biocrnpyler.mixtures.cell

Classes

ExpressionDilutionMixture([name])	In vivo gene expression with dilution but without cellular machinery.
SimpleTxTlDilutionMixture([name])	In vivo TX-TL with simple mechanisms and continuous dilution.
TxTlDilutionMixture([name, rnap, ribosome, ...])	In vivo TX-TL with explicit machinery, dilution, and background load.

class biocrnpyler.mixtures.cell.ExpressionDilutionMixture(name='', **kwargs)

In vivo gene expression with dilution but without cellular machinery.

A simplified mixture that models gene expression as a single direct reaction from DNA to protein, without explicitly representing transcription and translation as separate processes or cellular machinery (ribosomes, polymerases). This mixture lumps transcription and translation into a single ‘expression’ reaction and includes global dilution to model cell growth and division effects on all non-DNA species.

This mixture is appropriate for coarse-grained models of in vivo gene expression where mRNA dynamics are negligible and growth dilution is important.

Parameters:

namestr, default=’’

Name of the mixture for identification and parameter lookup.

mechanismsdict, list, or Mechanism, optional

Default mechanisms for components in this mixture. Can be a dict with mechanism types (str) as keys and mechanism objects as values, a list of mechanism objects, or a single Mechanism.

componentslist of Component or Component, optional

Components to include in the mixture. Components are deep-copied when added to prevent modification of original objects.

parametersdict, optional

Dictionary of parameter values. Keys follow the format (mechanism, part_id, param_name).

compartmentCompartment, optional

Default compartment for all components and species in this mixture.

parameter_filestr, optional

Path to a CSV or TSV file containing parameters to load.

overwrite_parametersbool, default=False

If True, parameters from file/dict overwrite existing parameters. If False, existing parameters are preserved.

global_mechanismsdict, list, or GlobalMechanism, optional

Global mechanisms that apply to all species after component compilation (e.g., dilution, global degradation). Can be a dict, list, or single GlobalMechanism.

specieslist of Species or Species, optional

Additional species to add directly to the CRN without going through component compilation.

initial_condition_dictionarydict, optional

Dictionary mapping species to initial concentration values. Deprecated in favor of using parameters with mechanism=’initial concentration’.

global_component_enumeratorslist, optional

List of global component enumerators for advanced component generation patterns (e.g., creating all pairwise interactions).

global_recursion_depthint, default=4

Maximum recursion depth for global component enumeration during compilation.

local_recursion_depthint, optional

Maximum recursion depth for local component enumeration. If None, defaults to global_recursion_depth + 2.

Attributes:

namestr

Name of the mixture.

compartmentCompartment or None

Default compartment for the mixture.

componentslist of Component

List of components in the mixture (deep copies of added components).

mechanismsdict

Mechanism: Stores mixture mechanisms.

global_mechanismsdict

Mechanism: Stores global mechanisms in the mixture.

parameter_databaseParameterDatabase

Database storing all parameters for this mixture.

added_specieslist of Species

List of species added directly to the mixture.

global_component_enumeratorslist

List of global component enumerators.

global_recursion_depthint

Recursion depth for global component enumeration.

local_recursion_depthint

Recursion depth for local component enumeration.

crnChemicalReactionNetwork or None

The compiled CRN, created by calling compile_crn.

See also

ExpressionExtract

Expression without dilution.

SimpleTxTlDilutionMixture

TX-TL with dilution.

TxTlDilutionMixture

TX-TL with machinery and dilution.

Mixture

Base class for all mixtures.

Notes

Default mechanisms included:

• ‘transcription’ : OneStepGeneExpression - Single-step gene expression (DNA –> DNA + Protein) without intermediate mRNA

• ‘translation’ : EmptyMechanism - Dummy mechanism that generates no reactions (translation is disabled)

• ‘catalysis’ : BasicCatalysis - Simple catalytic reactions without explicit enzyme binding

• ‘binding’ : One_Step_Binding - Simple multi-species binding

• ‘dilution’ : Dilution - Global dilution mechanism (Species –> ∅) applied to all non-DNA species to model growth/division

Key features of this mixture:

• No explicit transcription or translation steps

• No cellular machinery (RNAP, ribosomes, RNases)

• No intermediate mRNA species

• Global dilution of all species except DNA

• Models growth dilution effects in vivo

• Simplified parameter space

When compiled, this mixture automatically disables transcript generation in DNAassemblies that produce proteins, routing expression directly from DNA to protein.

Common applications include:

• In vivo gene circuit modeling with growth effects

• Steady-state gene expression in growing cells

• Models where mRNA dynamics are negligible

• High-level circuit design with dilution

Examples

Create an in vivo expression mixture with dilution for GFP:

>>> gfp_gene = bcp.DNAassembly(
...     name='gfp_construct',
...     promoter='pconst',
...     protein='GFP'
... )
>>> mixture = bcp.ExpressionDilutionMixture(
...     name='cell_mixture',
...     components=[gfp_gene],
...     parameter_file='mixtures/cell_parameters.tsv'
... )
>>> crn = mixture.compile_crn()

add_component(component)

Add a single component to the mixture.

Parameters:

componentComponent or list of Component

Component object to add to the mixture. If a list is provided, calls add_components instead. The component is deep-copied before being added.

Raises:

AssertionError

If the component is not a Component object.

ValueError

If a component with the same type and name already exists in the mixture.

Notes

Components are deep-copied when added to prevent modification of the original component. The copied component’s mixture attribute is set to this Mixture, and its compartment is set to the mixture’s compartment.

add_components(components: List[Component] | Component)

Add multiple components to the mixture.

Parameters:

componentsComponent or list of Component

Component object(s) to add to the mixture. Each component is deep-copied before being added.

Raises:

ValueError

If components is not a Component, list of Components, or if any duplicate components are detected.

See also

add_component

Add a single component to the mixture.

add_global_mechanism(mechanism, mech_type=None, overwrite=False)

Add a global mechanism to the mixture.

