3.1.1.7.1.4. etfl.optim.variables

Variables declarations

3.1.1.7.1.4.1. Module Contents

3.1.1.7.1.4.1.1. Classes

GrowthRate	Class to represent a growth rate
GrowthActivation	Class to represent a binary growth rate range activation in ME2 MILP
EnzymeVariable	Class to represent a enzyme variable
mRNAVariable	Class to represent a mRNA concentration
rRNAVariable	Class to represent a mRNA concentration
tRNAVariable	Class to represent a tRNA concentration
ForwardEnzyme	Represents assignment of an enzyme the a forward reaction flux
BackwardEnzyme	Represents assignment of an enzyme the a backward reaction flux
LinearizationVariable	Class to represent the product mu*[E] when performin linearization of the
DNAVariable	Class to represent DNA in the model
RibosomeUsage	Class to represent the ribosomes that are assigned to producing the enzyme
RNAPUsage	Class to represent the ribosomes that are assigned to producing the enzyme
FreeEnzyme	Class to represent the ribosomes that are affected to producing the enzyme
CatalyticActivator	Class to represent a binary variable that activates a catalytic constraint
BinaryActivator	Class to represent a binary variable that activates with growth levels
InterpolationVariable	Represents a variable that is interpolated
EnzymeRef	Represents a reference enzyme concentration - for example in dETFL
mRNARef	Represents a reference enzyme concentration - for example in dETFL
LipidVariable	Class to represent lipid in the model
CarbohydrateVariable	Class to represent carbohydrate in the model
IonVariable	Class to represent ion in the model

class ETFL.GrowthRate(model, **kwargs)

Bases: pytfa.optim.variables.ModelVariable

Class to represent a growth rate

prefix = MU_

class ETFL.GrowthActivation(model, id_, **kwargs)

Bases: pytfa.optim.variables.ModelVariable, pytfa.optim.variables.BinaryVariable

Class to represent a binary growth rate range activation in ME2 MILP

prefix = GA_

class ETFL.EnzymeVariable(enzyme, **kwargs)

Bases: pytfa.optim.variables.GenericVariable

Class to represent a enzyme variable

prefix = EZ_

property enzyme(self)

property id(self)

property model(self)

class ETFL.mRNAVariable

Bases: pytfa.optim.variables.GeneVariable

Class to represent a mRNA concentration

prefix = MR_

class ETFL.rRNAVariable

Bases: pytfa.optim.variables.GeneVariable

Class to represent a mRNA concentration

prefix = RR_

class ETFL.tRNAVariable

Bases: pytfa.optim.variables.ModelVariable

Class to represent a tRNA concentration

prefix = TR_

class ETFL.ForwardEnzyme(enzyme, **kwargs)

Bases: EnzymeVariable

Represents assignment of an enzyme the a forward reaction flux

prefix = FE_

class ETFL.BackwardEnzyme(enzyme, **kwargs)

Bases: EnzymeVariable

Represents assignment of an enzyme the a backward reaction flux

prefix = BE_

class ETFL.LinearizationVariable

Bases: pytfa.optim.variables.ModelVariable

Class to represent the product mu*[E] when performin linearization of the model

prefix = LZ_

class ETFL.DNAVariable

Bases: pytfa.optim.variables.ModelVariable

Class to represent DNA in the model

prefix = DN_

class ETFL.RibosomeUsage

Bases: pytfa.optim.variables.GeneVariable

Class to represent the ribosomes that are assigned to producing the enzyme for a reaction

prefix = RP_

class ETFL.RNAPUsage

Bases: pytfa.optim.variables.GeneVariable

Class to represent the ribosomes that are assigned to producing the enzyme for a reaction

prefix = RM_

class ETFL.FreeEnzyme(enzyme, **kwargs)

Bases: EnzymeVariable

Class to represent the ribosomes that are affected to producing the enzyme for a reaction

prefix = EF_

class ETFL.CatalyticActivator(reaction, **kwargs)

Bases: pytfa.optim.variables.ReactionVariable, pytfa.optim.variables.BinaryVariable

Class to represent a binary variable that activates a catalytic constraint or relaxes it

prefix = CA_

class ETFL.BinaryActivator(model, id_, **kwargs)

Bases: pytfa.optim.variables.ModelVariable, pytfa.optim.variables.BinaryVariable

Class to represent a binary variable that activates with growth levels

prefix = LA_

class ETFL.InterpolationVariable

Bases: pytfa.optim.variables.ModelVariable

Represents a variable that is interpolated

prefix = IV_

class ETFL.EnzymeRef(enzyme, **kwargs)

Bases: EnzymeVariable

Represents a reference enzyme concentration - for example in dETFL

prefix = EZ0_

class ETFL.mRNARef

Bases: mRNAVariable

Represents a reference enzyme concentration - for example in dETFL

prefix = MR0_

class ETFL.LipidVariable

Bases: pytfa.optim.variables.ModelVariable

Class to represent lipid in the model

prefix = LIP_

class ETFL.CarbohydrateVariable

Bases: pytfa.optim.variables.ModelVariable

Class to represent carbohydrate in the model

prefix = CAR_

class ETFL.IonVariable

Bases: pytfa.optim.variables.ModelVariable

Class to represent ion in the model

prefix = ION_