SyMBac.cell

class SyMBac.cell.Cell(length, width, resolution, position, angle, space, dt, growth_rate_constant, max_length, max_length_mean, max_length_var, width_var, width_mean, parent=None, daughter=None, lysis_p=0, pinching_sep=0)[source]

Cells are the agents in the simulation. This class allows for instantiating Cell object.

Note

Typically the user will not need to call this class, as it will be handled by SyMBac.cell_simulation(), specifically all cell setup happens when instantiating a simulation using SyMBac.simulation.Simulation()

__init__(length, width, resolution, position, angle, space, dt, growth_rate_constant, max_length, max_length_mean, max_length_var, width_var, width_mean, parent=None, daughter=None, lysis_p=0, pinching_sep=0)[source]

Initialising a cell

For info about the Pymunk objects, see the API reference. http://www.pymunk.org/en/latest/pymunk.html Cell class has been tested and works with pymunk version 6.0.0

Parameters

  • length (float) – Cell’s length

  • width (float) – Cell’s width

  • resolution (int) – Number of points defining cell’s geometry

  • position ((float, float)) – x,y coords of cell centroid

  • angle (float) – rotation in radians of cell (counterclockwise)

  • space (pymunk.space.Space) – The pymunk space of the cell

  • dt (float) – Timestep the cell experiences every iteration

  • growth_rate_constant (float) – The cell grows by a function of dt*growth_rate_constant depending on its growth model

  • max_length (float) – The maximum length a cell reaches before dividing

  • max_length_mean (float) – should be the same as max_length for reasons unless doing advanced simulations

  • max_length_var (float) – The variance defining a normal distribution around max_length

  • width_var (float) – The variance defining a normal distribution around width

  • width_mean (float) – For reasons should be set equal to width unless using advanced features

  • body (pymunk.body.Body) – The cell’s pymunk body object

  • shape (pymunk.shapes.Poly) – The cell’s pymunk body object

  • ID (int) – A unique identifier for each cell. At the moment just a number from 0 to 100_000_000 and cross fingers that we get no collisions.

create_pm_cell()[source]

Creates a pymunk (pm) cell object, and places it into the pymunk space given when initialising the cell. If the cell is dividing, then two cells will be created. Typically this function is called for every cell, in every timestep to update the entire simulation.

Note

The return type of this function is dependent on the value returned by SyMBac.cell.Cell.is_dividing(). This is not good, and will be changed in a future version.

Returns

If SyMBac.cell.Cell.is_dividing() returns True, then a dictionary of values for the daughter cell is returned. A daughter can then be created. E.g:

>>> daughter_details = cell.create_pm_cell()
>>> daughter = Cell(**daughter_details)

If SyMBac.cell.Cell.is_dividing() returns False, then only a tuple containing (pymunk.body, pymunk.shape) will be returned.

Return type

dict or (pymunk.body, pymunk.shape)

get_angle()[source]

Gets the angle of the cell’s pymunk body.

Returns

angle – The cell’s angle in radians.

Return type

float

get_centroid()[source]

Calculates the centroid of the cell from the vertices.

Returns

centroid – The cell’s centroid in coordinates relative to the pymunk space which the cell exists in.

Return type

float

get_vertex_list()[source]

Calculates the vertex list (a set of x,y coordinates) which parameterise the outline of the cell

Returns

vertices – A list of vertices, each in a tuple, where the order is (x, y). The coordinates are relative to the pymunk space in which the cell exists.

Return type

list(tuple(float, float))

is_dividing()[source]

Checks whether a cell is dividing by comparing its current length to its max length (defined when instnatiated).

Returns

output – True if self.length > self.max_length, else False.

Return type

bool

update_length()[source]

A method, typically called every timepoint to update the length of the cell according to self.length = self.length + self.growth_rate_constant*self.dt*self.length.

Contains additional logic to control the amount of cell pinching happening according to the difference between the maximum length and the current length.

Return type

None

update_parent(parent)[source]
Parameters

parent (SyMBac.cell.Cell) – The SyMBac cell object to assign as the parent to the current cell.

Return type

None

update_position()[source]

A method, typically called every timepoint to keep synchronised the cell position (self.position and self.angle) with the position of the cell’s corresponding body in the pymunk space (self.body.position and self.body.angle).

Return type

None