Global mechanisms are applied to all species after component compilation, enabling operations like dilution or global degradation.

Parameters:

mechanismGlobalMechanism

The global mechanism object to add. Must be a GlobalMechanism instance.

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 global mechanism with the same key. If False, raises ValueError when key already exists.

Raises:

TypeError

If mechanism is not a GlobalMechanism object, or if mech_type is not a string.

ValueError

If mechanism key already exists and overwrite is False.

Notes

Global mechanisms are applied during compile_crn after all component reactions have been generated.

add_mechanism(mechanism, mech_type=None, overwrite=False)

Add a mechanism to the mixture’s mechanism dictionary.

Parameters:

mechanismMechanism or GlobalMechanism

The mechanism object to add. If a GlobalMechanism is provided, it is automatically added to the global mechanisms dictionary.

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 mechanisms with the same keys. If False, raises ValueError when keys already exist. If None, ignores mechanisms that already exist.

Raises:

TypeError

If mechanism is not a Mechanism object, or if mech_type is not a string.

ValueError

If mechanism key already exists and overwrite is None.

See also

add_global_mechanism

Add a global mechanism specifically.

add_mechanisms(mechanisms, overwrite=False)

Add multiple mechanisms to the mixture.

Accepts mechanisms as a single object, list, or dictionary and adds them to the mixture’s mechanism dictionary. Can handle both regular Mechanism and GlobalMechanism objects.

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. If None, ignores mechanisms that already exist.

Raises:

ValueError

If mechanisms is not a valid type, or if mechanism key conflicts occur with overwrite=False.

See also

add_mechanism

Add a single mechanism to the mixture.

add_species(species: List[Species] | Species)

Add species directly to the mixture without component compilation.

Parameters:

speciesSpecies or list of Species

Species object(s) to add directly to the mixture. These species will be included in the CRN during compilation.

Raises:

AssertionError

If any element in the list is not a Species object.

Notes

Species added this way bypass component enumeration and are added directly to the CRN during compile_crn.

add_species_to_crn(new_species, component=None, no_initial_concentrations=False, copy_species=True, compartment=None)

Add species to the CRN with initial concentrations.

Helper method that adds species to the CRN and automatically looks up and assigns their initial concentrations.

Parameters:

new_speciesSpecies or list of Species

Species to add to the CRN.

componentComponent, optional

The component that generated these species. Used for component-specific initial concentration lookup.

no_initial_concentrationsbool, default=False

If True, skips initial concentration lookup and assignment.

copy_speciesbool, default=True

If True, deep-copies species before adding them to the CRN.

compartmentCompartment, optional

Compartment to assign to the species. Overrides species’ existing compartments.

Returns:

list of Species

All species in the CRN after addition (may include pre-existing species).

Notes

This method tracks which species are newly added and only assigns initial concentrations to those new species, preventing overwriting of previously set initial concentrations.

apply_global_mechanisms(species, compartment=None) → Tuple[List[Species], List[Reaction]]

Apply all global mechanisms to a set of species.

Calls each global mechanism’s update_species_global and update_reactions_global methods, then adds the resulting species and reactions to the CRN.

Parameters:

specieslist of Species

Species to which global mechanisms should be applied.

compartmentCompartment, optional

Compartment for newly generated species and reactions.

Returns:

tuple of (list of Species, list of Reaction)

New species and reactions generated by global mechanisms.

Notes

Global mechanisms are typically used for operations that affect all species uniformly, such as dilution, global degradation, or compartment transport.

compile_crn(**kwargs) → ChemicalReactionNetwork

Compile CRN with transcript generation disabled in gene expression.

Overrides the parent compile_crn method to automatically disable transcript generation in DNAassemblies that produce proteins. This ensures that gene expression proceeds directly from DNA to protein without intermediate mRNA species.

Parameters:

**kwargs

Additional keyword arguments passed to the parent Mixture compile_crn method.

Returns:

ChemicalReactionNetwork

Compiled chemical reaction network with expression and dilution reactions.

Notes

This method automatically modifies DNAassemblies before compilation:

• For assemblies with a protein product, sets transcript to False

• RNA-only assemblies (no protein) are not affected

• Mechanisms receive protein instead of transcript when transcript is disabled

This behavior enables the single-step expression mechanism to route production directly to protein.

See Mixture.compile_crn for a more detailed description of the parent method behavior.

component_enumeration(comps_to_enumerate=None, recursion_depth=10) → List[Component]

Recursively enumerate components to generate derived components.

Calls each component’s enumerate_components method repeatedly to expand high-level components into their constituent parts (e.g., DNA_construct –> RNA_construct –> Protein).

Parameters:

comps_to_enumeratelist of Component, optional

Initial components to enumerate. If None, uses all components in the mixture.

recursion_depthint, default=10

Maximum number of enumeration iterations. Prevents infinite recursion.

Returns:

list of Component

All components including the original components and all derived components generated through enumeration.

Warns:

UserWarning

Warns if unenumerated components remain after reaching the recursion depth limit.

get_component(component=None, name=None, index=None)

Retrieve components from the mixture by various criteria.

Exactly one of the three parameters must be provided.

Parameters:

componentComponent, optional

A component instance to search for. Returns components with matching type and name.

namestr, optional

Name of the component to search for. Returns all components with this name.

indexint, optional

Index of the component in the mixture’s component list.

Returns:

Component, list of Component, or None

• Single Component if exactly one match is found or index is used

• List of Components if multiple matches are found

• None if no matches are found

Raises:

ValueError

If zero or more than one parameter is provided, or if parameters are of incorrect types.

get_initial_concentration(S: List | Species, component=None)

Determine initial concentrations using parameter hierarchy.

Searches for initial concentration parameters for species following a hierarchical lookup strategy, defaulting to 0 if not found.

Parameters:

SSpecies or list of Species

Species object(s) for which to find initial concentrations. Lists are automatically flattened.

componentComponent, optional

The component that generated the species. Used for component-specific parameter lookup.

