goo.molecule

class goo.molecule.DiffusionSystem(molecules: list[Molecule], grid_size: tuple[int, int, int] = (50, 50, 50), grid_center: tuple[int, int, int] = (0, 0, 0), time_step: float = 0.1, total_time: int = 1, element_size=(0.5, 0.5, 0.5))

Bases: object

A diffusion system that simulates the diffusion of molecules in a 3D grid. It also handles the secretion and sensing of molecular signals by cells.

Parameters:

• molecules (list[Molecule]) – The list of molecules in the system.

• grid_size (Tuple[int, int, int], optional) – The size of the 3D grid. Defaults to (25, 25, 25).

• grid_center (Tuple[int, int, int], optional) – The center of the 3D grid. Defaults to (0, 0, 0).

• time_step (float, optional) – The time step of the simulation. Defaults to 0.1.

• total_time (int, optional) – The total time of the simulation. Defaults to 10.

• element_size (Tuple[float, float, float], optional) – The size of each element in the grid. Defaults to (1.0, 1.0, 1.0).

build_kdtree()

Initialize the grid and build its corresponding KD-Tree.

diffuse(mol: Molecule)

Simulate the diffusion of molecules in the grid using the Laplace operator.

Parameters:

mol (Molecule)

get_ball_concentrations(mol, center, radius)

Returns the coordinates and concentrations of a molecule of all the voxels within a sphere.

Parameters:

• mol – Molecule to get concentrations for

• center – Coordinates of sphere center

• radius – Radius of sphere

Returns:

(coordinates array, concentrations array) for points within sphere

Return type:

tuple

get_molecule_concentration(mol, point)

Get the concentration of a molecule at a certain point.

get_total_ball_concentrations(mol, center, radius)

Returns total concentration of a molecule within a sphere.

Parameters:

• mol – Molecule to get concentration for

• center – Coordinates of sphere center

• radius – Radius of sphere

Returns:

Total concentration of the molecule within the sphere

Return type:

float

simulate_diffusion(mol: Molecule)

Simulate the diffusion of molecules in the grid.

Parameters:

mol (Molecule)

update_concentrations_around_sphere(mol, center, radius, value)

Add a value to a molecule concentration at a certain point that is converted to the nearesrt voxel in the grid.

update_molecule_concentration(mol, point, value)

Add a value to a molecule concentration at a certain point that is converted to the nearesrt voxel in the grid.

class goo.molecule.Molecule(name: str, conc: float, D: float, gradient: str | None = None)

Bases: object

A molecule involved in the diffusion system.

Parameters:

• name (str) – The name of the molecule.

• conc (float) – The initial concentration of the molecule.

• D (float) – The diffusion rate of the molecule.

• gradient (str, optional) – The gradient of the molecule. Defaults to None.

property D

property conc

property gradient

property name