sbmlsim._deprecated.pk.pkpd

Methods specific to pkdb models.

Module Contents

Functions

init_concentrations_changes(r, skey, value)	Get changes to set initial concentrations for skey.
init_amounts_changes(r, skey, value)	Set initial amounts for skey.
_set_initial_values(r, sid, value, method='concentration')	Set the initial concentration of a distributing substance.
get_species_keys(skey, species_ids)	Get keys of substance in given list of ids.

Attributes

logger

sbmlsim._deprecated.pk.pkpd.logger

sbmlsim._deprecated.pk.pkpd.init_concentrations_changes(r, skey, value)

Get changes to set initial concentrations for skey.

Parameters

• r (roadrunner.RoadRunner) –

• value (float) –

sbmlsim._deprecated.pk.pkpd.init_amounts_changes(r, skey, value)

Set initial amounts for skey.

Parameters

r (roadrunner.RoadRunner) –

sbmlsim._deprecated.pk.pkpd._set_initial_values(r, sid, value, method='concentration')

Set the initial concentration of a distributing substance.

Takes care of all the compartment values so starting close/in steady state. Units are in model units

return: changeset for model

Parameters

r (roadrunner.RoadRunner) –

Return type

Dict

sbmlsim._deprecated.pk.pkpd.get_species_keys(skey, species_ids)

Get keys of substance in given list of ids.

Relies on naming patterns of ids. This does not get the species ids of the submodels, but only of the top model.

Parameters

• skey – substance key

• species_ids – list of species ids to filter from

Returns