biocrnpyler.components.membrane

Classes

`DiffusibleMolecule`(substrate[, ...])	Molecule that diffuses passively through a membrane.
`IntegralMembraneProtein`(membrane_protein, ...)	Transmembrane protein that integrates into the membrane.
`MembraneChannel`(integral_membrane_protein, ...)	Membrane channel for facilitated transport across membranes.
`MembranePump`(membrane_pump, substrate[, ...])	ATP-dependent membrane pump for active transport.
`MembraneSensor`(membrane_sensor_protein, ...)	Two-component system (TCS) membrane sensor protein.

class biocrnpyler.components.membrane.DiffusibleMolecule(substrate: Species | str | Component, internal_compartment: str | Compartment = 'Internal', external_compartment: str | Compartment = 'External', attributes=None, **kwargs)[source]

Molecule that diffuses passively through a membrane.

A DiffusibleMolecule component represents a molecule that undergoes passive diffusion across a membrane between two compartments. The component uses a ‘diffusion’ mechanism to generate bidirectional diffusion reactions based on concentration gradients.

Parameters:

substrateSpecies, str, or Component: The diffusible molecule species. Can be a Species object, string name, or Component with an associated species.
internal_compartmentstr or Compartment, default=’Internal’: The internal compartment. Can be a string name (creates new Compartment) or an existing Compartment object.
external_compartmentstr or Compartment, default=’External’: The external compartment. Can be a string name (creates new Compartment) or an existing Compartment object.
attributeslist of str, optional: List of attribute tags to associate with the substrate species.
**kwargs: Additional keyword arguments passed to the Component base class constructor.

Attributes:

substrateSpecies: The substrate species in the internal compartment.
productSpecies: The same substrate species in the external compartment (diffusion product).

See also

MembraneChannel: Active transport through membrane channels.
MembranePump: ATP-dependent active transport.
Component: Base class for biomolecular components.

Notes

Passive diffusion follows concentration gradients and does not require energy. The diffusion mechanism generates bidirectional reactions:

Forward: substrate_internal –> substrate_external
Reverse: substrate_external –> substrate_internal

If not specified using the name keyword, the component name is automatically generated as: ‘<substrate_name>_<internal_compartment_name>’

Examples

Create a simple diffusible molecule:

>>> glucose = bcp.DiffusibleMolecule(
...     substrate='Glucose',
...     internal_compartment='Cytoplasm',
...     external_compartment='Extracellular'
... )

Use with a mixture and diffusion mechanism:

>>> mixture = bcp.Mixture(
...     components=[glucose],
...     mechanisms={'diffusion': bcp.Simple_Diffusion()},
...     parameters={'k_diff': 0.01}
... )
>>> crn = mixture.compile_crn()

__hash__()[source]: Return hash(self).

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:

attributestr: 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:

mechanismMechanism: The mechanism object to add.
mech_typestr, optional: The type key under which to store the mechanism. If None, uses the mechanism’s mechanism_type attribute.
overwritebool, default=False: If True, replaces any existing mechanism with the same key. If False, raises ValueError when key already exists.
optional_mechanismbool, 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:

mechanismsMechanism, 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.
overwritebool, default=False: If True, replaces any existing mechanisms with the same keys. If False, raises ValueError when keys already exist.
optional_mechanismbool, 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: Compartment or None: The compartment containing this component.

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_enumeratedset or list, optional: Collection of components that have already been enumerated, used to prevent infinite recursion in component enumeration.

Returns:

list: List of new components created from this component. This base implementation returns an empty 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_typestr: The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).
optional_mechanismbool, default=False: If True, returns None when mechanism not found. If False, raises KeyError when mechanism not found.

Returns:

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

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_namestr: Name of the parameter to retrieve.
part_idstr, optional: Part identifier for the parameter lookup key.
mechanismstr, optional: Mechanism identifier for the parameter lookup key.
return_numericalbool, default=False: If True, returns the numerical value. If False, returns the Parameter object.
return_nonebool, default=False: If True, returns None when parameter not found. If False, raises ValueError when parameter not found.
check_mixturebool, default=True: If True, searches the mixture’s parameter database if not found in the component’s database.

