Tissue Forge Models Python API Reference

This is the API Reference page for the module: tissue_forge.models

Cell Polarity

This is the API Reference page for the module: cell_polarity. For details on the mathematics and modeling concepts, see the Cell Polarity Module Documentation.

tissue_forge.models.center.cell_polarity.getVectorAB(pId: int const &, current: bool const & = True) → TissueForge::FVector3

Gets the AB polarity vector of a cell

Parameters

  • pId (int) – particle id

  • current (boolean) – current value flag; default true

Return type

FVector3

Returns

FVector3

tissue_forge.models.center.cell_polarity.getVectorPCP(pId: int const &, current: bool const & = True) → TissueForge::FVector3

Gets the PCP polarity vector of a cell

Parameters

  • pId (int) – particle id

  • current (boolean) – current value flag; default true

Return type

FVector3

Returns

FVector3

tissue_forge.models.center.cell_polarity.setVectorAB(pId: int const &, pVec: fVector3, current: bool const & = True, init: bool const & = False) → void

Sets the AB polarity vector of a cell

Parameters

  • pId (int) – particle id

  • pVec (FVector3) – vector value

  • current (boolean) – current value flag; default true

  • init (boolean) – initialization flag; default false

tissue_forge.models.center.cell_polarity.setVectorPCP(pId: int const &, pVec: fVector3, current: bool const & = True, init: bool const & = False) → void

Sets the PCP polarity vector of a cell

Parameters

  • pId (int) – particle id

  • pVec (FVector3) – vector value

  • current (boolean) – current value flag; default true

  • init (boolean) – initialization flag; default false

tissue_forge.models.center.cell_polarity.registerParticle(ph: ParticleHandle) → void

Registers a particle as polar.

This must be called before the first integration step. Otherwise, the engine will not know that the particle is polar and will be ignored.

Parameters

ph (ParticleHandle) – handle of particle

tissue_forge.models.center.cell_polarity.unregister(ph: ParticleHandle) → void

Unregisters a particle as polar.

This must be called before destroying a registered particle.

Parameters

ph (ParticleHandle) – handle of particle

tissue_forge.models.center.cell_polarity.registerType(*args, **kwargs) → void

Registers a particle type as polar.

This must be called on a particle type before any other type-specific operations.

Parameters

  • pType (ParticleType) – particle type

  • initMode (string) – initialization mode for particles of this type

  • initPolarAB (FVector3) – initial value of AB polarity vector; only used when initMode=”value”

  • initPolarPCP (FVector3) – initial value of PCP polarity vector; only used when initMode=”value”

tissue_forge.models.center.cell_polarity.getInitMode(pType: ParticleType) → std::string const

Gets the name of the initialization mode of a type

Parameters

pType (ParticleType) – a type

Return type

string

Returns

const std::string

tissue_forge.models.center.cell_polarity.setInitMode(pType: ParticleType, value: std::string const &) → void

Sets the name of the initialization mode of a type

Parameters

  • pType (ParticleType) – a type

  • value (string) – initialization mode

tissue_forge.models.center.cell_polarity.getInitPolarAB(pType: ParticleType) → TissueForge::FVector3 const

Gets the initial AB polar vector of a type

Parameters

pType (ParticleType) – a type

Return type

FVector3

Returns

const FVector3

tissue_forge.models.center.cell_polarity.setInitPolarAB(pType: ParticleType, value: fVector3) → void

Sets the initial AB polar vector of a type

Parameters

  • pType (ParticleType) – a type

  • value (FVector3) – initial AB polar vector

tissue_forge.models.center.cell_polarity.getInitPolarPCP(pType: ParticleType) → TissueForge::FVector3 const

Gets the initial PCP polar vector of a type

Parameters

pType (ParticleType) – a type

Return type

FVector3

Returns

const FVector3

tissue_forge.models.center.cell_polarity.setInitPolarPCP(pType: ParticleType, value: fVector3) → void

Sets the initial PCP polar vector of a type

Parameters

  • pType (ParticleType) – a type

  • value (FVector3) – initial PCP polar vector

tissue_forge.models.center.cell_polarity.createPersistentForce(sensAB: FloatP_t const & = 0.0, sensPCP: FloatP_t const & = 0.0) → TissueForge::models::center::CellPolarity::PersistentForce *

Creates a persistent polarity force.

Parameters

  • sensAB (float) – sensitivity to AB vector

  • sensPCP (float) – sensitivity to PCP vector

Return type

PersistentForce

Returns

PersistentForce*

tissue_forge.models.center.cell_polarity.setDrawVectors(_draw: bool const &) → void

Toggles whether polarity vectors are rendered

Parameters

_draw (boolean) – rendering flag; vectors are rendered when true

tissue_forge.models.center.cell_polarity.setArrowColors(colorAB: std::string const &, colorPCP: std::string const &) → void

Sets rendered polarity vector colors.

Applies to subsequently created vectors and all current vectors.

Parameters

  • colorAB (string) – name of AB vector color

  • colorPCP (string) – name of PCP vector color

tissue_forge.models.center.cell_polarity.setArrowScale(_scale: FloatP_t const &) → void

Sets scale of rendered polarity vectors.

Applies to subsequently created vectors and all current vectors.

Parameters

_scale (float) – scale of rendered vectors

tissue_forge.models.center.cell_polarity.setArrowLength(_length: FloatP_t const &) → void

Sets length of rendered polarity vectors.

Applies to subsequently created vectors and all current vectors.

Parameters

_length (float) – length of rendered vectors

tissue_forge.models.center.cell_polarity.load() → void

Runs the polarity model along with a simulation. Must be called before doing any operations with this module.

tissue_forge.models.center.cell_polarity.createContactPotential(*args, **kwargs) → TissueForge::models::center::CellPolarity::ContactPotential *

Creates a contact-mediated polarity potential

Parameters

  • cutoff (float) – cutoff distance

  • mag (float) – magnitude of force

  • rate (float) – rate of state vector dynamics

  • distanceCoeff (float) – distance coefficient

  • couplingFlat (float) – flat coupling coefficient

  • couplingOrtho (float) – orthogonal coupling coefficient

  • couplingLateral (float) – lateral coupling coefficient

  • contactType (string) – type of contact; available are regular, isotropic, anisotropic

  • bendingCoeff (float) – bending coefficient

Return type

ContactPotential

Returns

ContactPotential*

tissue_forge.models.center.cell_polarity.ContactPotential

alias of _models_center_CellPolarity_ContactPotential

tissue_forge.models.center.cell_polarity.PersistentForce

alias of _models_center_CellPolarity_PersistentForce