biocrnpyler.mixtures.cell

Classes

ExpressionDilutionMixture([name])

A Model for in-vivo Gene Expression without any Machinery (eg Ribosomes, Polymerases, etc.).

SimpleTxTlDilutionMixture([name])

Mixture with continuous dilution for non-DNA species.

TxTlDilutionMixture([name, rnap, ribosome, ...])

A Model for Transcription and Translation with Ribosomes, Polymerases, and Endonucleases labelled as Machinery.
class biocrnpyler.mixtures.cell.ExpressionDilutionMixture(name='', **kwargs)[source]

A Model for in-vivo Gene Expression without any Machinery (eg Ribosomes, Polymerases, etc.).

Here transcription and Translation are lumped into one reaction: expression. A global mechanism is used to dilute all non-dna species

Initializes an ExpressionDilutionMixture instance.

Parameters:

  • name – name of the mixture

  • kwargs – keywords passed into the parent Class (Mixture)

add_component(component)[source]

this function adds a single component to the mixture.

add_components(components: List[Component] | Component)[source]

This function adds a list of components to the mixture.

add_global_mechanism(mechanism, mech_type=None, overwrite=False)[source]

adds a mechanism of type mech_type to the Mixture global_mechanism dictonary.

keywordS:

mechanism: a Mechanism instance mech_type: the type of mechanism. defaults to mechanism.mech_type if None overwrite: whether to overwrite existing mechanisms of the same type (default False)

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

adds a mechanism of type mech_type to the Mixture mechanism_dictionary.

Parameters:

  • mechanism – a Mechanism instance

  • mech_type – the type of mechanism. defaults to mechanism.mech_type if None

  • overwrite – whether to overwrite existing mechanisms of the same type (default False)

Returns:

add_mechanisms(mechanisms, overwrite=False)[source]

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

Can take both GlobalMechanisms and Mechanisms

Parameters:

  • mechanisms – a Mechanism instance

  • overwrite – whether to overwrite existing mechanisms of the same type (default False)

Returns:

compile_crn(**keywords) → ChemicalReactionNetwork[source]

Overwriting compile_crn to replace transcripts with proteins for all DNA_assemblies.

Overwriting compile_crn to turn off transcription in all DNAassemblies

Returns:

compiled CRN instance

get_component(component=None, name=None, index=None)[source]

Function to get components from Mixture._components.

One of the 3 keywords must not be None.

Parameters:

  • component – an instance of a component. Searches Mixture._components for a Component with the same type and name.

  • name – str. Searches Mixture._components for a Component with the same name

  • index – int. returns Mixture._components[index]

Returns:

if nothing is found, returns None.

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

Tries to find an initial condition of species s using the parameter hierarchy using the key:

  1. Searches Component’s ParameterDatabase using the key:

    mechanisms = “initial concentration” part_id = mixture.name parameter_name = str(s)

    if s == component.get_species, also checks with parameter_name=component.name

  2. Searches the Mixture’s ParameterDatabase using the key:

    mechanisms = “initial concentration” part_id = mixture.name parameter_name = str(s)

    if s == component.get_species, also checks with parameter_name=component.name

  3. Defaults to 0

get_mechanism(mechanism_type)[source]

Searches the Mixture for a Mechanism of the correct type.

If no Mechanism is found, None is returned.

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

components that produce other components infinitely

property global_mechanisms

global_mechanisms stores global Mechanisms in the Mixture.

property mechanisms

mechanisms stores Mixture Mechanisms.

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

Used to set internal species from strings, Species or Components

Parameters:

  • species – name of a species or a species instance

  • material_type – material type of a species as a string

  • attributes – Species attribute

Returns:

Species in the mixture

class biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture(name='', **keywords)[source]

Mixture with continuous dilution for non-DNA species.

Transcription and Translation are both modeled as catalytic with no cellular machinery. mRNA is also degraded via a separate reaction to represent endonucleases

Initializes a SimpleTxTlDilutionMixture instance.

Parameters:

  • name – name of the mixture

  • kwargs – keywords passed into the parent Class (Mixture)

add_component(component)[source]

this function adds a single component to the mixture.

add_components(components: List[Component] | Component)[source]

This function adds a list of components to the mixture.

add_global_mechanism(mechanism, mech_type=None, overwrite=False)[source]

adds a mechanism of type mech_type to the Mixture global_mechanism dictonary.

keywordS:

mechanism: a Mechanism instance mech_type: the type of mechanism. defaults to mechanism.mech_type if None overwrite: whether to overwrite existing mechanisms of the same type (default False)

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

adds a mechanism of type mech_type to the Mixture mechanism_dictionary.

Parameters:

  • mechanism – a Mechanism instance

  • mech_type – the type of mechanism. defaults to mechanism.mech_type if None

  • overwrite – whether to overwrite existing mechanisms of the same type (default False)

Returns:

add_mechanisms(mechanisms, overwrite=False)[source]

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

Can take both GlobalMechanisms and Mechanisms

Parameters:

  • mechanisms – a Mechanism instance

  • overwrite – whether to overwrite existing mechanisms of the same type (default False)

Returns:

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[source]

Creates a chemical reaction network from the species and reactions associated with a mixture object (with compartment). :param initial_concentration_dict: a dictionary to overwrite initial

concentrations at the end of compile time

Parameters:

  • recursion_depth – how deep to run the Local and Global Component Enumeration

  • return_enumerated_components – returns a list of all enumerated components along with the CRN

  • initial_concentrations_at_end – if True does not look in Components for Species’ initial concentrations and only checks the Mixture database at the end.

