cellular_raza_concepts/
reactions_old.rs

1use crate::CalcError;
2
3/// Defines how the cell uses the extracellular gradient.
4///
5/// This trait can also be derived with the [CellAgent](crate::CellAgent) derive macro.
6/// ```
7/// use cellular_raza_concepts::{reactions_old::InteractionExtracellularGradient,
8///     CalcError, CellAgent
9/// };
10///
11/// struct DoNothingGradient;
12///
13/// impl<C, G> InteractionExtracellularGradient<C, G> for DoNothingGradient {
14///     fn sense_gradient(
15///         cell: &mut C,
16///         gradient: &G,
17///     ) -> Result<(), CalcError> {
18///         Ok(())
19///     }
20/// }
21///
22/// #[derive(CellAgent)]
23/// struct MyAgent {
24///     #[ExtracellularGradient]
25///     gradient: DoNothingGradient,
26/// }
27/// ```
28pub trait InteractionExtracellularGradient<Cell, ConcGradientExtracellular> {
29    /// The cell-agent senses the gradient and changes the behaviour of the cell.
30    fn sense_gradient(
31        cell: &mut Cell,
32        gradient: &ConcGradientExtracellular,
33    ) -> Result<(), CalcError>;
34}
35
36/// Specify how cellular reactions are taking place.
37///
38/// This trait can also be derived with the [CellAgent](crate::CellAgent) derive macro.
39/// ```
40/// use cellular_raza_concepts::{reactions_old::CellularReactions, CellAgent, CalcError};
41/// struct MyReactions {
42///     intracellular: f64,
43///     half_time: f64,
44/// }
45///
46/// impl CellularReactions<f64> for MyReactions {
47///     fn get_intracellular(&self) -> f64 {
48///         self.intracellular
49///     }
50///
51///     fn set_intracellular(&mut self, intracellular: f64) {
52///         self.intracellular = intracellular;
53///     }
54///
55///     fn calculate_intra_and_extracellular_reaction_increment(
56///         &self,
57///         internal_concentration_vector: &f64,
58///         external_concentration_vector: &f64,
59///     ) -> Result<(f64, f64), CalcError> {
60///         Ok((-self.half_time * self.intracellular, self.half_time * self.intracellular))
61///     }
62/// }
63// #[derive(CellAgent)]
64// struct MyAgent {
65//     #[Reactions]
66//     reactions: MyReactions,
67// }
68/// ```
69pub trait CellularReactions<ConcVecIntracellular, ConcVecExtracellular = ConcVecIntracellular> {
70    /// Retrieves the current intracellular concentration.
71    fn get_intracellular(&self) -> ConcVecIntracellular;
72
73    /// Sets the intracellular concentration. This is used by the backend after values have been updated.
74    fn set_intracellular(&mut self, concentration_vector: ConcVecIntracellular);
75
76    /// Calculate the time-related change of the intracellular and extracellular concentrations.
77    /// This is not the increment itself (thus no parameter `dt` was specified) but rather the time-derivative.
78    /// Such an approach can be useful when designing addaptive solvers.
79    fn calculate_intra_and_extracellular_reaction_increment(
80        &self,
81        internal_concentration_vector: &ConcVecIntracellular,
82        external_concentration_vector: &ConcVecExtracellular,
83    ) -> Result<(ConcVecIntracellular, ConcVecExtracellular), CalcError>;
84}
85
86/// Obtain the current volume of the cell
87///
88/// This trait is used when updating extracellular reactions and processes.
89/// For more details see [domain](crate::Domain).
90pub trait Volume<F = f64> {
91    /// Obtain the cells current volume.
92    fn get_volume(&self) -> F;
93}
cellular_raza_concepts/reactions_old.rs

cellular_raza_concepts/
reactions_old.rs
