ecoli.processes.shape
Shape
Shape
is used to calculate shape properties using 3D capsule geometry.
Outputs length and `surface_area are determined from inputs volume and width.
These variables are required to plug into a Lattice Environment
- class ecoli.processes.shape.Shape(parameters=None)[source]
Bases:
Step
Shape Step
Derives cell length and surface area from width and volume.
Ports:
cell_global: Should be given the agent’s boundary store. Contains variables: volume, width, length, and surface_area.
periplasm_global: Contains the volume variable for the volume of the periplasm.
- Parameters:
parameters (dict) –
A dictionary that can contain the following configuration options:
width (
float
): Initial width of the cell in microns
-
defaults: Dict[str, Any]
{ 'cytoplasm_fraction': 0.8, 'initial_cell_volume': <Quantity(1.2, 'femtoliter')>, 'initial_mass': <Quantity(1339, 'femtogram')>, 'periplasm_fraction': 0.2, 'width': <Quantity(1.0, 'micrometer')>}
- name = 'ecoli-shape'
- ecoli.processes.shape.length_from_volume(volume, width)[source]
get cell length from volume, using the following equation for capsule volume, with V=volume, r=radius, a=length of cylinder without rounded caps, l=total length:
\(V = (4/3)*PI*r^3 + PI*r^2*a\) \(l = a + 2*r\)