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enzax.rate_equations

Drain

A drain reaction.

Source code in enzax/rate_equations/drain.py 
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class Drain(RateEquation):
    """A drain reaction."""

    sign: float

    def get_input(
        self,
        parameters: PyTree,
        reaction_id: str,
        reaction_stoichiometry: NDArray[np.float64],
        species_to_dgf_ix: NDArray[np.int16],
    ):
        return DrainInput(abs_v=jnp.exp(parameters["log_drain"][reaction_id]))

    def __call__(self, conc: ConcArray, drain_input: PyTree) -> Scalar:
        """Get the flux of a drain reaction."""
        return self.sign * drain_input.abs_v

__call__(conc, drain_input)

Get the flux of a drain reaction.

Source code in enzax/rate_equations/drain.py 
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def __call__(self, conc: ConcArray, drain_input: PyTree) -> Scalar:
    """Get the flux of a drain reaction."""
    return self.sign * drain_input.abs_v

IrreversibleMichaelisMenten

A reaction with irreversible Michaelis Menten kinetics.

Source code in enzax/rate_equations/michaelis_menten.py 
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class IrreversibleMichaelisMenten(RateEquation):
    """A reaction with irreversible Michaelis Menten kinetics."""

    ix_ki_species: NDArray[np.int16] = eqx.field(
        default_factory=lambda: np.array([], dtype=np.int64)
    )

    def get_input(
        self,
        parameters: PyTree,
        reaction_id: str,
        reaction_stoichiometry: NDArray[np.float64],
        species_to_dgf_ix: NDArray[np.int16],
    ):
        return get_irreversible_michaelis_menten_input(
            parameters=parameters,
            reaction_id=reaction_id,
            reaction_stoichiometry=reaction_stoichiometry,
            species_to_dgf_ix=species_to_dgf_ix,
            ci_ix=self.ix_ki_species,
        )

    def __call__(
        self,
        conc: Float[Array, " n"],
        imm_input: IrreversibleMichaelisMentenInput,
    ) -> Scalar:
        """Get flux of a reaction with irreversible Michaelis Menten kinetics."""  # noqa: E501
        numerator = numerator_mm(
            substrate_conc=conc[imm_input.ix_substrate],
            substrate_kms=imm_input.substrate_kms,
        )
        fer = free_enzyme_ratio_imm(
            substrate_conc=conc[imm_input.ix_substrate],
            substrate_km=imm_input.substrate_kms,
            ki=imm_input.ki,
            inhibitor_conc=conc[imm_input.ix_ki_species],
            substrate_stoichiometry=imm_input.substrate_stoichiometry,
        )
        return imm_input.kcat * imm_input.enzyme * numerator * fer

__call__(conc, imm_input)

Get flux of a reaction with irreversible Michaelis Menten kinetics.

Source code in enzax/rate_equations/michaelis_menten.py 
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def __call__(
    self,
    conc: Float[Array, " n"],
    imm_input: IrreversibleMichaelisMentenInput,
) -> Scalar:
    """Get flux of a reaction with irreversible Michaelis Menten kinetics."""  # noqa: E501
    numerator = numerator_mm(
        substrate_conc=conc[imm_input.ix_substrate],
        substrate_kms=imm_input.substrate_kms,
    )
    fer = free_enzyme_ratio_imm(
        substrate_conc=conc[imm_input.ix_substrate],
        substrate_km=imm_input.substrate_kms,
        ki=imm_input.ki,
        inhibitor_conc=conc[imm_input.ix_ki_species],
        substrate_stoichiometry=imm_input.substrate_stoichiometry,
    )
    return imm_input.kcat * imm_input.enzyme * numerator * fer

ReversibleMichaelisMenten

A reaction with reversible Michaelis Menten kinetics.

Source code in enzax/rate_equations/michaelis_menten.py 
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class ReversibleMichaelisMenten(RateEquation):
    """A reaction with reversible Michaelis Menten kinetics."""

    ix_ki_species: NDArray[np.int16] = eqx.field(
        default_factory=lambda: np.array([], dtype=np.int16)
    )
    water_stoichiometry: float = eqx.field(default_factory=lambda: 0.0)

    def get_input(
        self,
        parameters: PyTree,
        reaction_id: str,
        reaction_stoichiometry: NDArray[np.float64],
        species_to_dgf_ix: NDArray[np.int16],
    ):
        return get_reversible_michaelis_menten_input(
            parameters=parameters,
            reaction_id=reaction_id,
            reaction_stoichiometry=reaction_stoichiometry,
            species_to_dgf_ix=species_to_dgf_ix,
            ci_ix=self.ix_ki_species,
            water_stoichiometry=self.water_stoichiometry,
        )

    def __call__(
        self,
        conc: Float[Array, " n"],
        rmm_input: ReversibleMichaelisMentenInput,
    ) -> Scalar:
        """Get flux of a reaction with reversible Michaelis Menten kinetics.

        :param conc: A 1D array of non-negative numbers representing concentrations of the species that the reaction produces and consumes.

