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, current=1)

Gets the AB polarity vector of a cell

Parameters:

  • pId (int) – particle id

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

Return type:

FVector3

Returns:

FVector3

tissue_forge.models.center.cell_polarity.getVectorPCP(pId, current=1)

Gets the PCP polarity vector of a cell

Parameters:

  • pId (int) – particle id

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

Return type:

FVector3

Returns:

FVector3

tissue_forge.models.center.cell_polarity.setVectorAB(pId, pVec, current=1, init=0)

Sets the AB polarity vector of a cell

Parameters:

  • pId (int) – particle id

  • pVec (FVector3) – vector value

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

  • init (boolean, optional) – initialization flag; default false

tissue_forge.models.center.cell_polarity.setVectorPCP(pId, pVec, current=1, init=0)

Sets the PCP polarity vector of a cell

Parameters:

  • pId (int) – particle id

  • pVec (FVector3) – vector value

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

  • init (boolean, optional) – initialization flag; default false

tissue_forge.models.center.cell_polarity.registerParticle(ph)

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)

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)

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, optional) – initialization mode for particles of this type

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

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

tissue_forge.models.center.cell_polarity.getInitMode(pType)

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, value)

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)

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, value)

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)

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, value)

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=0.0, sensPCP=0.0)

Creates a persistent polarity force.

Parameters:

  • sensAB (float, optional) – sensitivity to AB vector

  • sensPCP (float, optional) – sensitivity to PCP vector

Return type:

PersistentForce

Returns:

PersistentForce*

tissue_forge.models.center.cell_polarity.setDrawVectors(_draw)

Toggles whether polarity vectors are rendered

Parameters:

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

tissue_forge.models.center.cell_polarity.setArrowColors(colorAB, colorPCP)

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)

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)

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()

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)

Creates a contact-mediated polarity potential

Parameters:

  • cutoff (float) – cutoff distance

  • mag (float, optional) – magnitude of force

  • rate (float, optional) – rate of state vector dynamics

  • distanceCoeff (float, optional) – distance coefficient

  • couplingFlat (float, optional) – flat coupling coefficient

  • couplingOrtho (float, optional) – orthogonal coupling coefficient

  • couplingLateral (float, optional) – lateral coupling coefficient

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

  • bendingCoeff (float, optional) – 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