ecoli.processes.environment.derive_globals

class ecoli.processes.environment.derive_globals.DeriveGlobals(parameters=None)[source]

Bases: Step

Process for deriving volume, mmol_to_counts, and shape from the cell mass

Parameters:

parameters (dict | None) –

defaults: Dict[str, Any]
{   'initial_mass': <Quantity(1339, 'femtogram')>,
    'width': <Quantity(1, 'micrometer')>}
name = 'globals_deriver'
next_update(timestep, states)[source]
ports_schema()[source]
ecoli.processes.environment.derive_globals.get_default_global_state()[source]
ecoli.processes.environment.derive_globals.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

ecoli.processes.environment.derive_globals.surface_area_from_length(length, width)[source]

SA = 3*PI*r^2 + 2*PI*r*a

ecoli.processes.environment.derive_globals.volume_from_length(length, width)[source]

inverse of length_from_volume