Struct BacteriaReactions

pub struct BacteriaReactions {
    pub potential_strength: f64,
    pub food_to_volume_conversion: f64,
    pub lag_phase_active: bool,
    pub species: Species,
    pub cell_volume: f64,
    pub uptake_rate: f64,
    pub inhibition_production_rate: f64,
    pub inhibition_coefficient: f64,
}

Implementation of the [cellular_raza_concepts::CellularReactions] trait and cellular_raza_concepts::Interaction trait for Bacteria.

Fields

potential_strength: f64

Overall interaction strength for physical interaction

food_to_volume_conversion: f64

Conversion of the consumed food to cellular volume. In units $\frac{\text{volume}}{\text{food}}$.

lag_phase_active: bool

flag if the cell is still in lag phase

species: Species

Species of the cell. This determines if a cell will secrete inhibitor or be affected by it.

cell_volume: f64

Total current volume of the cell

uptake_rate: f64

Uptake rate of nutrients

inhibition_production_rate: f64

Production rate of inhibitor

inhibition_coefficient: f64

Inhibition rate of the growth of the cell

Implementations

impl BacteriaReactions

pub fn new( potential_strength: f64, food_to_volume_conversion: f64, lag_phase_active: bool, species: Species, cell_volume: f64, uptake_rate: f64, inhibition_production_rate: f64, inhibition_coefficient: f64, ) -> BacteriaReactions

Available on crate feature cpu_os_threads only.

Construct a new BacteriaReactions object

pub fn cell_radius(&self) -> f64

Available on crate feature cpu_os_threads only.

Obtain current cell radius

Trait Implementations

impl CellularReactions<f64, Matrix<f64, Const<cellular_raza_building_blocks::::cell_models::pool_bacteria::ReactionVector::{constant#0}>, Const<1>, ArrayStorage<f64, cellular_raza_building_blocks::::cell_models::pool_bacteria::ReactionVector::{constant#0}, 1>>> for BacteriaReactions

fn calculate_intra_and_extracellular_reaction_increment( &self, _internal_concentration_vector: &f64, external_concentration_vector: &Matrix<f64, Const<cellular_raza_building_blocks::::cell_models::pool_bacteria::ReactionVector::{constant#0}>, Const<1>, ArrayStorage<f64, cellular_raza_building_blocks::::cell_models::pool_bacteria::ReactionVector::{constant#0}, 1>>, ) -> Result<(f64, Matrix<f64, Const<cellular_raza_building_blocks::::cell_models::pool_bacteria::ReactionVector::{constant#0}>, Const<1>, ArrayStorage<f64, cellular_raza_building_blocks::::cell_models::pool_bacteria::ReactionVector::{constant#0}, 1>>), CalcError>

Calculate the time-related change of the intracellular and extracellular concentrations. This is not the increment itself (thus no parameter dt was specified) but rather the time-derivative. Such an approach can be useful when designing addaptive solvers.

fn get_intracellular(&self) -> f64

Retrieves the current intracellular concentration.

fn set_intracellular(&mut self, new_volume: f64)

Sets the intracellular concentration. This is used by the backend after values have been updated.

impl Clone for BacteriaReactions

fn clone(&self) -> BacteriaReactions

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for BacteriaReactions

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for BacteriaReactions

fn deserialize<__D>( __deserializer: __D, ) -> Result<BacteriaReactions, <__D as Deserializer<'de>>::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Interaction<Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, f64> for BacteriaReactions

fn get_interaction_information(&self) -> f64

Get additional information of cellular properties (ie. for cell-specific interactions). For now, this can also be used to get the mass of the other cell-agent. In the future, we will probably provide a custom function for this.

fn calculate_force_between( &self, own_pos: &Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, _own_vel: &Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, ext_pos: &Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, _ext_vel: &Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, ext_radius: &f64, ) -> Result<(Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>, Matrix<f64, Const<2>, Const<1>, ArrayStorage<f64, 2, 1>>), CalcError>

Calculates the forces (velocity-derivative) on the corresponding external position given external velocity. By providing velocities, we can calculate terms that are related to friction. The function returns two forces, one acting on the current agent and the other on the external agent.

fn is_neighbor( &self, own_pos: &Pos, ext_pos: &Pos, ext_inf: &Inf, ) -> Result<bool, CalcError>

Checks if the other cell represented by position and information is a neighbor to the current one or not.

fn react_to_neighbors(&mut self, neighbors: usize) -> Result<(), CalcError>

Reacts to the results gathered by the Interaction::is_neighbor method and changes the state of the cell.

impl IntoPy<Py<PyAny>> for BacteriaReactions

fn into_py(self, py: Python<'_>) -> Py<PyAny>

👎Deprecated since 0.23.0: IntoPy is going to be replaced by IntoPyObject. See the migration guide (https://pyo3.rs/v0.23.0/migration) for more information.

Performs the conversion.

impl<'py> IntoPyObject<'py> for BacteriaReactions

type Target = BacteriaReactions

The Python output type

type Output = Bound<'py, <BacteriaReactions as IntoPyObject<'py>>::Target>

The smart pointer type to use.

type Error = PyErr

The type returned in the event of a conversion error.

fn into_pyobject( self, py: Python<'py>, ) -> Result<<BacteriaReactions as IntoPyObject<'py>>::Output, <BacteriaReactions as IntoPyObject<'py>>::Error>

Performs the conversion.

impl PyClass for BacteriaReactions

type Frozen = False

Whether the pyclass is frozen.

impl PyTypeInfo for BacteriaReactions

const NAME: &'static str = "BacteriaReactions"

Class name.

const MODULE: Option<&'static str> = ::core::option::Option::None

Module name, if any.

fn type_object_raw(py: Python<'_>) -> *mut PyTypeObject

Returns the PyTypeObject instance for this type.

fn type_object(py: Python<'_>) -> Bound<'_, PyType>

Returns the safe abstraction over the type object.

fn type_object_bound(py: Python<'_>) -> Bound<'_, PyType>

👎Deprecated since 0.23.0: renamed to PyTypeInfo::type_object

Deprecated name for [PyTypeInfo::type_object].

fn is_type_of(object: &Bound<'_, PyAny>) -> bool

Checks if object is an instance of this type or a subclass of this type.

fn is_type_of_bound(object: &Bound<'_, PyAny>) -> bool

👎Deprecated since 0.23.0: renamed to PyTypeInfo::is_type_of

Deprecated name for [PyTypeInfo::is_type_of].

fn is_exact_type_of(object: &Bound<'_, PyAny>) -> bool

Checks if object is an instance of this type.

fn is_exact_type_of_bound(object: &Bound<'_, PyAny>) -> bool

👎Deprecated since 0.23.0: renamed to PyTypeInfo::is_exact_type_of

Deprecated name for [PyTypeInfo::is_exact_type_of].

impl Serialize for BacteriaReactions

fn serialize<__S>( &self, __serializer: __S, ) -> Result<<__S as Serializer>::Ok, <__S as Serializer>::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl DerefToPyAny for BacteriaReactions