biocrnpyler.components.dna.promoter

Classes

ActivatablePromoter(name, activator[, ...])

A class for a promoter which can be activated by a single species, modelled as a positive hill function

CombinatorialPromoter(name, regulators[, ...])

A combinatorial promoter is something where binding multiple regulators result in qualitatively different transcription behaviour.

Promoter(name[, assembly, transcript, ...])

A basic Promoter class with no regulation.

RegulatedPromoter(name, regulators[, leak, ...])

A Promoter class with simple regulation.

RepressiblePromoter(name, repressor[, ...])

A class for a promoter which can be repressed by a single species, modelled as a negative hill function
class biocrnpyler.components.dna.promoter.ActivatablePromoter(name, activator, transcript=None, leak=False, **keywords)[source]

A class for a promoter which can be activated by a single species, modelled as a positive hill function

this represents a modular component sequence. These get compiled into working components

add_mechanism(mechanism: Mechanism, mech_type=None, overwrite=False, optional_mechanism=False)[source]

adds a mechanism of type mech_type to the Component Mechanism dictionary.

Parameters:

  • mechanism

  • mech_type

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

add_mechanisms(mechanisms: Mechanism | GlobalMechanism, overwrite=False, optional_mechanism=False)[source]

This function adds a list or dictionary of mechanisms to the mixture.

Parameters:

  • mechanisms – Can take both GlobalMechanisms and Mechanisms

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

clone(position, direction, parent_dna)[source]

this defines where the part is in what piece of DNA

property compartment

The compartment of the Component.

Returns:

Compartment

enumerate_components(**keywords) → List[source]

this is for component enumeration. Usually you will return a list of components that are copies of existing ones (first list) and new components (second list). For example, A DNA_construct makes a list of copies of its parts as the first output, and a list of RNA_constructs as the second output. An RNA_construct will make a list of copies of its parts as the first output, and a list of Protein components as its second output (if it makes any proteins)

classmethod from_promoter(name, assembly, transcript, protein)[source]

Helper function to initialize a promoter instance from another promoter or str.

Parameters:

  • name – either string or an other promoter instance

  • assembly

  • transcript

  • protein

Returns:

Promoter instance

get_mechanism(mechanism_type, optional_mechanism=False)[source]

Searches the Component for a Mechanism of the correct type.

If the Component does not have the mechanism, searches the Components’ Mixture for the Mechanism.

Parameters:

  • mechanism_type

  • optional_mechanism – toggles whether an error is thrown if no mechanism is found

Returns:

get_orphan()[source]

returns a copy of this monomer, except with no parent. But it still has a position and direction

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

Get a parameter from different objects that hold parameters.

Hierarchy:

  1. tries to find the Parameter in Component.parameter_database

  2. tries to find the parameter in Component.mixture.parameter_database

Parameters:

  • param_name

  • part_id

  • mechanism

  • return_numerical – numerical value or the parameter object is returned

  • return_none – returns None instead of throwing an error if a parameter isn’t found

  • check_mixture – toggle whether or not to check the Component’s Mixture as well

Returns:

Parameter object or a Real number

get_species()[source]

The subclasses should implement this method!

Returns:

None

set_mixture(mixture) → None[source]

Set the mixture the Component is in.

Parameters:

mixture

Returns:

None

classmethod set_species(species: Species | str, material_type=None, compartment=None, attributes=None) → Species[source]

Helper function that allows species to be set from strings, species, or Components

Parameters:

  • species – Species, str, Component

  • material_type

  • compartment

  • attributes

Returns:

Species

unclone()[source]

removes the current part from anything

update_component(internal_species=None, **keywords)[source]

returns a copy of this component, except with the proper fields updated

update_parameters(parameter_file=None, parameters=None, parameter_database=None, overwrite_parameters=True)[source]

Updates the ParameterDatabase inside a Component

Possible inputs:

parameter_file (string) parameters (dict) parameter_database (ParameterDatabase)

update_reactions(**keywords)[source]

The subclasses should implement this method!

Returns:

empty list

update_species(**keywords)[source]

The subclasses should implement this method!

Returns:

empty list

class biocrnpyler.components.dna.promoter.CombinatorialPromoter(name, regulators, leak=False, assembly=None, transcript=None, length=0, mechanisms=None, parameters=None, protein=None, tx_capable_list=None, cooperativity=None, **keywords)[source]

A combinatorial promoter is something where binding multiple regulators result in qualitatively different transcription behaviour. For example, maybe it’s an AND gate promoter where it only transcribes if two regulators are bound, but not if either one is bound.

inputs

name: the name of the promoter regulators: a list of strings or species indicating all the possible regualtors that can bind

leak: if true, then a promoter with nothing bound will transcribe

assembly: a DNA_assembly object that contains this promoter

transcript: the transcript that this promoter makes

length: the length in nt? I don’t think this is used for anything at the moment

mechanisms: additional mechanisms. formatted with {“mechanism_type”:mechanismObject(),…}

parameters: promoter-specific parameters. Formatted as {(“identifier1”,”identifier2”):value,…}

tx_capable_list: list of which combination of regulators bound will lead to transcription.

formatted as [[“regulator1”,”regulator2”],[“regulator1”],…] regulators can be strings or Species

cooperativity: a dictionary of cooperativity values. For example, {“regulator”:2,”regulator2”:1,….}

add_mechanism(mechanism: Mechanism, mech_type=None, overwrite=False, optional_mechanism=False)[source]

adds a mechanism of type mech_type to the Component Mechanism dictionary.

