physicool.datatypes

Module Contents

Classes

Domain
Overall
Substance
Volume
Mechanics
Motility
Secretion
CycleCode	Generic enumeration.
Cycle
DeathCode	Generic enumeration.
Death
CustomData
CellParameters

class physicool.datatypes.Domain

Bases: pydantic.BaseModel

x_min: int

x_max: int

y_min: int

y_max: int

z_min: int

z_max: int

dx: conint(ge=0)

dy: conint(ge=0)

dz: conint(ge=0)

use_2d: bool

class physicool.datatypes.Overall

Bases: pydantic.BaseModel

max_time: conint(ge=0)

dt_diffusion: confloat(ge=0)

dt_mechanics: confloat(ge=0)

dt_phenotype: confloat(ge=0)

class physicool.datatypes.Substance

Bases: pydantic.BaseModel

name: str

diffusion_coefficient: confloat(ge=0.0)

decay_rate: confloat(ge=0.0)

initial_condition: confloat(ge=0.0)

dirichlet_boundary_condition: confloat(ge=0.0)

class physicool.datatypes.Volume

Bases: pydantic.BaseModel

class Config

validate_assignment = True

total: confloat(ge=0.0)

fluid_fraction: confloat(ge=0.0, le=1.0)

nuclear: confloat(ge=0.0)

fluid_change_rate: confloat(ge=0.0)

cytoplasmic_biomass_change_rate: confloat(ge=0.0)

nuclear_biomass_change_rate: confloat(ge=0.0)

calcified_fraction: confloat(ge=0.0, le=1.0)

calcification_rate: confloat(ge=0.0)

relative_rupture_volume: confloat(ge=0.0)

class physicool.datatypes.Mechanics

Bases: pydantic.BaseModel

class Config

validate_assignment = True

cell_cell_adhesion_strength: confloat(ge=0.0)

cell_cell_repulsion_strength: confloat(ge=0.0)

relative_maximum_adhesion_distance: confloat(ge=0.0)

set_relative_equilibrium_distance: confloat(ge=0.0)

set_absolute_equilibrium_distance: confloat(ge=0.0)

class physicool.datatypes.Motility

Bases: pydantic.BaseModel

class Config

validate_assignment = True

speed: confloat(ge=0.0)

persistence_time: confloat(ge=0.0)

migration_bias: confloat(ge=0.0, le=1.0)

motility_enabled: bool

use_2d: bool

chemotaxis_enabled: bool

chemotaxis_substrate: str

chemotaxis_direction: float

class physicool.datatypes.Secretion

Bases: pydantic.BaseModel

class Config

validate_assignment = True

name: str

secretion_rate: confloat(ge=0.0)

secretion_target: confloat(ge=0.0)

uptake_rate: confloat(ge=0.0)

net_export_rate: confloat(ge=0.0)

class physicool.datatypes.CycleCode

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

LIVE = 0

FLOW_CYTOMETRY_SEPARATED = 6

class physicool.datatypes.Cycle

Bases: pydantic.BaseModel

class Config

validate_assignment = True

code: float

phase_durations: Optional[List[confloat(ge=0.0)]]

phase_transition_rates: Optional[List[confloat(ge=0.0)]]

class physicool.datatypes.DeathCode

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

APOPTOSIS = 100

NECROSIS = 101

class physicool.datatypes.Death

Bases: pydantic.BaseModel

class Config

validate_assignment = True

code: float

name: str

death_rate: confloat(ge=0.0)

phase_durations: Optional[List[confloat(ge=0.0)]]

phase_transition_rates: Optional[List[confloat(ge=0.0)]]

unlysed_fluid_change_rate: confloat(ge=0.0)

lysed_fluid_change_rate: confloat(ge=0.0)

cytoplasmic_biomass_change_rate: confloat(ge=0.0)

nuclear_biomass_change_rate: confloat(ge=0.0)

calcification_rate: confloat(ge=0.0)

relative_rupture_volume: confloat(ge=0.0)

class physicool.datatypes.CustomData

Bases: pydantic.BaseModel

name: str

value: float

class physicool.datatypes.CellParameters

Bases: pydantic.BaseModel

name: str

cycle: Cycle

death: List[Death]

volume: Volume

mechanics: Mechanics

motility: Motility

secretion: List[Secretion]

custom: List[CustomData]