3.1.1.2.1.11. etfl.core.reactions

ME-related Reaction subclasses and methods definition

3.1.1.2.1.11.1. Module Contents

3.1.1.2.1.11.1.1. Classes

ExpressionReaction

EnzymaticReaction

Subclass to describe reactions that are catalyzed by an enzyme.

TranscriptionReaction

Class describing transcription - Assembly of amino acids into peptides

TranslationReaction

Class describing translation - Assembly of amino acids into peptides

ProteinComplexation

Describes the assembly of peptides into an enzyme

DegradationReaction

Describes the degradation of macromolecules

DNAFormation

Describes the assembly of NTPs into DNA
class ETFL.ExpressionReaction(scaled, **kwargs)

Bases: cobra.Reaction

classmethod from_reaction(cls, reaction, scaled=False, **kwargs)

This method clones a cobra.Reaction object into a expression-related type of reaction

Parameters

reaction – the reaction to reproduce

Returns

an EnzymaticReaction object

add_metabolites(self, metabolites, rescale=True, **kwargs)

We need to override this method if the reaction is scaled

v_hat = v/vmax

dM/dt = n1*v1 + …

dM/dt = n1*vmax1 * v1_hat + …

Parameters

metabolites –

Returns

property scaling_factor(self)
property net(self)
property scaled_net(self)
class ETFL.EnzymaticReaction(enzymes=None, scaled=False, *args, **kwargs)

Bases: ExpressionReaction

Subclass to describe reactions that are catalyzed by an enzyme.

add_enzymes(self, enzymes)

` Method to add the enzymes to the reaction. :param enzymes: iterable of or single Enzyme object :return:

property scaling_factor(self)
class ETFL.TranscriptionReaction(id, name, gene_id, enzymes, **kwargs)

Bases: EnzymaticReaction

Class describing transcription - Assembly of amino acids into peptides

property gene(self)
property nucleotide_length(self)
add_rnap(self, rnap)

By definition this reaction will be catalyzed by RNA polymerase :param ribosome: :type ribosome: pytfa.me.RNAPolymerase :return:

property scaling_factor(self)
class ETFL.TranslationReaction(id, name, gene_id, enzymes, trna_stoich=None, **kwargs)

Bases: EnzymaticReaction

Class describing translation - Assembly of amino acids into peptides

property gene(self)
property aminoacid_length(self)
add_peptide(self, peptide)

According to the scaling rules, the coefficient of the scaled translation reaction for the peptide balance is 1:

dPep/dt = v_tsl - sum(ηj * vj_asm) = 0

v_tsl_hat - sum(ηj * L_aa/(krib * R_max) * kdegj * Ej_max * vj_asm_max)

Parameters

peptide –

Returns

add_ribosome(self, ribosome)

By definition this reaction will be catalyzed by a ribosome :param ribosome: :type ribosome: pytfa.me.Ribosome :return:

property scaling_factor(self)
class ETFL.ProteinComplexation(target, *args, **kwargs)

Bases: ExpressionReaction

Describes the assembly of peptides into an enzyme

property scaling_factor(self)
add_peptides(self, peptides)

/!Reaction must belong to a model

According to the scaling rules, the coefficient of the scaled complexation reaction for the peptide balance is L_aa/(krib * R_max):

dPep/dt = v_tsl - sum(ηj * vj_asm) = 0

v_tsl_hat - sum(ηj * L_aa/(krib * R_max) * kdegj * Ej_max * vj_asm_max)

Parameters

peptides – dict(Peptide: int)

Returns

class ETFL.DegradationReaction(macromolecule, *args, **kwargs)

Bases: ExpressionReaction

Describes the degradation of macromolecules

property scaling_factor(self)
class ETFL.DNAFormation(dna, mu_sigma=1, *args, **kwargs)

Bases: ExpressionReaction

Describes the assembly of NTPs into DNA

property scaling_factor(self)