biocrnpyler.mechanisms.enzyme

Classes

BasicCatalysis([name, mechanism_type])	Mechanism for the schema S + C --> P + C.
BasicProduction([name, mechanism_type])	Mechanism for the schema C --> P + C.
MichaelisMenten([name, mechanism_type])	Mechanism to automatically generate Michaelis-Menten Type Reactions.
MichaelisMentenCopy([name, mechanism_type])	In the Copy RXN version, the Substrate is not Consumed.
MichaelisMentenReversible([name, mechanism_type])	Mechanism to automatically generate Michaelis-Menten Type Reactions with products that can bind to enzymes.

class biocrnpyler.mechanisms.enzyme.BasicCatalysis(name: str = 'basic_catalysis', mechanism_type: str = 'catalysis', **keywords)

Mechanism for the schema S + C –> P + C.

Initializes a BasicCatalysis instance.

Parameters:

• name – name of the Mechanism, default: basic_catalysis

• mechanism_type – type of the Mechanism, default: catalysis

• keywords

update_reactions(Enzyme, Sub, Prod, component=None, part_id=None, kcat=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(Enzyme, Sub, Prod=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.enzyme.BasicProduction(name='basic_production', mechanism_type='catalysis', **keywords)

Mechanism for the schema C –> P + C.

Initializes a BasicProduction instance.

Parameters:

• name – name of the Mechanism, default: basic_production

• mechanism_type – type of the Mechanism, default: catalysis

• keywords

update_reactions(Enzyme, Sub, Prod, component=None, part_id=None, kcat=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(Enzyme, Sub=None, Prod=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.enzyme.MichaelisMenten(name='michalis_menten', mechanism_type='catalysis', **keywords)

Mechanism to automatically generate Michaelis-Menten Type Reactions.

In the Copy RXN version, the Substrate is not Consumed Sub+Enz <–> Sub:Enz –> Enz+Prod

Initializes a MichaelisMenten instance.

Parameters:

• name – name of the Mechanism, default: michalis_menten

• mechanism_type – type of the Mechanism, default: catalysis

• keywords

update_reactions(Enzyme, Sub, Prod, component=None, part_id=None, complex=None, kb=None, ku=None, kcat=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(Enzyme, Sub, Prod=None, complex=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.enzyme.MichaelisMentenCopy(name='michalis_menten_copy', mechanism_type='copy', **keywords)

In the Copy RXN version, the Substrate is not Consumed.

Sub+Enz <–> Sub:Enz –> Sub+Enz+Prod

Initializes a MichaelisMentenCopy instance.

Parameters:

• name – name of the Mechanism, default: michalis_menten_copy

• mechanism_type – type of the Mechanism, default: copy

• keywords

update_reactions(Enzyme, Sub, Prod, component=None, part_id=None, complex=None, kb=None, ku=None, kcat=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(Enzyme, Sub, complex=None, Prod=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.enzyme.MichaelisMentenReversible(name='michalis_menten_reverse_binding', mechanism_type='catalysis', **keywords)

Mechanism to automatically generate Michaelis-Menten Type Reactions with products that can bind to enzymes.

In the Copy RXN version, the Substrate is not Consumed Sub+Enz <–> Sub:Enz <–> Enz:Prod <–> Enz + Prod

Initializes a MichaelisMentenReversible instance.

Parameters:

• name – name of the Mechanism, default: michalis_menten_reverse_binding

• mechanism_type – type of the Mechanism, default: catalysis

• keywords

update_reactions(Enzyme, Sub, Prod, component=None, part_id=None, complex=None, complex2=None, kb=None, ku=None, kcat=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(Enzyme, Sub, Prod, complex=None, complex2=None, **keywords)

the child class should implement this method.

Returns:

empty list