initial_values¶

The initial values of a substance in every tissue of a model.

A substance which is transported in the body is initialized in every tissue to the same value, which removes the distribution kinetics: the simulation starts in (or close to) the steady state of the distribution. The functions return the changes of a simulation, [sid] for the concentration and sid for the amount of a species, and leave the urine alone.

The species of a substance are found by the naming pattern of the ids of the models, C<tissue>_<substance> for a concentration and A<tissue>_<substance> for an amount (Cve_len, Cli_plasma_len, Aurine_len), see get_species_keys.

init_concentrations_changes ¶

init_concentrations_changes(r, skey, value)

Get changes to set initial concentrations for skey.

Parameters:

Name	Type	Description	Default
`r`	`RoadRunner`	roadrunner model.	required
`skey`	`str`	substance key, e.g., `len` for the species `Cve_len`.	required
`value`	`float`	initial concentration in model units.	required

Returns:

Type	Description
`dict[str, float]`	Changes for the model, species selection to value.

init_amounts_changes ¶

init_amounts_changes(r, skey, value)

Get changes to set initial amounts for skey.

Parameters:

Name	Type	Description	Default
`r`	`RoadRunner`	roadrunner model.	required
`skey`	`str`	substance key, e.g., `len` for the species `Cve_len`.	required
`value`	`float`	initial amount in model units.	required

Returns:

Type	Description
`dict[str, float]`	Changes for the model, species selection to value.

get_species_keys ¶

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:

Name	Type	Description	Default
`skey`	`str`	substance key.	required
`species_ids`	`list[str]`	list of species ids to filter from.	required

Returns:

Type	Description
`list[str]`	Species ids of the substance.