Returns:

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

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()[source]

Get the substrate species in the internal compartment.

Returns:

Species: The substrate species in the internal compartment.

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:

attributeslist 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:

mixtureMixture 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:

speciesSpecies, 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_typestr, optional: Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). Only used when creating new Species from strings.
compartmentCompartment, optional: Compartment to assign to the species. Only used when creating new Species from strings.
attributeslist of str, optional: Attributes to assign to the species. Only used when creating new Species from strings.

Returns:

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

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_filestr, optional: Path to a CSV or TSV file containing parameters to load.
parametersdict, optional: Dictionary of parameters to add. Keys follow the format (mechanism, part_id, param_name).
parameter_databaseParameterDatabase, optional: Another parameter database to merge into component’s database.
overwrite_parametersbool, default=True: If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

update_reactions()[source]

Use ‘diffusion’ mechanism to generate diffusion reactions.

Uses the ‘diffusion’ mechanism to generate reactions for passive diffusion between compartments.

Returns:

list of Reaction: List of diffusion reactions (forward and reverse) between internal and external compartments.

update_species()[source]

Use ‘diffusion’ mechanism to generate diffusion species.

Uses the ‘diffusion’ mechanism to generate species in both compartments.

Returns:

list of Species: List of species in internal and external compartments generated by the diffusion mechanism.

class biocrnpyler.components.membrane.IntegralMembraneProtein(membrane_protein: Species | str | Component, product: Species | str | Component, direction: str = None, size: int = None, compartment: str | Compartment = 'Internal', membrane_compartment: str | Compartment = 'Membrane', attributes=None, **kwargs)[source]

Transmembrane protein that integrates into the membrane.

An IntegralMembraneProtein component represents a membrane protein that integrates into a membrane compartment. The component uses a ‘membrane_insertion’ mechanism to generate reactions for protein insertion into the membrane. The size parameter allows modeling of oligomeric channels (dimers, trimers, etc.).

Parameters:

membrane_proteinSpecies, str, or Component: The membrane protein species before insertion. Can be a Species object, string name, or Component with an associated species.
productSpecies, str, or Component: The integrated membrane protein species. Can be a Species object, string name, or Component.
directionstr, optional: Transport direction attribute for the integrated protein. Default is ‘Passive’. Common values: ‘Passive’, ‘Importer’, ‘Exporter’.
sizeint, optional: Number of monomers needed to form the functional channel. Used to model oligomeric channels (e.g., size=2 for dimers, size=3 for trimers). Default is 1.
compartmentstr or Compartment, default=’Internal’: The compartment containing the membrane protein before insertion. Can be a string name or Compartment object.
membrane_compartmentstr or Compartment, default=’Membrane’: The membrane compartment where the protein integrates. Can be a string name or Compartment object.
attributeslist of str, optional: List of attribute tags to associate with the membrane protein.
**kwargs: Additional keyword arguments passed to the Component base class constructor.

Attributes:

membrane_proteinSpecies: The membrane protein species before insertion.
productSpecies: The integrated transmembrane protein species in the membrane compartment.

See also

MembraneChannel: Membrane channel for substrate transport.
Component: Base class for biomolecular components.

Notes

The membrane_insertion mechanism generates reactions for protein integration into the membrane. For oligomeric channels, the size parameter determines the stoichiometry:

size=1: Monomer insertion
size=2: Dimer formation (2 proteins –> 1 channel)
size=3: Trimer formation (3 proteins –> 1 channel)

The component name is automatically generated as: ‘<membrane_protein_name>_<compartment_name>’

Examples

Create a simple membrane protein:

>>> channel = bcp.IntegralMembraneProtein(
...     membrane_protein='ChannelProtein',
...     product='ChannelProtein_membrane',
...     direction='Passive'
... )

Create a dimeric channel protein:

>>> dimer = bcp.IntegralMembraneProtein(
...     membrane_protein='Aquaporin',
...     product='Aquaporin_channel',
...     size=2,
...     direction='Passive'
... )

__hash__()[source]: Return hash(self).

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:

attributestr: 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:

mechanismMechanism: The mechanism object to add.
mech_typestr, optional: The type key under which to store the mechanism. If None, uses the mechanism’s mechanism_type attribute.
overwritebool, default=False: If True, replaces any existing mechanism with the same key. If False, raises ValueError when key already exists.
optional_mechanismbool, 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:

mechanismsMechanism, 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.
overwritebool, default=False: If True, replaces any existing mechanisms with the same keys. If False, raises ValueError when keys already exist.
optional_mechanismbool, 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: Compartment or None: The compartment containing this component.