Returns:

dict

Dictionary mapping each Species object to its initial concentration value (float).

Raises:

ValueError

If any element in S is not a Species object.

Notes

The parameter lookup hierarchy is:

1. Component’s ParameterDatabase with mechanism='initial concentration', part_id=mixture.name, and parameter names: str(s), s.name, or component.name (where s is the component’s primary species)

2. Mixture’s ParameterDatabase with the same keys

3. Defaults to 0 if not found

get_mechanism(mechanism_type)

Retrieve a mechanism by type from the mixture.

Parameters:

mechanism_typestr

The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).

Returns:

Mechanism or None

The requested mechanism object, or None if not found.

Raises:

TypeError

If mechanism_type is not a string.

get_parameter(mechanism, part_id, param_name)

Retrieve a parameter from the mixture’s parameter database.

Parameters:

mechanismstr

Mechanism identifier for the parameter lookup key.

part_idstr

Part identifier for the parameter lookup key.

param_namestr

Name of the parameter to retrieve.

Returns:

Parameter or None

The parameter object, or None if not found.

global_component_enumeration(comps_to_enumerate=None, recursion_depth=None) → List[Component]

Apply global component enumerators to generate new components.

Global component enumerators create new components based on patterns across all components (e.g., generating all pairwise binding interactions between proteins).

Parameters:

comps_to_enumeratelist of Component, optional

Initial components to pass to enumerators. If None, uses all components in the mixture.

recursion_depthint, optional

Maximum number of enumeration iterations. If None, uses self.global_recursion_depth.

Returns:

list of Component

All components including original and newly generated components from global enumeration.

Notes

This method is called during compile_crn before local component enumeration. Global enumerators are useful for creating complex interaction networks without manually specifying every interaction.

property global_mechanisms

Mechanism: Stores global mechanisms in the mixture.

property mechanisms

Mechanism: Stores mixture mechanisms.

set_species(species: Species | str, material_type=None, attributes=None)

Convert various inputs into Species objects.

Parameters:

speciesSpecies, str, or Component

The species to convert. Can be a Species object (returned as-is), a string (creates new Species), or a Component (extracts its species).

material_typestr, optional

Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). 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

The converted Species object.

Raises:

ValueError

If the input cannot be converted to a valid Species.

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

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).

overwrite_parametersbool, default=True

If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

class biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture(name='', **kwargs)

In vivo TX-TL with simple mechanisms and continuous dilution.

A mixture that models transcription and translation as separate catalytic reactions without explicitly representing cellular machinery (RNAP, ribosomes). This mixture uses simple mass-action kinetics where DNA and mRNA act as catalysts for transcript and protein production, respectively. Includes global dilution to model cell growth and division effects, plus separate RNA degradation to model endonuclease activity.

This mixture is appropriate for in vivo gene expression models where machinery is not limiting but explicit TX-TL steps and growth dilution are important.

Parameters:

namestr, default=’’

Name of the mixture for identification and parameter lookup.

mechanismsdict, list, or Mechanism, optional

Default mechanisms for components in this mixture. Can be a dict with mechanism types (str) as keys and mechanism objects as values, a list of mechanism objects, or a single Mechanism.

componentslist of Component or Component, optional

Components to include in the mixture. Components are deep-copied when added to prevent modification of original objects.

parametersdict, optional

Dictionary of parameter values. Keys follow the format (mechanism, part_id, param_name).

compartmentCompartment, optional

Default compartment for all components and species in this mixture.

parameter_filestr, optional

Path to a CSV or TSV file containing parameters to load.

overwrite_parametersbool, default=False

If True, parameters from file/dict overwrite existing parameters. If False, existing parameters are preserved.

global_mechanismsdict, list, or GlobalMechanism, optional

Global mechanisms that apply to all species after component compilation (e.g., dilution, global degradation). Can be a dict, list, or single GlobalMechanism.

specieslist of Species or Species, optional

Additional species to add directly to the CRN without going through component compilation.

initial_condition_dictionarydict, optional

Dictionary mapping species to initial concentration values. Deprecated in favor of using parameters with mechanism=’initial concentration’.

global_component_enumeratorslist, optional

List of global component enumerators for advanced component generation patterns (e.g., creating all pairwise interactions).

global_recursion_depthint, default=4

Maximum recursion depth for global component enumeration during compilation.

local_recursion_depthint, optional

Maximum recursion depth for local component enumeration. If None, defaults to global_recursion_depth + 2.

Attributes:

namestr

Name of the mixture.

compartmentCompartment or None

Default compartment for the mixture.

componentslist of Component

List of components in the mixture (deep copies of added components).

mechanismsdict

Mechanism: Stores mixture mechanisms.

global_mechanismsdict

Mechanism: Stores global mechanisms in the mixture.

parameter_databaseParameterDatabase

Database storing all parameters for this mixture.

added_specieslist of Species

List of species added directly to the mixture.

global_component_enumeratorslist

List of global component enumerators.

global_recursion_depthint

Recursion depth for global component enumeration.

local_recursion_depthint

Recursion depth for local component enumeration.

crnChemicalReactionNetwork or None

The compiled CRN, created by calling compile_crn.

See also

ExpressionDilutionMixture

Single-step expression with dilution.

TxTlDilutionMixture

TX-TL with machinery and dilution.

SimpleTxTlExtract

TX-TL without dilution.

Mixture

Base class for all mixtures.

