nskinetics.SpeciesSystem#

class nskinetics.SpeciesSystem(ID, all_sps, concentrations=None, compartments=None, default_volume=1.0)[source]#

Bases: object

Abstract class for a system containing defined chemical species. Note this class will, by convention, use “sp” to denote a single species and use “sps” to denote multiple species.

Parameters:

ID (str) – ID.
all_sps (list) – List of Species objects or strings. If the latter, new Species objects will be created.
concentrations (list or np.ndarray, optional) – Concentrations of species, indexed the same way as all_sps. Defaults to zero-array of length equal to that of all_sps.
compartments (dict) – Dictionary with keys as compartment IDs and values as volumes. Volumes can be either a float or a callable that returns a float given the SpeciesSystem object as an argument.

__init__(ID, all_sps, concentrations=None, compartments=None, default_volume=1.0)[source]#

Methods

`__init__`(ID, all_sps[, concentrations, ...])
`add_species`(species[, concentration])
`concentration`(sp_ID)
`contains`(sp)
`get_compartment_volume`(comp_ID)
`index`(sp)
`index_from_ID`(sp_ID)
`index_from_base_ID`(base_ID)
`indices`(some_sps)
`remove_species`(species)
`set_compartment_volume`(comp_ID, volume)
`species`(ID_or_index)

Attributes

`all_sp_IDs`
`amounts`	Amounts = concentration * compartment_volume for each species.
`compartments`	volume}
`concentrations`
`volume`

add_species(species, concentration=0.0)[source]#

property all_sp_IDs#

property amounts#: Amounts = concentration * compartment_volume for each species.

property compartments#

volume}

Type:: dict
Type:: {compartment_id

concentration(sp_ID)[source]#

property concentrations#

contains(sp)[source]#

get_compartment_volume(comp_ID)[source]#

index(sp)[source]#

index_from_ID(sp_ID)[source]#

Return type:: int

index_from_base_ID(base_ID)[source]#

Return type:: int

indices(some_sps)[source]#

remove_species(species)[source]#

set_compartment_volume(comp_ID, volume)[source]#

species(ID_or_index)[source]#

property volume#