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_enumeratedset or list, optional: Collection of components that have already been enumerated, used to prevent infinite recursion in component enumeration.

Returns:

list: List of new components created from this component. This base implementation returns an empty 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_typestr: The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).
optional_mechanismbool, default=False: If True, returns None when mechanism not found. If False, raises KeyError when mechanism not found.

Returns:

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

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_namestr: Name of the parameter to retrieve.
part_idstr, optional: Part identifier for the parameter lookup key.
mechanismstr, optional: Mechanism identifier for the parameter lookup key.
return_numericalbool, default=False: If True, returns the numerical value. If False, returns the Parameter object.
return_nonebool, default=False: If True, returns None when parameter not found. If False, raises ValueError when parameter not found.
check_mixturebool, default=True: If True, searches the mixture’s parameter database if not found in the component’s database.

Returns:

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

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()[source]

Get the membrane protein species before insertion.

Returns:

Species: The membrane protein species in the compartment before integration into the membrane.

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:

attributeslist 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:

mixtureMixture 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:

speciesSpecies, 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_typestr, optional: Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). Only used when creating new Species from strings.
compartmentCompartment, optional: Compartment to assign to the species. Only used when creating new Species from strings.
attributeslist of str, optional: Attributes to assign to the species. Only used when creating new Species from strings.

Returns:

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

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_filestr, optional: Path to a CSV or TSV file containing parameters to load.
parametersdict, optional: Dictionary of parameters to add. Keys follow the format (mechanism, part_id, param_name).
parameter_databaseParameterDatabase, optional: Another parameter database to merge into component’s database.
overwrite_parametersbool, default=True: If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

update_reactions()[source]

Use ‘membrane_insertion’ to generate membrane insertion reactions.

Uses the ‘membrane_insertion’ mechanism to generate reactions for protein integration into the membrane.

Returns:

list of Reaction: List of reactions for protein insertion into the membrane.

update_species()[source]

Use ‘membrane_insertion’ to generate membrane insertion species.

Uses the ‘membrane_insertion’ mechanism to generate species for the protein before and after insertion.

Returns:

list of Species: List of species generated by the membrane_insertion mechanism, including the protein and integrated product.

class biocrnpyler.components.membrane.MembraneChannel(integral_membrane_protein: Species | str | Component, substrate: Species | str | Component, direction: str = None, internal_compartment: str | Compartment = 'Internal', external_compartment: str | Compartment = 'External', attributes=None, **kwargs)[source]

Membrane channel for facilitated transport across membranes.

A MembraneChannel component represents a membrane channel or transporter that facilitates substrate movement across a membrane following concentration gradients. The direction of transport depends on the specific transporter type. The component uses a ‘transport’ mechanism to generate transport reactions.

Parameters:

integral_membrane_proteinSpecies, str, or Component: The integral membrane protein that forms the channel. Can be a Species object, string name, or Component. If a string, automatically creates a protein species with appropriate direction attribute.
substrateSpecies, str, or Component: The substrate to be transported through the channel. Can be a Species object, string name, or Component.
directionstr, optional: Direction of transport. If None, extracted from integral_membrane_protein attributes. Common values: ‘Importer’ (external –> internal), ‘Exporter’ (internal –> external), ‘Passive’ (bidirectional).
internal_compartmentstr or Compartment, default=’Internal’: The internal compartment. Can be a string name (creates new Compartment) or an existing Compartment object.
external_compartmentstr or Compartment, default=’External’: The external compartment. Can be a string name (creates new Compartment) or an existing Compartment object.
attributeslist of str, optional: List of attribute tags to associate with substrate species.
**kwargs: Additional keyword arguments passed to the Component base class constructor.