Notes

Default mechanisms included:

• ‘transcription’ : SimpleTranscription - Simple catalytic transcription (DNA –> DNA + mRNA) without explicit RNAP binding

• ‘translation’ : SimpleTranslation - Simple catalytic translation (mRNA –> mRNA + Protein) without explicit ribosome binding

• ‘catalysis’ : BasicCatalysis - Simple catalytic reactions without explicit enzyme binding

• ‘binding’ : One_Step_Binding - Simple multi-species binding

• ‘dilution’ : Dilution - Global dilution mechanism (Species –> ∅) applied to all non-DNA species to model growth/division

• ‘rna_degradation’ : Dilution - Separate RNA degradation mechanism (mRNA –> ∅) applied to all RNA species to model endonuclease activity

Key features of this mixture:

• Explicit transcription and translation steps

• Intermediate mRNA species

• Simple mass-action kinetics (no enzyme binding)

• No cellular machinery (RNAP, ribosomes)

• Global dilution of all non-DNA species

• Separate RNA degradation (faster than dilution)

• Models growth effects in vivo

Common applications include:

• In vivo gene circuit modeling with growth

• Models where machinery is not limiting

• Constitutive or weakly regulated promoters in growing cells

• mRNA dynamics with degradation and dilution

Examples

Create a simple in vivo TX-TL mixture with dilution for GFP:

>>> gfp_gene = bcp.DNAassembly(
...     name='gfp_construct',
...     promoter='pconst',
...     rbs='bcd2',
...     transcript='gfp_mrna',
...     protein='GFP'
... )
>>> mixture = bcp.SimpleTxTlDilutionMixture(
...     name='cell_mixture',
...     components=[gfp_gene],
...     parameter_file='mixtures/cell_parameters.tsv'
... )
>>> crn = mixture.compile_crn()

add_component(component)

Add a single component to the mixture.

Parameters:

componentComponent or list of Component

Component object to add to the mixture. If a list is provided, calls add_components instead. The component is deep-copied before being added.

Raises:

AssertionError

If the component is not a Component object.

ValueError

If a component with the same type and name already exists in the mixture.

Notes

Components are deep-copied when added to prevent modification of the original component. The copied component’s mixture attribute is set to this Mixture, and its compartment is set to the mixture’s compartment.

add_components(components: List[Component] | Component)

Add multiple components to the mixture.

Parameters:

componentsComponent or list of Component

Component object(s) to add to the mixture. Each component is deep-copied before being added.

Raises:

ValueError

If components is not a Component, list of Components, or if any duplicate components are detected.

See also

add_component

Add a single component to the mixture.

add_global_mechanism(mechanism, mech_type=None, overwrite=False)

Add a global mechanism to the mixture.

Global mechanisms are applied to all species after component compilation, enabling operations like dilution or global degradation.

Parameters:

mechanismGlobalMechanism

The global mechanism object to add. Must be a GlobalMechanism instance.

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 global mechanism with the same key. If False, raises ValueError when key already exists.

Raises:

TypeError

If mechanism is not a GlobalMechanism object, or if mech_type is not a string.

ValueError

If mechanism key already exists and overwrite is False.

Notes

Global mechanisms are applied during compile_crn after all component reactions have been generated.

add_mechanism(mechanism, mech_type=None, overwrite=False)

Add a mechanism to the mixture’s mechanism dictionary.

Parameters:

mechanismMechanism or GlobalMechanism

The mechanism object to add. If a GlobalMechanism is provided, it is automatically added to the global mechanisms dictionary.

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 mechanisms with the same keys. If False, raises ValueError when keys already exist. If None, ignores mechanisms that already exist.

Raises:

TypeError

If mechanism is not a Mechanism object, or if mech_type is not a string.

ValueError

If mechanism key already exists and overwrite is None.

See also

add_global_mechanism

Add a global mechanism specifically.

add_mechanisms(mechanisms, overwrite=False)

Add multiple mechanisms to the mixture.

Accepts mechanisms as a single object, list, or dictionary and adds them to the mixture’s mechanism dictionary. Can handle both regular Mechanism and GlobalMechanism objects.

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. If None, ignores mechanisms that already exist.

Raises:

ValueError

If mechanisms is not a valid type, or if mechanism key conflicts occur with overwrite=False.

See also

add_mechanism

Add a single mechanism to the mixture.

add_species(species: List[Species] | Species)

Add species directly to the mixture without component compilation.

Parameters:

speciesSpecies or list of Species

Species object(s) to add directly to the mixture. These species will be included in the CRN during compilation.

Raises:

AssertionError

If any element in the list is not a Species object.

Notes

Species added this way bypass component enumeration and are added directly to the CRN during compile_crn.

add_species_to_crn(new_species, component=None, no_initial_concentrations=False, copy_species=True, compartment=None)

Add species to the CRN with initial concentrations.

Helper method that adds species to the CRN and automatically looks up and assigns their initial concentrations.

Parameters:

new_speciesSpecies or list of Species

Species to add to the CRN.

componentComponent, optional

The component that generated these species. Used for component-specific initial concentration lookup.

no_initial_concentrationsbool, default=False

If True, skips initial concentration lookup and assignment.

copy_speciesbool, default=True

If True, deep-copies species before adding them to the CRN.

compartmentCompartment, optional

Compartment to assign to the species. Overrides species’ existing compartments.

Returns:

list of Species

All species in the CRN after addition (may include pre-existing species).

Notes

This method tracks which species are newly added and only assigns initial concentrations to those new species, preventing overwriting of previously set initial concentrations.

apply_global_mechanisms(species, compartment=None) → Tuple[List[Species], List[Reaction]]

Apply all global mechanisms to a set of species.

Calls each global mechanism’s update_species_global and update_reactions_global methods, then adds the resulting species and reactions to the CRN.

Parameters:

specieslist of Species

Species to which global mechanisms should be applied.

compartmentCompartment, optional

Compartment for newly generated species and reactions.

Returns:

tuple of (list of Species, list of Reaction)

New species and reactions generated by global mechanisms.

Notes

Global mechanisms are typically used for operations that affect all species uniformly, such as dilution, global degradation, or compartment transport.

compile_crn(recursion_depth: int = None, initial_concentration_dict: dict = None, return_enumerated_components: bool = False, initial_concentrations_at_end: bool = False, copy_objects: bool = True, add_reaction_species: bool = True, compartment: Compartment = None) → ChemicalReactionNetwork

Compile a chemical reaction network from the mixture.

Enumerates components, generates species and reactions from each component, applies global mechanisms, and returns a complete CRN.