        """  # noqa: E501
        rev = get_reversibility(
            reactant_conc=conc[rmm_input.ix_reactant],
            reactant_stoichiometry=rmm_input.reactant_stoichiometry,
            dgf=rmm_input.dgf,
            temperature=rmm_input.temperature,
            water_stoichiometry=rmm_input.water_stoichiometry,
        )
        numerator = numerator_mm(
            substrate_conc=conc[rmm_input.ix_substrate],
            substrate_kms=rmm_input.substrate_kms,
        )
        fer = free_enzyme_ratio_rmm(
            substrate_conc=conc[rmm_input.ix_substrate],
            product_conc=conc[rmm_input.ix_product],
            ix_ki_species=conc[rmm_input.ix_ki_species],
            substrate_kms=rmm_input.substrate_kms,
            product_kms=rmm_input.product_kms,
            substrate_stoichiometry=rmm_input.substrate_stoichiometry,
            product_stoichiometry=rmm_input.product_stoichiometry,
            ki=rmm_input.ki,
        )
        return rev * rmm_input.kcat * rmm_input.enzyme * numerator * fer

__call__(conc, rmm_input)

Get flux of a reaction with reversible Michaelis Menten kinetics.

Parameters:

Name Type Description Default
conc Float[Array, ' n']

A 1D array of non-negative numbers representing concentrations of the species that the reaction produces and consumes.

 required
Source code in enzax/rate_equations/michaelis_menten.py 
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def __call__(
    self,
    conc: Float[Array, " n"],
    rmm_input: ReversibleMichaelisMentenInput,
) -> Scalar:
    """Get flux of a reaction with reversible Michaelis Menten kinetics.

    :param conc: A 1D array of non-negative numbers representing concentrations of the species that the reaction produces and consumes.

    """  # noqa: E501
    rev = get_reversibility(
        reactant_conc=conc[rmm_input.ix_reactant],
        reactant_stoichiometry=rmm_input.reactant_stoichiometry,
        dgf=rmm_input.dgf,
        temperature=rmm_input.temperature,
        water_stoichiometry=rmm_input.water_stoichiometry,
    )
    numerator = numerator_mm(
        substrate_conc=conc[rmm_input.ix_substrate],
        substrate_kms=rmm_input.substrate_kms,
    )
    fer = free_enzyme_ratio_rmm(
        substrate_conc=conc[rmm_input.ix_substrate],
        product_conc=conc[rmm_input.ix_product],
        ix_ki_species=conc[rmm_input.ix_ki_species],
        substrate_kms=rmm_input.substrate_kms,
        product_kms=rmm_input.product_kms,
        substrate_stoichiometry=rmm_input.substrate_stoichiometry,
        product_stoichiometry=rmm_input.product_stoichiometry,
        ki=rmm_input.ki,
    )
    return rev * rmm_input.kcat * rmm_input.enzyme * numerator * fer

AllostericIrreversibleMichaelisMenten

A reaction with irreversible Michaelis Menten kinetics and allostery.

Source code in enzax/rate_equations/generalised_mwc.py 
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class AllostericIrreversibleMichaelisMenten(IrreversibleMichaelisMenten):
    """A reaction with irreversible Michaelis Menten kinetics and allostery."""

    ix_allosteric_inhibitors: NDArray[np.int16] = eqx.field(
        default_factory=lambda: np.array([], dtype=np.int16)
    )
    ix_allosteric_activators: NDArray[np.int16] = eqx.field(
        default_factory=lambda: np.array([], dtype=np.int16)
    )
    subunits: int = 1

    def get_input(
        self,
        parameters: PyTree,
        reaction_id: str,
        reaction_stoichiometry: NDArray[np.float64],
        species_to_dgf_ix: NDArray[np.int16],
    ):
        return get_allosteric_irreversible_michaelis_menten_input(
            parameters=parameters,
            reaction_id=reaction_id,
            reaction_stoichiometry=reaction_stoichiometry,
            species_to_dgf_ix=species_to_dgf_ix,
            ci_ix=self.ix_ki_species,
        )

    def __call__(
        self,
        conc: Float[Array, " n"],
        aimm_input: AllostericIrreversibleMichaelisMentenInput,
    ) -> Scalar:
        """The flux of an irreversible allosteric Michaelis Menten reaction."""
        fer = free_enzyme_ratio_imm(
            substrate_conc=conc[aimm_input.ix_substrate],
            substrate_km=aimm_input.substrate_kms,
            ki=aimm_input.ki,
            inhibitor_conc=conc[self.ix_ki_species],
            substrate_stoichiometry=aimm_input.substrate_stoichiometry,
        )
        allosteric_effect = generalised_mwc_effect(
            conc_inhibitor=conc[self.ix_allosteric_inhibitors],
            dc_inhibitor=aimm_input.dc_inhibitor,
            dc_activator=aimm_input.dc_activator,
            conc_activator=conc[self.ix_allosteric_activators],
            free_enzyme_ratio=fer,
            tc=aimm_input.tc,
            subunits=self.subunits,
        )
        non_allosteric_rate = super().__call__(conc, aimm_input)
        return non_allosteric_rate * allosteric_effect

__call__(conc, aimm_input)

The flux of an irreversible allosteric Michaelis Menten reaction.

