NutMEG.culture.horde package

Submodules

NutMEG.culture.horde.horde module

class NutMEG.culture.horde.horde.horde(name, locale, metabolism, num, maintenance=None, CHNOPS=None, mass=1e-15, dry_mass=3e-16, *args, **kwargs)

Bases: NutMEG.culture.base_organism.base_organism.base_organism

Class for a horde of organisms acting as one for better efficiency., albeit losing some fidelity. For the majority of applications using a horde is much better than using a colony. A horde shares most attributes with base-organism like objects (and using them as per-cell parameters), but has a couple of its own.

num

The number of organisms the horde represents.

Type

int

volume

The total volume of the horde.

Type

float

deathnum

The number of dead cells which are inactive, but still represent biomass.

Type

int

biomass_cell_ratio

To be used for conversion between cell numbers and volumes, because some cells will be mid growth and bigger than others. Default 1.5.

Type

float, kwarg

get_mass(inactive=False)

return the total (approximate) biomass of the horde in kg

get_population(inactive=False)

Return total number of cells in the horde

get_volume(inactive=False)

return the total volume of the horde in m^3

reproduce()

Hordes don’t reproduce, throw an error if something tries to make it do so.

select_timestep(factorup=1.01, returncop=False)

work out a suitable time step for the horde to grow by factorup times. return the timestep. If returncop is passed as True, also return the copy used to calculate the timestep.

take_step(t)

Overwrite base_organisms take_step. Send the horde forward by time t. Perform all metabolic reactions and grow the horde if possible.

update_num(t)

After updating the volume, correct the number of organisms.

workoutID()

NutMEG.culture.horde.horde_output module

class NutMEG.culture.horde.horde_output.horde_output(hosthorde)

Bases: object

helper class for managing the output of a horde, either to terminal or to a database.

hosthorde

The host for this output generator, Where we get our numbers from.

Type

horde

params

Dictionary of parameters to output.

Type

dict

appendvals(startnum, dt)

Add parameters at the present time to params.

Parameters

  • startnum (int) – Previous number of organisms, assuming this is output after a time step. Used to calculate thr gorwth rate

  • dt (float) – Amount of time that has passed since the previous step.

buildbaseparams()
params = {}
paramtypelst()
refreshparams()

reset the parameter dictionary to have empty numpy arrays.

Inherit and adjust this method for saved organisms which have specific parameters you want to monitor.

Module contents