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*

class tissue_forge.models.center.cell_polarity.ContactPotential(tissue_forge.Potential)
couplingFlat

Flat interaction coefficient

couplingOrtho

Orthogonal interaction coefficient

couplingLateral

Lateral interaction coefficient

distanceCoeff

Distance coefficient

cType

Contact type (e.g., normal, isotropic or anisotropic)

mag

Magnitude of force due to potential

rate

State vector dynamics rate due to potential

bendingCoeff

Bending coefficient

class tissue_forge.models.center.cell_polarity.PersistentForce(tissue_forge.Force)
sensAB

Proportionality of force to AB vector

sensPCP

Proportionality of force to PCP vector