Parameters:

recursion_depthint, optional

Maximum recursion depth for both local and global component enumeration. If None, uses self.global_recursion_depth.

initial_concentration_dictdict, optional

Dictionary mapping species to initial concentrations. This overrides all other initial concentration settings and is applied at the very end of compilation.

return_enumerated_componentsbool, default=False

If True, returns a tuple of (CRN, enumerated_components) instead of just the CRN.

initial_concentrations_at_endbool, default=False

If True, initial concentrations are only set at the end using the mixture’s parameter database, ignoring component-specific initial concentrations during compilation.

copy_objectsbool, default=True

If True, species and reactions are deep-copied when added to the CRN. Protects CRN validity at the expense of compilation speed.

add_reaction_speciesbool, default=True

If True, species appearing in reactions are automatically added to the CRN. Ensures no missing species at the expense of compilation speed.

compartmentCompartment, optional

Compartment to assign to all species and reactions that are not already assigned to a compartment. If None, uses self.compartment.

Returns:

ChemicalReactionNetwork or tuple

If return_enumerated_components is False, returns the compiled ChemicalReactionNetwork. If True, returns a tuple of (ChemicalReactionNetwork, list of enumerated Components).

Notes

The compilation process follows these steps:

1. Add any directly-added species to the CRN

2. Global component enumeration (generates component interactions)

3. Local component enumeration (e.g., DNA –> RNA –> Protein)

4. Generate species from all enumerated components

5. Generate reactions from all enumerated components

6. Apply global mechanisms to all species

7. Set initial concentrations

Examples

Basic compilation:

>>> gene = bcp.DNAassembly(
...     'GFP', promoter='pconst', rbs='RBS', protein='GFP')
>>> mixture = bcp.Mixture(
...     name="txtl_extract",
...     components=[gene],
...     mechanisms={
...         'transcription': bcp.SimpleTranscription(),
...         'translation': bcp.SimpleTranslation()
...     },
...     parameters={'ktx': 0.05, 'ktl': 0.01}
... )
>>> crn = mixture.compile_crn()

Compilation with custom initial concentrations:

>>> crn = mixture.compile_crn(
...     initial_concentration_dict={gene.dna: 1, gene.transcript: 50}
... )

Get both CRN and enumerated components:

>>> crn, components = mixture.compile_crn(
...     return_enumerated_components=True
... )

component_enumeration(comps_to_enumerate=None, recursion_depth=10) → List[Component]

Recursively enumerate components to generate derived components.

Calls each component’s enumerate_components method repeatedly to expand high-level components into their constituent parts (e.g., DNA_construct –> RNA_construct –> Protein).

Parameters:

comps_to_enumeratelist of Component, optional

Initial components to enumerate. If None, uses all components in the mixture.

recursion_depthint, default=10

Maximum number of enumeration iterations. Prevents infinite recursion.

Returns:

list of Component

All components including the original components and all derived components generated through enumeration.

Warns:

UserWarning

Warns if unenumerated components remain after reaching the recursion depth limit.

get_component(component=None, name=None, index=None)

Retrieve components from the mixture by various criteria.

Exactly one of the three parameters must be provided.

Parameters:

componentComponent, optional

A component instance to search for. Returns components with matching type and name.

namestr, optional

Name of the component to search for. Returns all components with this name.

indexint, optional

Index of the component in the mixture’s component list.

Returns:

Component, list of Component, or None

• Single Component if exactly one match is found or index is used

• List of Components if multiple matches are found

• None if no matches are found

Raises:

ValueError

If zero or more than one parameter is provided, or if parameters are of incorrect types.

get_initial_concentration(S: List | Species, component=None)

Determine initial concentrations using parameter hierarchy.

Searches for initial concentration parameters for species following a hierarchical lookup strategy, defaulting to 0 if not found.

Parameters:

SSpecies or list of Species

Species object(s) for which to find initial concentrations. Lists are automatically flattened.

componentComponent, optional

The component that generated the species. Used for component-specific parameter lookup.

Returns:

dict

Dictionary mapping each Species object to its initial concentration value (float).

Raises:

ValueError

If any element in S is not a Species object.

Notes

The parameter lookup hierarchy is:

1. Component’s ParameterDatabase with mechanism='initial concentration', part_id=mixture.name, and parameter names: str(s), s.name, or component.name (where s is the component’s primary species)

2. Mixture’s ParameterDatabase with the same keys

3. Defaults to 0 if not found

get_mechanism(mechanism_type)

Retrieve a mechanism by type from the mixture.

Parameters:

mechanism_typestr

The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).

Returns:

Mechanism or None

The requested mechanism object, or None if not found.

Raises:

TypeError

If mechanism_type is not a string.

get_parameter(mechanism, part_id, param_name)

Retrieve a parameter from the mixture’s parameter database.

Parameters:

mechanismstr

Mechanism identifier for the parameter lookup key.

part_idstr

Part identifier for the parameter lookup key.

param_namestr

Name of the parameter to retrieve.

Returns:

Parameter or None

The parameter object, or None if not found.

global_component_enumeration(comps_to_enumerate=None, recursion_depth=None) → List[Component]

Apply global component enumerators to generate new components.

Global component enumerators create new components based on patterns across all components (e.g., generating all pairwise binding interactions between proteins).

Parameters:

comps_to_enumeratelist of Component, optional

Initial components to pass to enumerators. If None, uses all components in the mixture.

recursion_depthint, optional

Maximum number of enumeration iterations. If None, uses self.global_recursion_depth.

Returns:

list of Component

All components including original and newly generated components from global enumeration.

Notes

This method is called during compile_crn before local component enumeration. Global enumerators are useful for creating complex interaction networks without manually specifying every interaction.

property global_mechanisms

Mechanism: Stores global mechanisms in the mixture.

property mechanisms

Mechanism: Stores mixture mechanisms.

set_species(species: Species | str, material_type=None, attributes=None)

Convert various inputs into Species objects.

