biocrnpyler.mechanisms.binding

Classes

Combinatorial_Cooperative_Binding([name, ...])	a reaction where some number of binders bind combinatorially to a bindee
One_Step_Binding([name, mechanism_type])	A mechanism to model the binding of a list of species, eg S1 + S2 .
One_Step_Cooperative_Binding([name, ...])	A reaction where n binders (A) bind to 1 bindee (B) in one step n A + B <--> nA:B
Two_Step_Cooperative_Binding([name, ...])	A reaction where n binders (s1) bind to 1 bindee (s2) in two steps.

class biocrnpyler.mechanisms.binding.Combinatorial_Cooperative_Binding(name='Combinatorial_Cooperative_binding', mechanism_type='cooperative_binding')

a reaction where some number of binders bind combinatorially to a bindee

Initializes a Combinatorial_Cooperative_Binding instance

Parameters:

• name – name of the Mechanism, default: Combinatorial_Cooperative_binding

• mechanism_type – type of the Mechanism, default: cooperative_binding

make_cooperative_complex(combo, bindee, cooperativity)

given a list of binders and their cooperativities, make a complex that contains the binders present N number of times where N is each one’s cooperativity.

update_reactions(binders, bindee, component=None, kbs=None, kus=None, part_id=None, cooperativity=None, **kwords)

the child class should implement this method.

Returns:

empty list

update_species(binders, bindee, cooperativity=None, component=None, part_id=None, **kwords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.binding.One_Step_Binding(name='one_step_binding', mechanism_type='binding')

A mechanism to model the binding of a list of species, eg S1 + S2 … SN <–> S1:S2:…:SN

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(binder, bindee, component=None, complex_species=None, part_id=None, kb=None, ku=None, **keywords)

the child class should implement this method.

Returns:

empty list

update_species(binder, bindee, component=None, complex_species=None, part_id=None, **keywords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.binding.One_Step_Cooperative_Binding(name='one_step_cooperative_binding', mechanism_type='cooperative_binding')

A reaction where n binders (A) bind to 1 bindee (B) in one step n A + B <–> nA:B

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(binder, bindee, complex_species=None, component=None, kb=None, ku=None, part_id=None, cooperativity=None, **kwords)

the child class should implement this method.

Returns:

empty list

update_species(binder, bindee, complex_species=None, cooperativity=None, component=None, part_id=None, **kwords)

the child class should implement this method.

Returns:

empty list

class biocrnpyler.mechanisms.binding.Two_Step_Cooperative_Binding(name='two_step_cooperative_binding', mechanism_type='cooperative_binding')

A reaction where n binders (s1) bind to 1 bindee (s2) in two steps.

n A <–> nx_A nx_A <–> nx_A:B

Initializes a Mechanism instance.

Parameters:

• name – name of the Mechanism

• mechanism_type – mechanism_type in string

update_reactions(binder, bindee, kb=None, ku=None, component=None, part_id=None, cooperativity=None, complex_species=None, n_mer_species=None, **keywords)

Returns reactions: cooperativity binder <–> n_mer, kf = kb1, kr = ku1 n_mer + bindee <–> complex, kf = kb2, kr = ku2 :param s1: :param s2: :param kb: :param ku: :param cooperativity: :param keywords: :return:

update_species(binder, bindee, component=None, complex_species=None, n_mer_species=None, cooperativity=None, part_id=None, **keywords)

the child class should implement this method.

Returns:

empty list