Parameters:

  • mechanism

  • mech_type

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

add_mechanisms(mechanisms: Mechanism | GlobalMechanism, overwrite=False, optional_mechanism=False)[source]

This function adds a list or dictionary of mechanisms to the mixture.

Parameters:

  • mechanisms – Can take both GlobalMechanisms and Mechanisms

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

clone(position, direction, parent_dna)[source]

this defines where the part is in what piece of DNA

property compartment

The compartment of the Component.

Returns:

Compartment

enumerate_components(**keywords) → List[source]

this is for component enumeration. Usually you will return a list of components that are copies of existing ones (first list) and new components (second list). For example, A DNA_construct makes a list of copies of its parts as the first output, and a list of RNA_constructs as the second output. An RNA_construct will make a list of copies of its parts as the first output, and a list of Protein components as its second output (if it makes any proteins)

classmethod from_promoter(name, assembly, transcript, protein)[source]

Helper function to initialize a promoter instance from another promoter or str.

Parameters:

  • name – either string or an other promoter instance

  • assembly

  • transcript

  • protein

Returns:

Promoter instance

get_mechanism(mechanism_type, optional_mechanism=False)[source]

Searches the Component for a Mechanism of the correct type.

If the Component does not have the mechanism, searches the Components’ Mixture for the Mechanism.

Parameters:

  • mechanism_type

  • optional_mechanism – toggles whether an error is thrown if no mechanism is found

Returns:

get_orphan()[source]

returns a copy of this monomer, except with no parent. But it still has a position and direction

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

Get a parameter from different objects that hold parameters.

Hierarchy:

  1. tries to find the Parameter in Component.parameter_database

  2. tries to find the parameter in Component.mixture.parameter_database

Parameters:

  • param_name

  • part_id

  • mechanism

  • return_numerical – numerical value or the parameter object is returned

  • return_none – returns None instead of throwing an error if a parameter isn’t found

  • check_mixture – toggle whether or not to check the Component’s Mixture as well

Returns:

Parameter object or a Real number

get_species()[source]

The subclasses should implement this method!

Returns:

None

set_mixture(mixture) → None[source]

Set the mixture the Component is in.

Parameters:

mixture

Returns:

None

classmethod set_species(species: Species | str, material_type=None, compartment=None, attributes=None) → Species[source]

Helper function that allows species to be set from strings, species, or Components

Parameters:

  • species – Species, str, Component

  • material_type

  • compartment

  • attributes

Returns:

Species

unclone()[source]

removes the current part from anything

update_component(internal_species=None, **keywords)[source]

returns a copy of this component, except with the proper fields updated

update_parameters(parameter_file=None, parameters=None, parameter_database=None, overwrite_parameters=True)[source]

Updates the ParameterDatabase inside a Component

Possible inputs:

parameter_file (string) parameters (dict) parameter_database (ParameterDatabase)

update_reactions()[source]

The subclasses should implement this method!

Returns:

empty list

update_species()[source]

The subclasses should implement this method!

Returns:

empty list

class biocrnpyler.components.dna.promoter.Promoter(name, assembly=None, transcript=None, length=0, mechanisms=None, parameters=None, protein=None, dna_to_bind=None, **keywords)[source]

A basic Promoter class with no regulation. Needs to be included in a DNAassembly or DNAconstruct to function.

this represents a modular component sequence. These get compiled into working components

add_mechanism(mechanism: Mechanism, mech_type=None, overwrite=False, optional_mechanism=False)[source]

adds a mechanism of type mech_type to the Component Mechanism dictionary.

Parameters:

  • mechanism

  • mech_type

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

add_mechanisms(mechanisms: Mechanism | GlobalMechanism, overwrite=False, optional_mechanism=False)[source]

This function adds a list or dictionary of mechanisms to the mixture.

Parameters:

  • mechanisms – Can take both GlobalMechanisms and Mechanisms

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

clone(position, direction, parent_dna)[source]

this defines where the part is in what piece of DNA

property compartment

The compartment of the Component.