  • copy_objects – Species and Reactions will be copied when placed into the CRN. Protects CRN validity at the expense of compilation speed.

  • add_reaction_species – Species inside reactions will be added to the CRN. Ensures no missing species at the expense of compilation speed.

Returns:

ChemicalReactionNetwork

get_component(component=None, name=None, index=None)[source]

Function to get components from Mixture._components.

One of the 3 keywords must not be None.

Parameters:

  • component – an instance of a component. Searches Mixture._components for a Component with the same type and name.

  • name – str. Searches Mixture._components for a Component with the same name

  • index – int. returns Mixture._components[index]

Returns:

if nothing is found, returns None.

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

Tries to find an initial condition of species s using the parameter hierarchy using the key:

  1. Searches Component’s ParameterDatabase using the key:

    mechanisms = “initial concentration” part_id = mixture.name parameter_name = str(s)

    if s == component.get_species, also checks with parameter_name=component.name

  2. Searches the Mixture’s ParameterDatabase using the key:

    mechanisms = “initial concentration” part_id = mixture.name parameter_name = str(s)

    if s == component.get_species, also checks with parameter_name=component.name

  3. Defaults to 0

get_mechanism(mechanism_type)[source]

Searches the Mixture for a Mechanism of the correct type.

If no Mechanism is found, None is returned.

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

components that produce other components infinitely

property global_mechanisms

global_mechanisms stores global Mechanisms in the Mixture.

property mechanisms

mechanisms stores Mixture Mechanisms.

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

Used to set internal species from strings, Species or Components

Parameters:

  • species – name of a species or a species instance

  • material_type – material type of a species as a string

  • attributes – Species attribute

Returns:

Species in the mixture

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

A Model for Transcription and Translation with Ribosomes, Polymerases, and Endonucleases labelled as Machinery.

This model includes a background load “cellular processes” which represents innate loading effects in the cell. Effects of loading on cell growth are not modelled. Unlike TxTlExtract, has global dilution for non-DNA and non-Machinery This model does not include any energy

Initializes a TxTlDilutionMixture instance.

Parameters:

  • name – name of the mixture

  • rnap – name of the RNA polymerase, default: RNAP

  • ribosome – name of the ribosome, default: Ribo

  • rnaase – name of the Ribonuclease, default: RNAase

  • kwargs – keywords passed into the parent Class (Mixture)

add_component(component)[source]

this function adds a single component to the mixture.

add_components(components: List[Component] | Component)[source]

This function adds a list of components to the mixture.

add_global_mechanism(mechanism, mech_type=None, overwrite=False)[source]

adds a mechanism of type mech_type to the Mixture global_mechanism dictonary.

keywordS:

mechanism: a Mechanism instance mech_type: the type of mechanism. defaults to mechanism.mech_type if None overwrite: whether to overwrite existing mechanisms of the same type (default False)

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

adds a mechanism of type mech_type to the Mixture mechanism_dictionary.

Parameters:

  • mechanism – a Mechanism instance

  • mech_type – the type of mechanism. defaults to mechanism.mech_type if None

  • overwrite – whether to overwrite existing mechanisms of the same type (default False)

Returns:

add_mechanisms(mechanisms, overwrite=False)[source]

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

Can take both GlobalMechanisms and Mechanisms

Parameters:

  • mechanisms – a Mechanism instance

  • overwrite – whether to overwrite existing mechanisms of the same type (default False)

Returns:

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[source]

Creates a chemical reaction network from the species and reactions associated with a mixture object (with compartment). :param initial_concentration_dict: a dictionary to overwrite initial

concentrations at the end of compile time

Parameters:

  • recursion_depth – how deep to run the Local and Global Component Enumeration

  • return_enumerated_components – returns a list of all enumerated components along with the CRN

  • initial_concentrations_at_end – if True does not look in Components for Species’ initial concentrations and only checks the Mixture database at the end.

  • copy_objects – Species and Reactions will be copied when placed into the CRN. Protects CRN validity at the expense of compilation speed.

  • add_reaction_species – Species inside reactions will be added to the CRN. Ensures no missing species at the expense of compilation speed.

Returns:

ChemicalReactionNetwork

get_component(component=None, name=None, index=None)[source]

Function to get components from Mixture._components.

One of the 3 keywords must not be None.

Parameters:

  • component – an instance of a component. Searches Mixture._components for a Component with the same type and name.

  • name – str. Searches Mixture._components for a Component with the same name

  • index – int. returns Mixture._components[index]

Returns:

if nothing is found, returns None.

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

Tries to find an initial condition of species s using the parameter hierarchy using the key:

  1. Searches Component’s ParameterDatabase using the key:

    mechanisms = “initial concentration” part_id = mixture.name parameter_name = str(s)

    if s == component.get_species, also checks with parameter_name=component.name

  2. Searches the Mixture’s ParameterDatabase using the key:

    mechanisms = “initial concentration” part_id = mixture.name parameter_name = str(s)

    if s == component.get_species, also checks with parameter_name=component.name

  3. Defaults to 0

get_mechanism(mechanism_type)[source]

Searches the Mixture for a Mechanism of the correct type.

If no Mechanism is found, None is returned.

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

components that produce other components infinitely

property global_mechanisms

global_mechanisms stores global Mechanisms in the Mixture.

property mechanisms

mechanisms stores Mixture Mechanisms.

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

Used to set internal species from strings, Species or Components

Parameters:

  • species – name of a species or a species instance

  • material_type – material type of a species as a string

  • attributes – Species attribute

Returns:

Species in the mixture