Struct MetabolicPathway

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pub struct MetabolicPathway {
    pub name: String,
    pub enzymes: Vec<EnzymeDefinition>,
    pub metabolites: Vec<String>,
    pub stoichiometry_matrix: Array2<f64>,
    pub regulations: Vec<Regulation>,
    pub external_metabolites: HashMap<usize, f64>,
}

Expand description

Metabolic pathway definition

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§name: String

Pathway name

§enzymes: Vec<EnzymeDefinition>

Enzyme definitions

§metabolites: Vec<String>

Metabolite names

§stoichiometry_matrix: Array2<f64>

Stoichiometric matrix (reactions × metabolites)

§regulations: Vec<Regulation>

Regulatory relationships

§external_metabolites: HashMap<usize, f64>

External metabolite concentrations (fixed)

Implementations§

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impl MetabolicPathway

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pub fn new(_name: String, num_metabolites: usize, numenzymes: usize) -> Self

Create a new empty metabolic pathway

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pub fn add_enzyme(&mut self, enzyme: EnzymeDefinition)

Add an enzyme to the pathway

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pub fn add_regulation(&mut self, regulation: Regulation)

Add a regulatory relationship

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pub fn set_external_metabolite( &mut self, _metaboliteidx: usize, concentration: f64, )

Set external metabolite concentration

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pub fn calculate_reaction_rates( &self, concentrations: &Array1<f64>, ) -> Array1<f64>

Calculate reaction rates for all enzymes

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pub fn calculate_derivatives(&self, concentrations: &Array1<f64>) -> Array1<f64>

Calculate concentration time derivatives

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pub fn control_analysis( &self, _steady_stateconcentrations: &Array1<f64>, ) -> PathwayAnalysis

Perform metabolic control analysis

Trait Implementations§

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impl Clone for MetabolicPathway

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fn clone(&self) -> MetabolicPathway

Returns a duplicate of the value. Read more

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fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source. Read more

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impl Debug for MetabolicPathway

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fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter. Read more

Auto Trait Implementations§

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impl UnwindSafe for MetabolicPathway

Blanket Implementations§

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impl<T> Any for T
where T: 'static + ?Sized,

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

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impl<T> Borrow<T> for T
where T: ?Sized,

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fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

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impl<T> BorrowMut<T> for T
where T: ?Sized,

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fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

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impl<T> CloneToUninit for T
where T: Clone,

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unsafe fn clone_to_uninit(&self, dest: *mut u8)

🔬This is a nightly-only experimental API. (clone_to_uninit)

Performs copy-assignment from self to dest. Read more

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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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impl<T, U> Into for T
where U: From<T>,

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fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

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impl<T> IntoEither for T

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fn into_either(self, into_left: bool) -> Either<Self, Self>

Converts self into a Left variant of Either<Self, Self> if into_left is true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

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fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
where F: FnOnce(&Self) -> bool,

Converts self into a Left variant of Either<Self, Self> if into_left(&self) returns true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

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