Crate cellular_raza_building_blocks

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§cellular_raza - Building Blocks

Building blocks allow users to quickly construct complex cellular agents. The simplest approach is to use fully-defined cell models. However, users can also build their own complex models by combining existing ones.

To create your own agent with physical mechanics and interactions, we need to include the building blocks for them as fields of our agent struct.

struct MyAgent {
    mechanics: NewtonDamped2D,
    interaction: BoundLennardJones,
}

Furthermore, we can derive desired concepts by using the CellAgent derive macro.

#[derive(CellAgent)]
struct MyAgent {
    #[Mechanics]
    mechanics: NewtonDamped2D,
    #[Interaction]
    interaction: BoundLennardJones,
}

For technical reasons, we are required to also once more specify the types for position, velocity and force when specifying which struct field to derive from. The optional Inf generic parameter of the Interaction trait was left out and thus defaults to (). It can and needs to also be specified when choosing interactions with non-trivial interaction information.

§Optional Features

Features guard implementations which introduce additional dependencies. To simplify usability, we enable commonly used features by default.

pyo3 Rust bindings to the Python interpreter

Modules§

cartesian_cuboid_n_oldplotters: Contains deprecated cartesian cuboid implementations
pool_bacteriapyo3: Objects and definitions surrounding the bacterial pool model

Structs§

BoundLennardJones: Lennard-Jones interaction potential with numerical upper and lower limit.
BoundLennardJonesF32: Identical to BoundLennardJones but for f32 type.
Brownian1D: Brownian motion of particles
Brownian1DF32: Brownian motion of particles
Brownian2D: Brownian motion of particles
Brownian2DF32: Brownian motion of particles
Brownian3D: Brownian motion of particles
Brownian3DF32: Brownian motion of particles
CartesianCuboid: A generic Domain with a cuboid layout.
CartesianCuboidRods: Cells are represented by rods
CartesianDiffusion2D: Domain based on CartesianCuboid in 2 dimensions with extracellular diffusion.
CartesianDiffusion2DSubDomain: Subdomain for the CartesianDiffusion2D domain.
CartesianSubDomain: Subdomain corresponding to the CartesianCuboid struct.
CartesianSubDomainRods: The corresponding SubDomain of the CartesianCuboidRods domain.
Langevin1D: Langevin dynamics
Langevin1DF32: Langevin dynamics
Langevin2D: Langevin dynamics
Langevin2DF32: Langevin dynamics
Langevin3D: Langevin dynamics
Langevin3DF32: Langevin dynamics
MiePotential: Generalizeation of the BoundLennardJones potential.
MiePotentialF32: Generalizeation of the BoundLennardJones potential.
ModularCell: Superseded by the CellAgent derive macro.
MorsePotential: Famous Morse potential for diatomic molecules.
MorsePotentialF32: Famous Morse potential for diatomic molecules.
NewtonDamped1D: Newtonian dynamics governed by mass and damping.
NewtonDamped1DF32: Newtonian dynamics governed by mass and damping.
NewtonDamped2D: Newtonian dynamics governed by mass and damping.
NewtonDamped2DF32: Newtonian dynamics governed by mass and damping.
NewtonDamped3D: Newtonian dynamics governed by mass and damping.
NewtonDamped3DF32: Newtonian dynamics governed by mass and damping.
NoCellularReactions: Do not model intracellular reactions at all.
NoCycle: No cycle of the cell.
NoExtracellularGradientSensing: Type which allows to simply not model gradients.
NoInteraction: No interaction of the cell with any other.
RodInteraction: Automatically derives a Interaction suitable for rods from a point-wise interaction.
RodMechanics: A mechanical model for Bacterial Rods
VertexDerivedInteraction: Derives an interaction potential from a point-like potential.
VertexMechanics2D: Mechanics model which represents cells as vertices with edges between them.

Functions§

calculate_morse_interaction: Calculates the interaction strength behind the MorsePotential and MorsePotentialF32 structs.
nearest_point_from_point_to_line: Calculate the point on a line which is closest to an external given point.
nearest_point_from_point_to_multiple_lines: Generalizes the nearest_point_from_point_to_line function for a collection of line segments.
ray_intersects_line_segment: Implements the ray-casting algorithm to check if a ray intersects with a given line segment.
wiener_process: Generate a vector corresponding to a wiener process.

Type Aliases§

Nothing: Type alias used when not wanting to simulate any cellular reactions for example.