for setting direction in a fluent interface style.

Parameters:

direction (str, int, or None) – The direction to assign to this monomer.

Returns:

Returns self for method chaining.

Return type:

OrderedMonomer

Examples

>>> monomer = bcp.OrderedMonomer().set_dir('forward')
>>> monomer.direction
'forward'

set_mixture(mixture) → None

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

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.

subhash()

Compute hash contribution from monomer properties.

Computes a hash value based on the monomer’s position, direction, and name (if present), excluding the parent reference.

Returns:

Hash value based on monomer-specific properties.

Return type:

int

Notes

This method is used by __hash__ to compute the monomer’s hash contribution. It excludes the parent to avoid circular dependencies in hash computation.

unclone()

Remove this part from its parent construct.

Detaches the part from any parent construct or assembly, resetting its position and parent references.

Returns:

Returns self after removal from parent.

Return type:

DNA_part

Notes

This method calls the remove method from the OrderedMonomer base class to detach the part from its parent polymer structure.

After calling this method, the part becomes “orphaned” and can be attached to a different construct using clone.

See also

clone

Attach the part to a construct at a specific position.

update_component(internal_species=None, **kwargs)

Create a copy of the promoter with updated DNA binding target.

Used for component enumeration when promoters are part of larger constructs that need to be duplicated with different species.

Parameters:

• internal_species (Species, optional) – The new DNA species to use as the binding target.

• **kwargs – Additional keyword arguments (currently unused).

Returns:

A shallow copy of this promoter with the updated dna_to_bind attribute. Returns None if parent is RNA.

Return type:

Promoter or None

Raises:

TypeError – If parent is neither DNA nor RNA construct.

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

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()

Generate reactions for conformation changes and transcription.

Generates reactions from both conformational changes (via CombinatorialConformation) and transcription (via Promoter) for conformations that are transcriptionally active.

Returns:

List of all reactions including conformation change reactions and transcription reactions (RNAP binding, elongation, etc.) for active conformations.

Return type:

list of Reaction

Notes

For each conformation, determines if it is transcriptionally active using the same logic as update_species(). Only active conformations generate transcription reactions via Promoter.update_reactions.

The component name is temporarily changed to a state-specific name for each conformation to ensure unique reaction identifiers.

update_species()

Generate species for conformation changes and transcription.

Generates species from both conformational changes (via CombinatorialConformation) and transcription (via Promoter) for conformations that are transcriptionally active.

Returns:

List of all unique species including conformation states and transcription-related species (RNAP complexes, transcripts, etc.) for active conformations.

Return type:

list of Species

Notes

For each conformation, determines if it is transcriptionally active based on:

• Whether it is in promoter_states (and promoter_states_on setting)

• Presence of activating_complexes

• Absence of inactivating_complexes

Only active conformations generate transcription species via Promoter.update_species().