3.1.1.7.1.2. `etfl.optim.constraints`¶

Constraints declarations

3.1.1.7.1.2.1. Module Contents¶

3.1.1.7.1.2.1.1. Classes¶

`CatalyticConstraint`	Class to represent a enzymatic constraint
`ForwardCatalyticConstraint`	Class to represent a enzymatic constraint
`BackwardCatalyticConstraint`	Class to represent a enzymatic constraint
`EnzymeConstraint`	Class to represent a variable attached to a enzyme
`EnzymeMassBalance`	Class to represent a enzymatic mass balance constraint
`mRNAMassBalance`	Class to represent a mRNA mass balance constraint
`rRNAMassBalance`	Class to represent a mRNA mass balance constraint
`tRNAMassBalance`	Class to represent a tRNA mass balance constraint
`DNAMassBalance`	Class to represent a DNA mass balance constraint
`SynthesisConstraint`	Class to represent a Translation constraint
`GrowthCoupling`	Class to represent a growth capacity constraint
`TotalCapacity`	Class to represent the total capacity of constraint of a species, e.g
`TotalEnzyme`	Class to represent the total amount of an enzyme species, forwards and backwards
`ExpressionCoupling`	Add the coupling between mRNA availability and ribosome charging
`MinimalCoupling`	Add the minimal activity of ribosome based on the availability of mRNA.
`RNAPAllocation`	Add the coupling between DNA availability and RNAP charging
`MinimalAllocation`	Add the minimal activity of RNAP based on the availability of gene.
`EnzymeRatio`	Represents the availability of free enzymes, e.g ribosomes (non bound)
`RibosomeRatio`	(Legacy) represents the availability of free ribosomes, e.g ribosomes (non bound)
`EnzymeDegradation`	v_deg = k_deg [E]
`mRNADegradation`	v_deg = k_deg [mRNA]
`GrowthChoice`	Class to represent a variable attached to a reaction
`LinearizationConstraint`	Class to represent a variable attached to a reaction
`SOS1Constraint`	Class to represent SOS 1 constraint
`InterpolationConstraint`	Class to represent an interpolation constraint
`EnzymeDeltaPos`	Represents a positive enzyme concentration variation for dETFL
`EnzymeDeltaNeg`	Represents a negative enzyme concentration variation for dETFL
`mRNADeltaPos`	Represents a positive mRNA concentration variation for dETFL
`mRNADeltaNeg`	Represents a negative mRNA concentration variation for dETFL
`ConstantAllocation`	Represents a similar share to FBA for RNA and protein
`LipidMassBalance`	Class to represent a lipid mass balance constraint
`CarbohydrateMassBalance`	Class to represent a carbohydrate mass balance constraint
`IonMassBalance`	Class to represent a ion mass balance constraint

class ETFL.CatalyticConstraint¶

Bases: pytfa.optim.ReactionConstraint

Class to represent a enzymatic constraint

prefix = CC_¶

class ETFL.ForwardCatalyticConstraint¶

Bases: pytfa.optim.ReactionConstraint

Class to represent a enzymatic constraint

prefix = FC_¶

class ETFL.BackwardCatalyticConstraint¶

Bases: pytfa.optim.ReactionConstraint

Class to represent a enzymatic constraint

prefix = BC_¶

class ETFL.EnzymeConstraint(enzyme, expr, **kwargs)¶

Bases: pytfa.optim.GenericConstraint

Class to represent a variable attached to a enzyme

prefix = EZ_¶

property enzyme(self)¶

property id(self)¶

property model(self)¶

class ETFL.EnzymeMassBalance(enzyme, expr, **kwargs)¶

Bases: EnzymeConstraint

Class to represent a enzymatic mass balance constraint

prefix = EB_¶

class ETFL.mRNAMassBalance¶

Bases: pytfa.optim.GeneConstraint

Class to represent a mRNA mass balance constraint

prefix = MB_¶

class ETFL.rRNAMassBalance¶

Bases: pytfa.optim.GeneConstraint

Class to represent a mRNA mass balance constraint

prefix = RB_¶

class ETFL.tRNAMassBalance¶

Bases: pytfa.optim.ModelConstraint

Class to represent a tRNA mass balance constraint

prefix = TB_¶

class ETFL.DNAMassBalance¶

Bases: pytfa.optim.ModelConstraint

Class to represent a DNA mass balance constraint

prefix = DB_¶

class ETFL.SynthesisConstraint¶

Bases: pytfa.optim.ReactionConstraint

Class to represent a Translation constraint

prefix = TR_¶

class ETFL.GrowthCoupling¶

Bases: pytfa.optim.ReactionConstraint

Class to represent a growth capacity constraint

prefix = GC_¶

class ETFL.TotalCapacity¶

Bases: pytfa.optim.ModelConstraint

Class to represent the total capacity of constraint of a species, e.g Ribosome or RNA

prefix = TC_¶

class ETFL.TotalEnzyme¶

Bases: TotalCapacity

Class to represent the total amount of an enzyme species, forwards and backwards

prefix = TE_¶

class ETFL.ExpressionCoupling¶

Bases: pytfa.optim.GeneConstraint

Add the coupling between mRNA availability and ribosome charging The number of ribosomes assigned to a mRNA species is lower than the number of such mRNA times the max number of ribosomes that can sit on the mRNA: [RPi] <= loadmax_i*[mRNAi]

prefix = EX_¶

class ETFL.MinimalCoupling¶

Bases: pytfa.optim.GeneConstraint

Add the minimal activity of ribosome based on the availability of mRNA. We modeled it as a fraction of the maximum loadmax and the fraction depends on the affinity of ribosome to the mRNA: [RPi] >= Fraction*loadmax_i*[mRNAi]

prefix = MC_¶

class ETFL.RNAPAllocation¶

Bases: pytfa.optim.GeneConstraint

Add the coupling between DNA availability and RNAP charging The number of RNAP assigned to a gene locus is lower than the number of such loci times the max number of RNAP that can sit on the locus: [RNAPi] <= loadmax_i*[# of loci]*[DNA]

prefix = RA_¶

class ETFL.MinimalAllocation¶

Bases: pytfa.optim.GeneConstraint

Add the minimal activity of RNAP based on the availability of gene. We modeled it as a fraction of the maximum loadmax and the fraction depends on the affinity of RNAP to the gene, i.e. the strength of the promoter: [RPi] >= Fraction*loadmax_i*[mRNAi]