biocrnpyler.mechanisms.transport

Classes

Facilitated_Transport_MM([name, mechanism_type])	A mechanism to model the transport of a substrate through a membrane carrier.
Membrane_Protein_Integration([name, ...])	A simple mehanism to integrate into the membrane protein in the membrane.
Primary_Active_Transport_MM([name, ...])	A mechanism to model the transport of a substrate through a membrane carrier.
Simple_Diffusion([name, mechanism_type])	A mechanism to model the diffusion of a substrate through a membrane channel.
Simple_Transport([name, mechanism_type])	A mechanism to model the transport of a substrate through a membrane channel.

class biocrnpyler.mechanisms.transport.Facilitated_Transport_MM(name='facilitated_membrane_protein_transport', mechanism_type='transport', **keywords)

A mechanism to model the transport of a substrate through a membrane carrier. Mechanism follows Michaelis-Menten Type Reactions with products that can bind to membrane carriers. Mechanism for the schema: Sub+MC <–> Sub:MC –> Prod:MC –> Prod + MC

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(membrane_carrier, substrate, product, complex_dict=None, component=None, part_id=None, **keywords)

This always requires the inputs component and part_id to find the relevant parameters

update_species(membrane_carrier, substrate, product, complex_dict=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.transport.Membrane_Protein_Integration(name='membrane_protein_integration', mechanism_type='membrane_insertion', **keywords)

A simple mehanism to integrate into the membrane protein in the membrane. Reaction schema for monomers: monomer -> intergral membrane protein Reaction schema for oligomer: monomer*[size] -> oligomer -> intergral membrane protein

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(integral_membrane_protein, product, complex=None, component=None, part_id=None, **keywords)

This always requires the inputs component and part_id to find the relevant parameters

update_species(integral_membrane_protein, product, complex=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.transport.Primary_Active_Transport_MM(name='active_membrane_protein_transport', mechanism_type='transport', **keywords)

A mechanism to model the transport of a substrate through a membrane carrier. Mechanism follows Michaelis-Menten Type Reactions with products that can bind to membrane carriers. Mechanism for the schema: Sub+MP <–> Sub:MP + E –> Sub:MP:E –> MP:Prod:E –> Prod + MP:W –> Prod + MP+ W

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(membrane_pump, substrate, product, energy, waste, complex_dict=None, component=None, part_id=None, **keywords)

This always requires the inputs component and part_id to find the relevant parameters

update_species(membrane_pump, substrate, product, energy, waste, complex_dict=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.transport.Simple_Diffusion(name='simple_diffusion', mechanism_type='diffusion', **keywords)

A mechanism to model the diffusion of a substrate through a membrane channel. Does not require energy and follows diffusion rules. Reaction schema: substrate <-> product

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(substrate, product, component=None, part_id=None, k_diff=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(substrate, product, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.transport.Simple_Transport(name='simple_membrane_protein_transport', mechanism_type='transport', **keywords)

A mechanism to model the transport of a substrate through a membrane channel. Does not require energy and has unidirectional transport, following diffusion rules. Reaction schema: membrane_channel + substrate <-> membrane_channel + product

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(membrane_channel, substrate, product, component=None, part_id=None, k_trnsp=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(membrane_channel, substrate, product, **keywords)

the child class should implement this method.

Returns:

empty list