biocrnpyler.components.dna.IntegraseSite

class biocrnpyler.components.dna.IntegraseSite(name, site_type='attB', integrase='int1', dinucleotide=1, no_stop_codons=None, integrase_binding=True, **kwargs)

Bases: DNABindingSite

Integrase attachment site for site-specific recombination.

An IntegraseSite represents a specialized DNA binding site where integrase proteins can bind and catalyze site-specific recombination. This component uses the ‘binding’ mechanism to model integrase-DNA binding and the ‘integration’ mechanism to generate recombination reactions. The class handles both intramolecular (same DNA molecule) and intermolecular (different DNA molecules) recombination events between compatible attachment sites (attB/attP producing attL/attR, or similar).

Parameters:

• name (str) – Name of the integrase site.

• site_type (str, default 'attB') – Type of attachment site. Common types include ‘attB’, ‘attP’, ‘attL’, ‘attR’, ‘FLP’, ‘CRE’. Determines recombination compatibility.

• integrase (str or Species, default 'int1') – The integrase protein that recognizes this site. Can be a string name or Species object.

• dinucleotide (int, default 1) – Specific dinucleotide variant of the attachment site. Different dinucleotides allow orthogonal recombination systems.

• no_stop_codons (bool, optional) – If True, indicates the sequence has no stop codons.

• integrase_binding (bool, default True) – If True, integrase must bind before recombination. If False, recombination occurs without explicit binding (simplified model).

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

Attributes:

• integrase (Species) – The integrase protein species that catalyzes recombination.

• dinucleotide (int) – The dinucleotide variant identifier.

• site_type (str) – The type of attachment site (attB, attP, etc.).

• other_dna (Species or None) – Reference to DNA from another molecule (for intermolecular events).

• linked_sites (dict) – Dictionary tracking connected recombination partner sites.

• complexed_version (Species or None) – The integrase-bound version of this site.

• integrase_binding (bool) – Whether explicit integrase binding is modeled.

See also

DNABindingSite

Parent class for general DNA binding sites.

BasicIntegration

Mechanism for integrase-mediated recombination.

One_Step_Cooperative_Binding

Mechanism for integrase binding.

Notes

Integrase sites follow specific recombination rules:

• attB + attP \(\rightarrow\) attL + attR (integration)

• attL + attR \(\rightarrow\) attB + attP (excision)

• Compatible sites must have matching integrases and dinucleotides

The linked_sites dictionary maintains connections between compatible recombination partners, enabling the generation of appropriate recombination reactions during CRN compilation.

Recombination can be intramolecular (creating loops or deletions) or intermolecular (joining or exchanging DNA segments between molecules).

Examples

Create a basic attB site for phage integration:

>>> attB = bcp.IntegraseSite(
...     name='attB',
...     site_type='attB',
...     integrase='int_phiC31'
... )

Create orthogonal integration sites with different dinucleotides:

>>> site1 = bcp.IntegraseSite(
...     name='att1',
...     site_type='attB',
...     dinucleotide=1,
...     integrase='int1'
... )
>>> site2 = bcp.IntegraseSite(
...     name='att2',
...     site_type='attB',
...     dinucleotide=2,
...     integrase='int1'
... )

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.
enumerate_components	Enumerate derived components created from this component.
find_polymer_component	Find the polymer component within this monomer or its species.
get_complexed_species	Create the integrase-bound complex for this site.
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_removed	Create a fully detached copy of this monomer.
get_species	Get the primary species associated with this component.
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 integrase site with updated DNA reference.
update_integrase	Set or update the integrase protein for this site.
update_parameters	Update the parameter database with new parameters.
update_reactions	Use 'binding' and 'integration' mechanisms to generate reactions.
update_species	Generate species associated with binding and integration.

__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

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

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.

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.

get_complexed_species(dna)

Create the integrase-bound complex for this site.

Parameters:

dna (Species) – The DNA species containing this integrase site.

Returns:

A complex containing the DNA bound by two integrase molecules (dimeric binding typical of integrases).

Return type:

Complex

Notes

Most integrases bind as dimers to catalyze recombination, hence the complex contains two integrase molecules.

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_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() → None

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.

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.

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 integrase site with updated DNA reference.

This method handles the complex task of copying integrase sites during component enumeration, maintaining proper linkages between recombination partner sites.

Parameters:

• internal_species (Species, optional) – The new DNA species containing this integrase site.

• **kwargs – Additional keyword arguments. If ‘practice_run’ is True, performs special handling to preserve initial site linkage configuration.

Returns:

A copy of this integrase site with updated dna_to_bind and properly managed linked site references. Returns None if the parent DNABindingSite.update_component returns None.

Return type:

IntegraseSite or None

Notes

This method manages the complex bookkeeping required for integrase site recombination:

Practice Run Mode (‘practice_run’=True): During combinatorial enumeration’s practice run, the method preserves the initial configuration of linked sites by updating references in partner sites to point to the newly created copy.

Normal Mode (‘practice_run’=False or not specified):

• For intramolecular reactions: Only populates linked sites if both recombination partners are bound by integrase (or both unbound if integrase_binding is False)

• For intermolecular reactions: Always populates linked sites to enable proper reaction generation

The method ensures that only one site of a recombination pair generates the reaction, preventing duplicate reactions in the CRN.

update_integrase(int_name)

Set or update the integrase protein for this site.

Parameters:

int_name (str or Species) – Name of the integrase protein or a Species object.

Notes

Converts the input to a protein Species object and stores it in the integrase attribute.

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()

Use ‘binding’ and ‘integration’ mechanisms to generate reactions.

Creates binding reactions (if integrase_binding is True) and recombination reactions with linked partner sites. Handles both intramolecular (same DNA) and intermolecular (different DNA) recombination events.

Returns:

List containing:

• Integrase binding reactions (if integrase_binding is True)

• Recombination reactions with each linked partner site

Returns empty list if no linked sites exist.

Return type:

list of Reaction

Notes

For each linked partner site, the method determines whether to generate a recombination reaction based on:

1. Intramolecular reactions (same DNA molecule):

   • Only generates reaction if both sites are properly bound (or unbound if integrase_binding is False)

   • Prevents duplicate reactions by checking if complex_parent is already in the linked sites data

   • Creates DNA loops, deletions, or inversions

2. Intermolecular reactions (different DNA molecules):

   • Generates reactions for all DNA molecules listed in linked_sites

   • These DNAs are added by partner sites that were processed earlier

   • Creates DNA joining, exchange, or integration events

The method uses the ‘integration’ mechanism to generate the actual recombination reactions with appropriate kinetic parameters identified by the integrase name as part_id.

Each site pair generates only one reaction (not two) to avoid duplicates, with the reaction generation responsibility determined by the update order and population status of linked sites.

update_species()

Generate species associated with binding and integration.

Generate the list of species associated with the binding site, including integrase-DNA complexes generated by the parent DNA binding site if integrase_binding is True.

Returns:

If integrase_binding is True, returns species from parent DNABindingSite including integrase-DNA complexes. If False, returns only the binder proteins without generating complexes.

Return type:

list of Species

Notes

When integrase_binding is False, the model assumes simplified recombination without explicit binding steps, useful for simplified models where binding kinetics are not important.