Returns:

Compartment

enumerate_components(**keywords) → List[source]

this is for component enumeration. Usually you will return a list of components that are copies of existing ones (first list) and new components (second list). For example, A DNA_construct makes a list of copies of its parts as the first output, and a list of RNA_constructs as the second output. An RNA_construct will make a list of copies of its parts as the first output, and a list of Protein components as its second output (if it makes any proteins)

classmethod from_promoter(name, assembly, transcript, protein)[source]

Helper function to initialize a promoter instance from another promoter or str.

Parameters:

  • name – either string or an other promoter instance

  • assembly

  • transcript

  • protein

Returns:

Promoter instance

get_mechanism(mechanism_type, optional_mechanism=False)[source]

Searches the Component for a Mechanism of the correct type.

If the Component does not have the mechanism, searches the Components’ Mixture for the Mechanism.

Parameters:

  • mechanism_type

  • optional_mechanism – toggles whether an error is thrown if no mechanism is found

Returns:

get_orphan()[source]

returns a copy of this monomer, except with no parent. But it still has a position and direction

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

Get a parameter from different objects that hold parameters.

Hierarchy:

  1. tries to find the Parameter in Component.parameter_database

  2. tries to find the parameter in Component.mixture.parameter_database

Parameters:

  • param_name

  • part_id

  • mechanism

  • return_numerical – numerical value or the parameter object is returned

  • return_none – returns None instead of throwing an error if a parameter isn’t found

  • check_mixture – toggle whether or not to check the Component’s Mixture as well

Returns:

Parameter object or a Real number

get_species()[source]

The subclasses should implement this method!

Returns:

None

set_mixture(mixture) → None[source]

Set the mixture the Component is in.

Parameters:

mixture

Returns:

None

classmethod set_species(species: Species | str, material_type=None, compartment=None, attributes=None) → Species[source]

Helper function that allows species to be set from strings, species, or Components

Parameters:

  • species – Species, str, Component

  • material_type

  • compartment

  • attributes

Returns:

Species

unclone()[source]

removes the current part from anything

update_component(internal_species=None, **keywords)[source]

returns a copy of this component, except with the proper fields updated

update_parameters(parameter_file=None, parameters=None, parameter_database=None, overwrite_parameters=True)[source]

Updates the ParameterDatabase inside a Component

Possible inputs:

parameter_file (string) parameters (dict) parameter_database (ParameterDatabase)

update_reactions()[source]

The subclasses should implement this method!

Returns:

empty list

update_species()[source]

The subclasses should implement this method!

Returns:

empty list

class biocrnpyler.components.dna.promoter.RegulatedPromoter(name: str, regulators, leak=True, assembly=None, transcript=None, length=0, mechanisms=None, parameters=None, **keywords)[source]

A Promoter class with simple regulation. regulators = [list of species] Each regulator binds independently to the Promoter to regulate it.

this represents a modular component sequence. These get compiled into working components

add_mechanism(mechanism: Mechanism, mech_type=None, overwrite=False, optional_mechanism=False)[source]

adds a mechanism of type mech_type to the Component Mechanism dictionary.

Parameters:

  • mechanism

  • mech_type

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

add_mechanisms(mechanisms: Mechanism | GlobalMechanism, overwrite=False, optional_mechanism=False)[source]

This function adds a list or dictionary of mechanisms to the mixture.

Parameters:

  • mechanisms – Can take both GlobalMechanisms and Mechanisms

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

clone(position, direction, parent_dna)[source]

this defines where the part is in what piece of DNA

property compartment

The compartment of the Component.

Returns:

Compartment

enumerate_components(**keywords) → List[source]

this is for component enumeration. Usually you will return a list of components that are copies of existing ones (first list) and new components (second list). For example, A DNA_construct makes a list of copies of its parts as the first output, and a list of RNA_constructs as the second output. An RNA_construct will make a list of copies of its parts as the first output, and a list of Protein components as its second output (if it makes any proteins)

classmethod from_promoter(name, assembly, transcript, protein)[source]

Helper function to initialize a promoter instance from another promoter or str.

Parameters:

  • name – either string or an other promoter instance

  • assembly

  • transcript

  • protein

Returns:

Promoter instance

get_mechanism(mechanism_type, optional_mechanism=False)[source]

Searches the Component for a Mechanism of the correct type.

If the Component does not have the mechanism, searches the Components’ Mixture for the Mechanism.

Parameters:

  • mechanism_type

  • optional_mechanism – toggles whether an error is thrown if no mechanism is found

Returns:

get_orphan()[source]

returns a copy of this monomer, except with no parent. But it still has a position and direction

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

Get a parameter from different objects that hold parameters.

Hierarchy:

  1. tries to find the Parameter in Component.parameter_database

  2. tries to find the parameter in Component.mixture.parameter_database

Parameters:

  • param_name

  • part_id

  • mechanism

  • return_numerical – numerical value or the parameter object is returned

  • return_none – returns None instead of throwing an error if a parameter isn’t found

  • check_mixture – toggle whether or not to check the Component’s Mixture as well

Returns:

Parameter object or a Real number

get_species()[source]

The subclasses should implement this method!

