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 valuecurrent (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 valuecurrent (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 typeinitMode (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 typevalue (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 typevalue (
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 typevalue (
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:
- 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:
- 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