Reactions and Species

mechanica.Species

alias of mechanica.mechanica.MxSpecies

class mechanica.MxSpecies(*args)

The Mechanica species object.

Mostly, this is a wrap of libSBML Species.

__str__() → mechanica.mechanica.MxSpecies.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

MxSpecies

Returns

MxSpecies*

__reduce__()

Helper for pickle.

property id: mechanica.mechanica.MxSpecies.str

property name: mechanica.mechanica.MxSpecies.str

property species_type: mechanica.mechanica.MxSpecies.str

property compartment: mechanica.mechanica.MxSpecies.str

property initial_amount: float

property initial_concentration: float

property substance_units: mechanica.mechanica.MxSpecies.str

property spatial_size_units: mechanica.mechanica.MxSpecies.str

property units: mechanica.mechanica.MxSpecies.str

property has_only_substance_units: bool

property boundary_condition: bool

property charge: int

property constant: bool

property conversion_factor: mechanica.mechanica.MxSpecies.str

mechanica.SpeciesValue

alias of mechanica.mechanica.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 mechanica.mechanica.MxSpeciesList

class mechanica.MxSpeciesList

__str__() → mechanica.mechanica.MxSpeciesList.str

Return str(self).

__len__() → int

__getattr__(item: mechanica.mechanica.MxSpeciesList.str)

__setattr__(item: mechanica.mechanica.MxSpeciesList.str, value) → None

Implement setattr(self, name, value).

__getitem__(item) → mechanica.mechanica.MxSpecies

__setitem__(item, value) → None

item(*args) → MxSpecies *

Overload 1:

Get a species by index

Parameters

index (int) – index of the species

Return type

MxSpecies

Returns

MxSpecies*

Overload 2:

Get a species by name

Parameters

s (string) – name of species

Return type

MxSpecies

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

MxSpeciesList

Returns

MxSpeciesList*

__reduce__()

Helper for pickle.

mechanica.StateVector

alias of mechanica.mechanica.MxStateVector

class mechanica.MxStateVector(*args)

A state vector of an object.

__str__() → mechanica.mechanica.MxStateVector.str

Return str(self).

__len__() → int

__getattr__(item: mechanica.mechanica.MxStateVector.str)

__setattr__(item: mechanica.mechanica.MxStateVector.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

MxStateVector

Returns

MxStateVector*

__reduce__()

Helper for pickle.

species

Species of the state vector