Returns:

None

set_mixture(mixture) → None[source]

Set the mixture the Component is in.

Parameters:

mixture

Returns:

None

classmethod set_species(species: Species | str, material_type=None, compartment=None, attributes=None) → Species[source]

Helper function that allows species to be set from strings, species, or Components

Parameters:

  • species – Species, str, Component

  • material_type

  • compartment

  • attributes

Returns:

Species

unclone()[source]

removes the current part from anything

update_component(internal_species=None, **keywords)[source]

returns a copy of this component, except with the proper fields updated

update_parameters(parameter_file=None, parameters=None, parameter_database=None, overwrite_parameters=True)[source]

Updates the ParameterDatabase inside a Component

Possible inputs:

parameter_file (string) parameters (dict) parameter_database (ParameterDatabase)

update_reactions()[source]

The subclasses should implement this method!

Returns:

empty list

update_species()[source]

The subclasses should implement this method!

Returns:

empty list

class biocrnpyler.components.dna.promoter.RepressiblePromoter(name, repressor, transcript=None, leak=False, **keywords)[source]

A class for a promoter which can be repressed by a single species, modelled as a negative hill function

this represents a modular component sequence. These get compiled into working components

add_mechanism(mechanism: Mechanism, mech_type=None, overwrite=False, optional_mechanism=False)[source]

adds a mechanism of type mech_type to the Component Mechanism dictionary.

Parameters:

  • mechanism

  • mech_type

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

add_mechanisms(mechanisms: Mechanism | GlobalMechanism, overwrite=False, optional_mechanism=False)[source]

This function adds a list or dictionary of mechanisms to the mixture.

Parameters:

  • mechanisms – Can take both GlobalMechanisms and Mechanisms

  • overwrite – toggles whether the mechanism is added overwriting any mechanism with the same key.

  • optional_mechanism – toggles whether an error is thrown if a Mechanism is added that conflicts with an exising Mechanism

Returns:

clone(position, direction, parent_dna)[source]

this defines where the part is in what piece of DNA

property compartment

The compartment of the Component.

Returns:

Compartment

enumerate_components(**keywords) → List[source]

this is for component enumeration. Usually you will return a list of components that are copies of existing ones (first list) and new components (second list). For example, A DNA_construct makes a list of copies of its parts as the first output, and a list of RNA_constructs as the second output. An RNA_construct will make a list of copies of its parts as the first output, and a list of Protein components as its second output (if it makes any proteins)

classmethod from_promoter(name, assembly, transcript, protein)[source]

Helper function to initialize a promoter instance from another promoter or str.

Parameters:

  • name – either string or an other promoter instance

  • assembly

  • transcript

  • protein

Returns:

Promoter instance

get_mechanism(mechanism_type, optional_mechanism=False)[source]

Searches the Component for a Mechanism of the correct type.

If the Component does not have the mechanism, searches the Components’ Mixture for the Mechanism.

Parameters:

  • mechanism_type

  • optional_mechanism – toggles whether an error is thrown if no mechanism is found

Returns:

get_orphan()[source]

returns a copy of this monomer, except with no parent. But it still has a position and direction

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

Get a parameter from different objects that hold parameters.

Hierarchy:

  1. tries to find the Parameter in Component.parameter_database

  2. tries to find the parameter in Component.mixture.parameter_database

Parameters:

  • param_name

  • part_id

  • mechanism

  • return_numerical – numerical value or the parameter object is returned

  • return_none – returns None instead of throwing an error if a parameter isn’t found

  • check_mixture – toggle whether or not to check the Component’s Mixture as well

Returns:

Parameter object or a Real number

get_species()[source]

The subclasses should implement this method!

Returns:

None

set_mixture(mixture) → None[source]

Set the mixture the Component is in.

Parameters:

mixture

Returns:

None

classmethod set_species(species: Species | str, material_type=None, compartment=None, attributes=None) → Species[source]

Helper function that allows species to be set from strings, species, or Components

Parameters:

  • species – Species, str, Component

  • material_type

  • compartment

  • attributes

Returns:

Species

unclone()[source]

removes the current part from anything

update_component(internal_species=None, **keywords)[source]

returns a copy of this component, except with the proper fields updated

update_parameters(parameter_file=None, parameters=None, parameter_database=None, overwrite_parameters=True)[source]

Updates the ParameterDatabase inside a Component

Possible inputs:

parameter_file (string) parameters (dict) parameter_database (ParameterDatabase)

update_reactions(**keywords)[source]

The subclasses should implement this method!

Returns:

empty list

update_species(**keywords)[source]

The subclasses should implement this method!

Returns:

empty list