5.1.1.1.3. etfba.core.reaction

Difine the Reaction class.

5.1.1.1.3.1. Attributes

DEFAULT_MW

DEFAULT_KCAT

DEFAULT_KM

DEFAULT_DGPM

5.1.1.1.3.2. Classes

ReactantDict

dict() -> new empty dictionary

Reaction

5.1.1.1.3.3. Module Contents

etfba.core.reaction.DEFAULT_MW = 40[source]
etfba.core.reaction.DEFAULT_KCAT = 200[source]
etfba.core.reaction.DEFAULT_KM = 0.2[source]
etfba.core.reaction.DEFAULT_DGPM = 0[source]
class etfba.core.reaction.ReactantDict(*args, **kwargs)[source]

Bases: etfba.io.results.PrettyDict

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

caller = None[source]
role = None[source]
__getitem__(key)[source]

x.__getitem__(y) <==> x[y]

class etfba.core.reaction.Reaction(rxnid, enzyme_name=None, category=None, *, forward_kcat=None, backward_kcat=None, molecular_weight=None, standard_gibbs_energy=None, standard_gibbs_energy_error=None, reversible=True, is_biomass_formation=False, is_exch_reaction=False, is_h_transport=False, is_h2o_transport=False)[source]
substrates[source]

Key is the metabolite ID, value is the Metabolite instances as substrates.

Type:

PrettyDict

products[source]

Key is the metabolite ID, value is the Metabolite instances as products.

Type:

PrettyDict

forward_kcat/fkcat

Catalytic rate constant in the forward direction.

Type:

float

backward_kcat/bkcat

Catalytic rate constant in the backward direction .

Type:

float

molecular_weight/mw

Molecular weight of the catalytic enzyme.

Type:

float

standard_gibbs_energy/dgpm

Standard Gibbs energy of the reaction.

Type:

float

standard_gibbs_energy_error/dgpm_error

Standard error of the standard reaction Gibbs energy.

Type:

float

reversible/rev

Reaction reversibility.

Type:

bool

is_biomass_formation[source]

Indicates if it’s the biomass formation reaction.

Type:

bool

is_exch_reaction[source]

Indicates if it’s an exchange reaction.

Type:

bool

is_h_transport[source]

Indicates if it’s a proton transport reaction.

Type:

bool

is_h2o_transport[source]

Indicates if it’s a water transport reaction.

Type:

bool

is_constrained_by_thermodynamics[source]

Indicates if it’s constrained by thermodynamics.

Type:

bool

rxnid[source]
enzyme[source]
category[source]
fkcat[source]
bkcat[source]
mw[source]
dgpm[source]
dgpm_error[source]
rev[source]
is_biomass_formation[source]
is_exch_reaction[source]
is_h_transport[source]
is_h2o_transport[source]
_substrates[source]
_products[source]
is_constrained_by_thermodynamics = False[source]
_add_reactants(coes, kms, label)[source]
add_substrates(coes, kms=None)[source]
Parameters:

  • coes (dict) – Dictionary mapping substrates to their corresponding stoichiometric coefficients (positive values). All substrates should have a provided stoichiometric coefficient.

  • kms (dict) – Dictionary mapping substrates to their corresponding Km values. Km values should only be provided as a subset of substrates present in the ‘coes’ dictionary. An empty dict is acceptable if no Km values are available.

add_products(coes, kms=None)[source]
Parameters:

  • coes (dict) – Dictionary mapping products to their corresponding stoichiometric coefficients (positive values). All products should have a provided stoichiometric coefficient.

  • kms (dict) – Dictionary mapping products to their corresponding Km values. Km values should only be provided as a subset of products present in the ‘coes’ dictionary. An empty dict is acceptable if no Km values are available.

_remove_reactants(reactants, label)[source]
remove_substrates(substrates)[source]
Parameters:

substrates (list of Metabolite) – List of substrates to be removed from the current reaction.

remove_products(products)[source]
Parameters:

products (list of Metabolites) – List of products to be removed from current reaction.

property substrates[source]
property products[source]
property forward_kcat[source]
property backward_kcat[source]
property molecular_weight[source]
property standard_gibbs_energy[source]
property standard_gibbs_energy_error[source]
property reversible[source]
__repr__()[source]

Return repr(self).