Reactions and Species
- class mechanica.MxSpecies(*args)
The Mechanica species object.
Mostly, this is a wrap of libSBML Species.
- __str__() str
Return str(self).
- toString() std::string
Get a JSON string representation
- Return type
string
- Returns
std::string
- static fromString(str: std::string const &) MxSpecies *
Create from a JSON string representation.
- Parameters
str (string) –
- Return type
- Returns
MxSpecies*
- __reduce__()
Helper for pickle.
- property id: str
- property name: str
- property species_type: str
- property compartment: str
- property initial_amount: float
- property initial_concentration: float
- property substance_units: str
- property spatial_size_units: str
- property units: str
- property has_only_substance_units: bool
- property boundary_condition: bool
- property charge: int
- property constant: bool
- property conversion_factor: str
- mechanica.SpeciesValue
alias of
MxSpeciesValue
- class mechanica.MxSpeciesValue(*args)
A working valued-object of an underlying MxSpecies attached to an object.
- property boundary_condition: bool
- property initial_amount: float
- property initial_concentration: float
- property constant: bool
- secrete(amount, to=None, distance=None)
Secrete this species into a neighborhood.
Requires either a list of neighboring particles or neighborhood distance.
- Parameters
amount (float) – Amount to secrete.
to (MxParticleList) – Optional list of particles to secrete to.
distance (float) – Neighborhood distance.
- Returns
Amount actually secreted, accounting for availability and other subtleties.
- Return type
float
- mechanica.SpeciesList
alias of
MxSpeciesList
- class mechanica.MxSpeciesList
- __str__() str
Return str(self).
- __len__() int
- __getattr__(item: str)
- __setattr__(item: str, value) None
Implement setattr(self, name, value).
- __setitem__(item, value) None
- item(*args) MxSpecies *
Overload 1:
Get a species by index
- Parameters
index (int) – index of the species
- Return type
- Returns
MxSpecies*
Overload 2:
Get a species by name
- Parameters
s (string) – name of species
- Return type
- Returns
MxSpecies*
- insert(*args) HRESULT
Overload 1:
Insert a species
- Return type
int
- Returns
HRESULT
Overload 2:
Insert a species by name
- Parameters
s (string) – name of the species
- Return type
int
- Returns
HRESULT
- toString() std::string
Get a JSON string representation
- Return type
string
- Returns
std::string
- static fromString(str: std::string const &) MxSpeciesList *
Create from a JSON string representation.
- Parameters
str (string) –
- Return type
- Returns
MxSpeciesList*
- __reduce__()
Helper for pickle.
- mechanica.StateVector
alias of
MxStateVector
- class mechanica.MxStateVector(*args)
A state vector of an object.
- __str__() str
Return str(self).
- __len__() int
- __getattr__(item: str)
- __setattr__(item: str, value: float) None
Implement setattr(self, name, value).
- __getitem__(item: int)
- __setitem__(item: int, value: float) None
- toString() std::string
Get a JSON string representation
- Return type
string
- Returns
std::string
- static fromString(str: std::string const &) MxStateVector *
Create from a JSON string representation.
- Parameters
str (string) –
- Return type
- Returns
MxStateVector*
- __reduce__()
Helper for pickle.
- species
Species of the state vector