Reactions and Species

class tissue_forge.state.Species(*args)

__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 &) → TissueForge::state::Species *

Create from a JSON string representation.

Parameters:

str (string) –

Return type:

Species

Returns:

Species*

__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

class tissue_forge.state.SpeciesValue(state_vector: _state_StateVector, index: uint32_t)

property boundary_condition: bool

property initial_amount: float

property initial_concentration: float

property constant: bool

property value: float

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 (ParticleList) – Optional list of particles to secrete to.

• distance (float) – Neighborhood distance.

Returns:

Amount actually secreted, accounting for availability and other subtleties.

Return type:

float

class tissue_forge.state.SpeciesList

__str__() → str

Return str(self).

__len__() → int

__getattr__(item: str)

__setattr__(item: str, value) → None

Implement setattr(self, name, value).

__getitem__(item) → _state_Species

__setitem__(item, value) → None

item(*args) → TissueForge::state::Species *

Overload 1:

Get a species by index

Parameters:

index (int) – index of the species

Return type:

Species

Returns:

Species*

Overload 2:

Get a species by name

Parameters:

s (string) – name of species

Return type:

Species

Returns:

Species*

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 &) → TissueForge::state::SpeciesList *

Create from a JSON string representation.

Parameters:

str (string) –

Return type:

SpeciesList

Returns:

SpeciesList*

__reduce__()

Helper for pickle.

class tissue_forge.state.StateVector(*args)

__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 &) → TissueForge::state::StateVector *

Create from a JSON string representation.

Parameters:

str (string) –

Return type:

StateVector

Returns:

StateVector*

__reduce__()

Helper for pickle.

species

Species of the state vector