Attributes:

integral_membrane_proteinSpecies: The membrane channel protein species.
substrateSpecies: The substrate species in the source compartment (depends on direction).
productSpecies: The same substrate in the destination compartment.

See also

IntegralMembraneProtein: Protein insertion into membranes.
MembranePump: ATP-dependent active transport.
DiffusibleMolecule: Passive diffusion without channels.
Component: Base class for biomolecular components.

Notes

The transport mechanism generates reactions based on the direction:

‘Importer’: substrate_external + channel
–> substrate_internal + channel
‘Exporter’: substrate_internal + channel
–> substrate_external + channel
‘Passive’: bidirectional transport following gradients

The component name is automatically generated as: ‘<integral_membrane_protein_name>_<compartment_name>’

Examples

Create a glucose importer:

>>> importer = bcp.MembraneChannel(
...     integral_membrane_protein='GlucoseTransporter',
...     substrate='Glucose',
...     direction='Importer'
... )

Create a passive channel:

>>> channel = bcp.MembraneChannel(
...     integral_membrane_protein='WaterChannel',
...     substrate='Water',
...     direction='Passive'
... )

Use with a mixture:

>>> mixture = bcp.Mixture(
...     components=[importer],
...     mechanisms={'transport': bcp.Facilitated_Transport_MM()},
...     parameter_file='mechanisms/transport_parameters.tsv'
... )
>>> crn = mixture.compile_crn()

__hash__()[source]: Return hash(self).

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:

attributestr: 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:

mechanismMechanism: The mechanism object to add.
mech_typestr, optional: The type key under which to store the mechanism. If None, uses the mechanism’s mechanism_type attribute.
overwritebool, default=False: If True, replaces any existing mechanism with the same key. If False, raises ValueError when key already exists.
optional_mechanismbool, 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:

mechanismsMechanism, 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.
overwritebool, default=False: If True, replaces any existing mechanisms with the same keys. If False, raises ValueError when keys already exist.
optional_mechanismbool, 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: Compartment or None: The compartment containing this component.

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_enumeratedset or list, optional: Collection of components that have already been enumerated, used to prevent infinite recursion in component enumeration.

Returns:

list: List of new components created from this component. This base implementation returns an empty 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_typestr: The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).
optional_mechanismbool, default=False: If True, returns None when mechanism not found. If False, raises KeyError when mechanism not found.

Returns:

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

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_namestr: Name of the parameter to retrieve.
part_idstr, optional: Part identifier for the parameter lookup key.
mechanismstr, optional: Mechanism identifier for the parameter lookup key.
return_numericalbool, default=False: If True, returns the numerical value. If False, returns the Parameter object.
return_nonebool, default=False: If True, returns None when parameter not found. If False, raises ValueError when parameter not found.
check_mixturebool, default=True: If True, searches the mixture’s parameter database if not found in the component’s database.

Returns:

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

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()[source]

Get the integral membrane protein species.

Returns:

Species: The integral membrane protein species that forms the channel.

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:

attributeslist 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:

mixtureMixture 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:

speciesSpecies, 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_typestr, optional: Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). Only used when creating new Species from strings.
compartmentCompartment, optional: Compartment to assign to the species. Only used when creating new Species from strings.
attributeslist of str, optional: Attributes to assign to the species. Only used when creating new Species from strings.

Returns:

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

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_filestr, optional: Path to a CSV or TSV file containing parameters to load.
parametersdict, optional: Dictionary of parameters to add. Keys follow the format (mechanism, part_id, param_name).
parameter_databaseParameterDatabase, optional: Another parameter database to merge into component’s database.
overwrite_parametersbool, default=True: If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

update_reactions()[source]

Use ‘transport’ mechanism to generate channel-mediated reactions.

Uses the ‘transport’ mechanism to generate reactions for substrate transport through the channel.

Returns:

list of Reaction: List of transport reactions through the membrane channel.

update_species()[source]

Use ‘transport’ mechanism to generate channel-mediated species.