Parameters:

speciesSpecies, str, or Component

The species to convert. Can be a Species object (returned as-is), a string (creates new Species), or a Component (extracts its species).

material_typestr, optional

Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). 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

The converted Species object.

Raises:

ValueError

If the input cannot be converted to a valid Species.

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

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).

overwrite_parametersbool, default=True

If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.

class biocrnpyler.mixtures.cell.TxTlDilutionMixture(name='', rnap='RNAP', ribosome='Ribo', rnaase='RNAase', **kwargs)

In vivo TX-TL with explicit machinery, dilution, and background load.

A mixture that models transcription and translation with explicit representation of RNA polymerase (RNAP), ribosomes, and RNases for in vivo contexts. This mixture uses Michaelis-Menten kinetics for TX-TL, explicitly tracking enzyme-substrate binding and catalysis. Includes global dilution to model cell growth effects and a background load component representing endogenous cellular processes that compete for shared machinery.

Unlike TxTlExtract, this mixture includes dilution for non-DNA and non-machinery species. Machinery components (RNAP, ribosomes, RNases) are protected from dilution via the ‘machinery’ attribute. This model does not include explicit energy species.

Parameters:

namestr, default=’’

Name of the mixture for identification and parameter lookup.

rnapstr, default=’RNAP’

Name for the RNA polymerase protein species.

ribosomestr, default=’Ribo’

Name for the ribosome protein species.

rnaasestr, default=’RNAase’

Name for the ribonuclease protein species.

mechanismsdict, list, or Mechanism, optional

Default mechanisms for components in this mixture. Can be a dict with mechanism types (str) as keys and mechanism objects as values, a list of mechanism objects, or a single Mechanism.

componentslist of Component or Component, optional

Components to include in the mixture. Components are deep-copied when added to prevent modification of original objects.

parametersdict, optional

Dictionary of parameter values. Keys follow the format (mechanism, part_id, param_name).

compartmentCompartment, optional

Default compartment for all components and species in this mixture.

parameter_filestr, optional

Path to a CSV or TSV file containing parameters to load.

overwrite_parametersbool, default=False

If True, parameters from file/dict overwrite existing parameters. If False, existing parameters are preserved.

global_mechanismsdict, list, or GlobalMechanism, optional

Global mechanisms that apply to all species after component compilation (e.g., dilution, global degradation). Can be a dict, list, or single GlobalMechanism.

specieslist of Species or Species, optional

Additional species to add directly to the CRN without going through component compilation.

initial_condition_dictionarydict, optional

Dictionary mapping species to initial concentration values. Deprecated in favor of using parameters with mechanism=’initial concentration’.

global_component_enumeratorslist, optional

List of global component enumerators for advanced component generation patterns (e.g., creating all pairwise interactions).

global_recursion_depthint, default=4

Maximum recursion depth for global component enumeration during compilation.

local_recursion_depthint, optional

Maximum recursion depth for local component enumeration. If None, defaults to global_recursion_depth + 2.

Attributes:

namestr

Name of the mixture.

rnapProtein

RNA polymerase component with ‘machinery’ attribute.

ribosomeProtein

Ribosome component with ‘machinery’ attribute.

rnaaseProtein

Ribonuclease component with ‘machinery’ attribute.

compartmentCompartment or None

Default compartment for the mixture.

componentslist of Component

List of components in the mixture (deep copies of added components).

mechanismsdict

Mechanism: Stores mixture mechanisms.

global_mechanismsdict

Mechanism: Stores global mechanisms in the mixture.

parameter_databaseParameterDatabase

Database storing all parameters for this mixture.

added_specieslist of Species

List of species added directly to the mixture.

global_component_enumeratorslist

List of global component enumerators.

global_recursion_depthint

Recursion depth for global component enumeration.

local_recursion_depthint

Recursion depth for local component enumeration.

crnChemicalReactionNetwork or None

The compiled CRN, created by calling compile_crn.

See also

SimpleTxTlDilutionMixture

TX-TL without machinery, with dilution.

TxTlExtract

TX-TL with machinery, without dilution.

ExpressionDilutionMixture

Single-step expression with dilution.

Mixture

Base class for all mixtures.

Notes

This mixture automatically adds the following components:

• RNA polymerase (RNAP) with ‘machinery’ attribute

• Ribosome with ‘machinery’ attribute

• Ribonuclease (RNase) with ‘machinery’ attribute

• Background processes DNAassembly representing cellular load

Default mechanisms included:

• ‘transcription’ : Transcription_MM - Michaelis-Menten transcription with explicit RNAP binding (DNA + RNAP <–> DNA:RNAP –> DNA + RNAP + mRNA)

• ‘translation’ : Translation_MM - Michaelis-Menten translation with explicit ribosome binding (mRNA + Rib <–> mRNA:Rib –> mRNA + Rib + Protein)

• ‘rna_degradation’ : Degradation_mRNA_MM - Global RNA degradation by RNase using Michaelis-Menten kinetics

• ‘catalysis’ : MichaelisMenten - General Michaelis-Menten enzyme catalysis

• ‘binding’ : One_Step_Binding - Simple multi-species binding

• ‘dilution’ : Dilution - Global dilution mechanism (Species –> ∅) applied to all species except DNA and machinery

Key features of this mixture:

• Explicit modeling of transcription and translation machinery

• Resource competition (genes and background processes compete for machinery)

• Enzyme sequestration in complexes

• RNA degradation dynamics

• Global dilution modeling cell growth

• Machinery protected from dilution

• Background load representing cellular processes

• Suitable for modeling in vivo gene expression with resource limits

Background processes:

• Implemented as a DNAassembly component (‘cellular_processes’)

• Represents endogenous genes competing for machinery

• Uses average promoter and RBS parameters

• Creates realistic loading effects on available machinery

• Does not model effects of loading on cell growth rate

Common applications include:

• In vivo gene circuit modeling with growth

• Resource allocation in growing cells

• Gene expression burden studies

• Competition between heterologous and endogenous genes

• Synthetic biology in cellular contexts

Examples

Create an in vivo TX-TL mixture with machinery and dilution for GFP:

>>> gfp_gene = bcp.DNAassembly(
...     name='gfp_construct',
...     promoter='pconst',
...     rbs='bcd2',
...     transcript='gfp_mrna',
...     protein='GFP'
... )
>>> mixture = bcp.TxTlDilutionMixture(
...     name='cell_mixture',
...     components=[gfp_gene],
...     parameter_file='mixtures/cell_parameters.tsv'
... )
>>> crn = mixture.compile_crn()

add_component(component)

Add a single component to the mixture.