Source code in enzax/rate_equations/generalised_mwc.py 
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def __call__(
    self,
    conc: Float[Array, " n"],
    aimm_input: AllostericIrreversibleMichaelisMentenInput,
) -> Scalar:
    """The flux of an irreversible allosteric Michaelis Menten reaction."""
    fer = free_enzyme_ratio_imm(
        substrate_conc=conc[aimm_input.ix_substrate],
        substrate_km=aimm_input.substrate_kms,
        ki=aimm_input.ki,
        inhibitor_conc=conc[self.ix_ki_species],
        substrate_stoichiometry=aimm_input.substrate_stoichiometry,
    )
    allosteric_effect = generalised_mwc_effect(
        conc_inhibitor=conc[self.ix_allosteric_inhibitors],
        dc_inhibitor=aimm_input.dc_inhibitor,
        dc_activator=aimm_input.dc_activator,
        conc_activator=conc[self.ix_allosteric_activators],
        free_enzyme_ratio=fer,
        tc=aimm_input.tc,
        subunits=self.subunits,
    )
    non_allosteric_rate = super().__call__(conc, aimm_input)
    return non_allosteric_rate * allosteric_effect

AllostericReversibleMichaelisMenten

A reaction with reversible Michaelis Menten kinetics and allostery.

Source code in enzax/rate_equations/generalised_mwc.py 
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class AllostericReversibleMichaelisMenten(ReversibleMichaelisMenten):
    """A reaction with reversible Michaelis Menten kinetics and allostery."""

    ix_allosteric_inhibitors: NDArray[np.int16] = eqx.field(
        default_factory=lambda: np.array([], dtype=np.int16)
    )
    ix_allosteric_activators: NDArray[np.int16] = eqx.field(
        default_factory=lambda: np.array([], dtype=np.int16)
    )
    subunits: int = 1

    def get_input(
        self,
        parameters: PyTree,
        reaction_id: str,
        reaction_stoichiometry: NDArray[np.float64],
        species_to_dgf_ix: NDArray[np.int16],
    ):
        return get_allosteric_reversible_michaelis_menten_input(
            parameters=parameters,
            reaction_id=reaction_id,
            reaction_stoichiometry=reaction_stoichiometry,
            species_to_dgf_ix=species_to_dgf_ix,
            ci_ix=self.ix_ki_species,
            water_stoichiometry=self.water_stoichiometry,
        )

    def __call__(
        self,
        conc: Float[Array, " n"],
        armm_input: AllostericReversibleMichaelisMentenInput,
    ) -> Scalar:
        """The flux of an irreversible allosteric Michaelis Menten reaction."""
        fer = free_enzyme_ratio_rmm(
            substrate_conc=conc[armm_input.ix_substrate],
            product_conc=conc[armm_input.ix_product],
            substrate_kms=armm_input.substrate_kms,
            product_kms=armm_input.product_kms,
            ix_ki_species=conc[self.ix_ki_species],
            ki=armm_input.ki,
            substrate_stoichiometry=armm_input.substrate_stoichiometry,
            product_stoichiometry=armm_input.product_stoichiometry,
        )
        allosteric_effect = generalised_mwc_effect(
            conc_inhibitor=conc[self.ix_allosteric_inhibitors],
            dc_inhibitor=armm_input.dc_inhibitor,
            dc_activator=armm_input.dc_activator,
            conc_activator=conc[self.ix_allosteric_activators],
            free_enzyme_ratio=fer,
            tc=armm_input.tc,
            subunits=self.subunits,
        )
        non_allosteric_rate = super().__call__(conc, armm_input)
        return non_allosteric_rate * allosteric_effect

__call__(conc, armm_input)

The flux of an irreversible allosteric Michaelis Menten reaction.

Source code in enzax/rate_equations/generalised_mwc.py 
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def __call__(
    self,
    conc: Float[Array, " n"],
    armm_input: AllostericReversibleMichaelisMentenInput,
) -> Scalar:
    """The flux of an irreversible allosteric Michaelis Menten reaction."""
    fer = free_enzyme_ratio_rmm(
        substrate_conc=conc[armm_input.ix_substrate],
        product_conc=conc[armm_input.ix_product],
        substrate_kms=armm_input.substrate_kms,
        product_kms=armm_input.product_kms,
        ix_ki_species=conc[self.ix_ki_species],
        ki=armm_input.ki,
        substrate_stoichiometry=armm_input.substrate_stoichiometry,
        product_stoichiometry=armm_input.product_stoichiometry,
    )
    allosteric_effect = generalised_mwc_effect(
        conc_inhibitor=conc[self.ix_allosteric_inhibitors],
        dc_inhibitor=armm_input.dc_inhibitor,
        dc_activator=armm_input.dc_activator,
        conc_activator=conc[self.ix_allosteric_activators],
        free_enzyme_ratio=fer,
        tc=armm_input.tc,
        subunits=self.subunits,
    )
    non_allosteric_rate = super().__call__(conc, armm_input)
    return non_allosteric_rate * allosteric_effect