Uses the ‘transport’ mechanism to generate species including the channel protein, substrate, and product.

Returns:

list of Species: List of species generated by the transport mechanism.

class biocrnpyler.components.membrane.MembranePump(membrane_pump: Species | str | Component, substrate: Species | str | Component, direction: str = None, internal_compartment: str | Compartment = 'Internal', external_compartment: str | Compartment = 'External', ATP: int = None, attributes=None, **kwargs)[source]

ATP-dependent membrane pump for active transport.

A MembranePump component represents an active transporter or pump that uses ATP to transport substrates across membranes against concentration gradients. The pump operates unidirectionally and requires energy in the form of ATP. The component uses a ‘transport’ mechanism to generate ATP-dependent transport reactions.

Parameters:

membrane_pumpSpecies, str, or Component: The membrane pump protein species. Can be a Species object, string name, or Component. If a string, automatically creates a protein species with appropriate direction attribute.
substrateSpecies, str, or Component: The substrate to be transported by the pump. Can be a Species object, string name, or Component.
directionstr, optional: Direction of active transport. Common values: ‘Importer’ (external –> internal), ‘Exporter’ (internal –> external), ‘Passive’ (default). Affects substrate and ATP compartment placement.
internal_compartmentstr or Compartment, default=’Internal’: The internal compartment. Can be a string name (creates new Compartment) or an existing Compartment object.
external_compartmentstr or Compartment, default=’External’: The external compartment. Can be a string name (creates new Compartment) or an existing Compartment object.
ATPint, optional: Number of ATP molecules required per transport cycle. Default is 1.
attributeslist of str, optional: List of attribute tags to associate with substrate species.
**kwargs: Additional keyword arguments passed to the Component base class constructor.

Attributes:

membrane_pumpSpecies: The membrane pump protein species.
substrateSpecies: The substrate species in the source compartment.
productSpecies: The same substrate in the destination compartment.
energySpecies: ATP species used for energy (compartment depends on direction).
wasteSpecies: ADP species produced (compartment depends on direction).

See also

MembraneChannel: Facilitated transport without ATP.
DiffusibleMolecule: Passive diffusion.
Component: Base class for biomolecular components.

Notes

Active transport requires ATP hydrolysis and can move substrates against concentration gradients. The typical reaction scheme is:

Exporter: substrate_internal + ATP + pump –>
substrate_external + ADP + pump
Importer: substrate_external + ATP + pump –>
substrate_internal + ADP + pump

The ATP parameter controls the stoichiometry of ATP consumption per transport event.

The component name is automatically generated as: ‘<membrane_pump_name>_<compartment_name>’

Examples

Create a simple ATP-dependent exporter:

>>> pump = bcp.MembranePump(
...     membrane_pump='CalciumPump',
...     substrate='Calcium',
...     direction='Exporter',
...     ATP=2
... )

Create an ABC transporter (importer):

>>> abc = bcp.MembranePump(
...     membrane_pump='ABC_Transporter',
...     substrate='Maltose',
...     direction='Importer',
...     ATP=1
... )

Use with a mixture:

>>> mixture = bcp.Mixture(
...     components=[pump],
...     mechanisms={'transport': bcp.Primary_Active_Transport_MM()},
...     parameter_file='mechanisms/transport_parameters.tsv'
... )
>>> crn = mixture.compile_crn()

__hash__()[source]: Return hash(self).

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:

attributestr: 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:

mechanismMechanism: The mechanism object to add.
mech_typestr, optional: The type key under which to store the mechanism. If None, uses the mechanism’s mechanism_type attribute.
overwritebool, default=False: If True, replaces any existing mechanism with the same key. If False, raises ValueError when key already exists.
optional_mechanismbool, 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:

mechanismsMechanism, 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.
overwritebool, default=False: If True, replaces any existing mechanisms with the same keys. If False, raises ValueError when keys already exist.
optional_mechanismbool, 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: Compartment or None: The compartment containing this component.

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_enumeratedset or list, optional: Collection of components that have already been enumerated, used to prevent infinite recursion in component enumeration.