Parameters:

componentComponent or list of Component

Component object to add to the mixture. If a list is provided, calls add_components instead. The component is deep-copied before being added.

Raises:

AssertionError

If the component is not a Component object.

ValueError

If a component with the same type and name already exists in the mixture.

Notes

Components are deep-copied when added to prevent modification of the original component. The copied component’s mixture attribute is set to this Mixture, and its compartment is set to the mixture’s compartment.

add_components(components: List[Component] | Component)

Add multiple components to the mixture.

Parameters:

componentsComponent or list of Component

Component object(s) to add to the mixture. Each component is deep-copied before being added.

Raises:

ValueError

If components is not a Component, list of Components, or if any duplicate components are detected.

See also

add_component

Add a single component to the mixture.

add_global_mechanism(mechanism, mech_type=None, overwrite=False)

Add a global mechanism to the mixture.

Global mechanisms are applied to all species after component compilation, enabling operations like dilution or global degradation.

Parameters:

mechanismGlobalMechanism

The global mechanism object to add. Must be a GlobalMechanism instance.

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 global mechanism with the same key. If False, raises ValueError when key already exists.

Raises:

TypeError

If mechanism is not a GlobalMechanism object, or if mech_type is not a string.

ValueError

If mechanism key already exists and overwrite is False.

Notes

Global mechanisms are applied during compile_crn after all component reactions have been generated.

add_mechanism(mechanism, mech_type=None, overwrite=False)

Add a mechanism to the mixture’s mechanism dictionary.

Parameters:

mechanismMechanism or GlobalMechanism

The mechanism object to add. If a GlobalMechanism is provided, it is automatically added to the global mechanisms dictionary.

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 mechanisms with the same keys. If False, raises ValueError when keys already exist. If None, ignores mechanisms that already exist.

Raises:

TypeError

If mechanism is not a Mechanism object, or if mech_type is not a string.

ValueError

If mechanism key already exists and overwrite is None.

See also

add_global_mechanism

Add a global mechanism specifically.

add_mechanisms(mechanisms, overwrite=False)

Add multiple mechanisms to the mixture.

Accepts mechanisms as a single object, list, or dictionary and adds them to the mixture’s mechanism dictionary. Can handle both regular Mechanism and GlobalMechanism objects.

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. If None, ignores mechanisms that already exist.

Raises:

ValueError

If mechanisms is not a valid type, or if mechanism key conflicts occur with overwrite=False.

See also

add_mechanism

Add a single mechanism to the mixture.

add_species(species: List[Species] | Species)

Add species directly to the mixture without component compilation.

Parameters:

speciesSpecies or list of Species

Species object(s) to add directly to the mixture. These species will be included in the CRN during compilation.

Raises:

AssertionError

If any element in the list is not a Species object.

Notes

Species added this way bypass component enumeration and are added directly to the CRN during compile_crn.

add_species_to_crn(new_species, component=None, no_initial_concentrations=False, copy_species=True, compartment=None)

Add species to the CRN with initial concentrations.

Helper method that adds species to the CRN and automatically looks up and assigns their initial concentrations.

Parameters:

new_speciesSpecies or list of Species

Species to add to the CRN.

componentComponent, optional

The component that generated these species. Used for component-specific initial concentration lookup.

no_initial_concentrationsbool, default=False

If True, skips initial concentration lookup and assignment.

copy_speciesbool, default=True

If True, deep-copies species before adding them to the CRN.

compartmentCompartment, optional

Compartment to assign to the species. Overrides species’ existing compartments.

Returns:

list of Species

All species in the CRN after addition (may include pre-existing species).

Notes

This method tracks which species are newly added and only assigns initial concentrations to those new species, preventing overwriting of previously set initial concentrations.

apply_global_mechanisms(species, compartment=None) → Tuple[List[Species], List[Reaction]]

Apply all global mechanisms to a set of species.

Calls each global mechanism’s update_species_global and update_reactions_global methods, then adds the resulting species and reactions to the CRN.

Parameters:

specieslist of Species

Species to which global mechanisms should be applied.

compartmentCompartment, optional

Compartment for newly generated species and reactions.

Returns:

tuple of (list of Species, list of Reaction)

New species and reactions generated by global mechanisms.

Notes

Global mechanisms are typically used for operations that affect all species uniformly, such as dilution, global degradation, or compartment transport.

compile_crn(recursion_depth: int = None, initial_concentration_dict: dict = None, return_enumerated_components: bool = False, initial_concentrations_at_end: bool = False, copy_objects: bool = True, add_reaction_species: bool = True, compartment: Compartment = None) → ChemicalReactionNetwork

Compile a chemical reaction network from the mixture.

Enumerates components, generates species and reactions from each component, applies global mechanisms, and returns a complete CRN.

Parameters:

recursion_depthint, optional

Maximum recursion depth for both local and global component enumeration. If None, uses self.global_recursion_depth.

initial_concentration_dictdict, optional

Dictionary mapping species to initial concentrations. This overrides all other initial concentration settings and is applied at the very end of compilation.

return_enumerated_componentsbool, default=False

If True, returns a tuple of (CRN, enumerated_components) instead of just the CRN.

initial_concentrations_at_endbool, default=False

If True, initial concentrations are only set at the end using the mixture’s parameter database, ignoring component-specific initial concentrations during compilation.

copy_objectsbool, default=True

If True, species and reactions are deep-copied when added to the CRN. Protects CRN validity at the expense of compilation speed.

add_reaction_speciesbool, default=True

If True, species appearing in reactions are automatically added to the CRN. Ensures no missing species at the expense of compilation speed.

compartmentCompartment, optional

Compartment to assign to all species and reactions that are not already assigned to a compartment. If None, uses self.compartment.