Returns:

list: List of new components created from this component. This base implementation returns an empty 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_typestr: The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).
optional_mechanismbool, default=False: If True, returns None when mechanism not found. If False, raises KeyError when mechanism not found.

Returns:

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

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_namestr: Name of the parameter to retrieve.
part_idstr, optional: Part identifier for the parameter lookup key.
mechanismstr, optional: Mechanism identifier for the parameter lookup key.
return_numericalbool, default=False: If True, returns the numerical value. If False, returns the Parameter object.
return_nonebool, default=False: If True, returns None when parameter not found. If False, raises ValueError when parameter not found.
check_mixturebool, default=True: If True, searches the mixture’s parameter database if not found in the component’s database.

Returns:

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

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()[source]

Get the membrane pump protein species.

Returns:

Species: The membrane pump protein 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:

attributeslist 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:

mixtureMixture 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:

speciesSpecies, 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_typestr, optional: Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). Only used when creating new Species from strings.
compartmentCompartment, optional: Compartment to assign to the species. Only used when creating new Species from strings.
attributeslist of str, optional: Attributes to assign to the species. Only used when creating new Species from strings.

Returns:

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

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_filestr, optional: Path to a CSV or TSV file containing parameters to load.
parametersdict, optional: Dictionary of parameters to add. Keys follow the format (mechanism, part_id, param_name).
parameter_databaseParameterDatabase, optional: Another parameter database to merge into component’s database.
overwrite_parametersbool, default=True: If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

update_reactions()[source]

Use ‘trasnport’ mechanism to generate ATP-dependent reactions.

Uses the ‘transport’ mechanism to generate reactions for active transport coupled to ATP hydrolysis.

Returns:

list of Reaction: List of ATP-dependent transport reactions.

update_species()[source]

Use ‘trasnport’ mechanism to generate ATP-dependent species.

Uses the ‘transport’ mechanism to generate species including the pump protein, substrate, product, ATP, and ADP.

Returns:

list of Species: List of species generated by the transport mechanism, including pump, substrate, product, energy, and waste.

Two-component system (TCS) membrane sensor protein.

A MembraneSensor component represents a membrane sensor protein in a two-component signaling system. The sensor detects external signal substrates and catalyzes the transfer of a chemical group (typically phosphate) to a response protein, activating it. The component uses a ‘membrane_sensor’ mechanism to generate signal transduction reactions.

Parameters:

membrane_sensor_proteinSpecies, str, or Component: The membrane sensor protein (histidine kinase) that detects the signal. Can be a Species object, string name, or Component.
response_proteinSpecies, str, or Component: The cytoplasmic response regulator protein that receives the signal. Can be a Species object, string name, or Component.
assigned_substrateSpecies, str, or Component: The chemical group to be transferred (typically phosphate). Can be a Species object, string name, or Component.
signal_substrateSpecies, str, or Component: The external signal molecule that activates the sensor. Can be a Species object, string name, or Component.
productSpecies, str, or Component, optional: The activated response protein product. If None, automatically named as ‘<response_protein>active’.
internal_compartmentstr or Compartment, default=’Internal’: The internal compartment containing response protein. Can be a string name (creates new Compartment) or an existing Compartment object.
external_compartmentstr or Compartment, default=’External’: The external compartment containing signal. Can be a string name (creates new Compartment) or an existing Compartment object.
ATPint, default=2: Number of ATP molecules required for the signaling process.
attributeslist of str, optional: List of attribute tags to associate with species.
**kwargs: Additional keyword arguments passed to the Component base class constructor.

Attributes:

membrane_sensor_proteinSpecies: The membrane sensor protein species.
response_proteinSpecies: The response regulator protein species.
assigned_substrateSpecies: The substrate to be transferred (e.g., phosphate).
signal_substrateSpecies: The external signal molecule species.
productSpecies: The activated response protein species.
energySpecies: ATP species used for energy.
wasteSpecies: ADP species produced.

See also

Component: Base class for biomolecular components.

Notes

Two-component systems (TCS) are common bacterial signal transduction pathways. The typical mechanism involves:

Signal detection by membrane sensor (histidine kinase)
Autophosphorylation of sensor using ATP
Phosphotransfer to response regulator
Activated response regulator regulates gene expression

The general reaction scheme:

signal + sensor + ATP + response_protein –> signal + sensor + ADP + response_protein-P

The component name is automatically generated as: ‘<membrane_sensor_protein_name>_<compartment_name>’

Examples

Create a simple two-component system:

>>> tcs = bcp.MembraneSensor(
...     membrane_sensor_protein='EnvZ',
...     response_protein='OmpR',
...     assigned_substrate='Phosphate',
...     signal_substrate='Osmolarity',
...     ATP=2
... )

Create a chemotaxis receptor:

>>> chemoreceptor = bcp.MembraneSensor(
...     membrane_sensor_protein='CheA',
...     response_protein='CheY',
...     assigned_substrate='Phosphate',
...     signal_substrate='Aspartate',
...     product='CheY_P'
... )

Use with a mixture:

>>> mixture = bcp.Mixture(
...     components=[tcs],
...     mechanisms={
...         'membrane_sensor': bcp.Membrane_Signaling_Pathway_MM()},
...     parameter_file='mechanisms/transport_parameters.tsv'
... )
>>> crn = mixture.compile_crn()

__hash__()[source]: Return hash(self).

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:

attributestr: 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:

mechanismMechanism: The mechanism object to add.
mech_typestr, optional: The type key under which to store the mechanism. If None, uses the mechanism’s mechanism_type attribute.
overwritebool, default=False: If True, replaces any existing mechanism with the same key. If False, raises ValueError when key already exists.
optional_mechanismbool, 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:

mechanismsMechanism, 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.
overwritebool, default=False: If True, replaces any existing mechanisms with the same keys. If False, raises ValueError when keys already exist.
optional_mechanismbool, 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: Compartment or None: The compartment containing this component.

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_enumeratedset or list, optional: Collection of components that have already been enumerated, used to prevent infinite recursion in component enumeration.

Returns:

list: List of new components created from this component. This base implementation returns an empty 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_typestr: The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).
optional_mechanismbool, default=False: If True, returns None when mechanism not found. If False, raises KeyError when mechanism not found.

Returns:

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

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_namestr: Name of the parameter to retrieve.
part_idstr, optional: Part identifier for the parameter lookup key.
mechanismstr, optional: Mechanism identifier for the parameter lookup key.
return_numericalbool, default=False: If True, returns the numerical value. If False, returns the Parameter object.
return_nonebool, default=False: If True, returns None when parameter not found. If False, raises ValueError when parameter not found.
check_mixturebool, default=True: If True, searches the mixture’s parameter database if not found in the component’s database.

Returns:

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

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()[source]

Get the membrane sensor protein species.

Returns:

Species: The membrane sensor protein (histidine kinase) 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:

attributeslist 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:

mixtureMixture 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:

speciesSpecies, 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_typestr, optional: Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). Only used when creating new Species from strings.
compartmentCompartment, optional: Compartment to assign to the species. Only used when creating new Species from strings.
attributeslist of str, optional: Attributes to assign to the species. Only used when creating new Species from strings.

Returns:

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

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_filestr, optional: Path to a CSV or TSV file containing parameters to load.
parametersdict, optional: Dictionary of parameters to add. Keys follow the format (mechanism, part_id, param_name).
parameter_databaseParameterDatabase, optional: Another parameter database to merge into component’s database.
overwrite_parametersbool, default=True: If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

update_reactions()[source]

Use ‘membrane_sensor’ to generate species signaling reactions.

Uses the ‘membrane_sensor’ mechanism to generate reactions for signal detection, ATP-dependent phosphorylation, and phosphotransfer to the response regulator.

Returns:

list of Reaction: List of signal transduction reactions including sensing, autophosphorylation, and phosphotransfer.

update_species()[source]

Use ‘membrane_sensor’ to generate species signaling species.

Uses the ‘membrane_sensor’ mechanism to generate all species involved in the signaling pathway including sensor, response protein, substrates, signal, product, ATP, and ADP.

Returns:

list of Species: List of species generated by the membrane_sensor mechanism.