Returns:

ChemicalReactionNetwork or tuple

If return_enumerated_components is False, returns the compiled ChemicalReactionNetwork. If True, returns a tuple of (ChemicalReactionNetwork, list of enumerated Components).

Notes

The compilation process follows these steps:

1. Add any directly-added species to the CRN

2. Global component enumeration (generates component interactions)

3. Local component enumeration (e.g., DNA –> RNA –> Protein)

4. Generate species from all enumerated components

5. Generate reactions from all enumerated components

6. Apply global mechanisms to all species

7. Set initial concentrations

Examples

Basic compilation:

>>> gene = bcp.DNAassembly(
...     'GFP', promoter='pconst', rbs='RBS', protein='GFP')
>>> mixture = bcp.Mixture(
...     name="txtl_extract",
...     components=[gene],
...     mechanisms={
...         'transcription': bcp.SimpleTranscription(),
...         'translation': bcp.SimpleTranslation()
...     },
...     parameters={'ktx': 0.05, 'ktl': 0.01}
... )
>>> crn = mixture.compile_crn()

Compilation with custom initial concentrations:

>>> crn = mixture.compile_crn(
...     initial_concentration_dict={gene.dna: 1, gene.transcript: 50}
... )

Get both CRN and enumerated components:

>>> crn, components = mixture.compile_crn(
...     return_enumerated_components=True
... )

component_enumeration(comps_to_enumerate=None, recursion_depth=10) → List[Component]

Recursively enumerate components to generate derived components.

Calls each component’s enumerate_components method repeatedly to expand high-level components into their constituent parts (e.g., DNA_construct –> RNA_construct –> Protein).

Parameters:

comps_to_enumeratelist of Component, optional

Initial components to enumerate. If None, uses all components in the mixture.

recursion_depthint, default=10

Maximum number of enumeration iterations. Prevents infinite recursion.

Returns:

list of Component

All components including the original components and all derived components generated through enumeration.

Warns:

UserWarning

Warns if unenumerated components remain after reaching the recursion depth limit.

get_component(component=None, name=None, index=None)

Retrieve components from the mixture by various criteria.

Exactly one of the three parameters must be provided.

Parameters:

componentComponent, optional

A component instance to search for. Returns components with matching type and name.

namestr, optional

Name of the component to search for. Returns all components with this name.

indexint, optional

Index of the component in the mixture’s component list.

Returns:

Component, list of Component, or None

• Single Component if exactly one match is found or index is used

• List of Components if multiple matches are found

• None if no matches are found

Raises:

ValueError

If zero or more than one parameter is provided, or if parameters are of incorrect types.

get_initial_concentration(S: List | Species, component=None)

Determine initial concentrations using parameter hierarchy.

Searches for initial concentration parameters for species following a hierarchical lookup strategy, defaulting to 0 if not found.

Parameters:

SSpecies or list of Species

Species object(s) for which to find initial concentrations. Lists are automatically flattened.

componentComponent, optional

The component that generated the species. Used for component-specific parameter lookup.

Returns:

dict

Dictionary mapping each Species object to its initial concentration value (float).

Raises:

ValueError

If any element in S is not a Species object.

Notes

The parameter lookup hierarchy is:

1. Component’s ParameterDatabase with mechanism='initial concentration', part_id=mixture.name, and parameter names: str(s), s.name, or component.name (where s is the component’s primary species)

2. Mixture’s ParameterDatabase with the same keys

3. Defaults to 0 if not found

get_mechanism(mechanism_type)

Retrieve a mechanism by type from the mixture.

Parameters:

mechanism_typestr

The type identifier of the mechanism to retrieve (e.g., ‘transcription’, ‘translation’, ‘binding’).

Returns:

Mechanism or None

The requested mechanism object, or None if not found.

Raises:

TypeError

If mechanism_type is not a string.

get_parameter(mechanism, part_id, param_name)

Retrieve a parameter from the mixture’s parameter database.

Parameters:

mechanismstr

Mechanism identifier for the parameter lookup key.

part_idstr

Part identifier for the parameter lookup key.

param_namestr

Name of the parameter to retrieve.

Returns:

Parameter or None

The parameter object, or None if not found.

global_component_enumeration(comps_to_enumerate=None, recursion_depth=None) → List[Component]

Apply global component enumerators to generate new components.

Global component enumerators create new components based on patterns across all components (e.g., generating all pairwise binding interactions between proteins).

Parameters:

comps_to_enumeratelist of Component, optional

Initial components to pass to enumerators. If None, uses all components in the mixture.

recursion_depthint, optional

Maximum number of enumeration iterations. If None, uses self.global_recursion_depth.

Returns:

list of Component

All components including original and newly generated components from global enumeration.

Notes

This method is called during compile_crn before local component enumeration. Global enumerators are useful for creating complex interaction networks without manually specifying every interaction.

property global_mechanisms

Mechanism: Stores global mechanisms in the mixture.

property mechanisms

Mechanism: Stores mixture mechanisms.

set_species(species: Species | str, material_type=None, attributes=None)

Convert various inputs into Species objects.

Parameters:

speciesSpecies, str, or Component

The species to convert. Can be a Species object (returned as-is), a string (creates new Species), or a Component (extracts its species).

material_typestr, optional

Material type for the species (e.g., ‘dna’, ‘rna’, ‘protein’). 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

The converted Species object.

Raises:

ValueError

If the input cannot be converted to a valid Species.

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

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).

overwrite_parametersbool, default=True

If True, new parameter values overwrite existing ones. If False, existing parameters are preserved.