Implements model with additional features defined in Nielsen, Bjarke Frost, et al. "Model to link cell shape and polarity with organogenesis." Iscience 23.2 (2020): 100830. More...

#include <tfParticle.h>
#include <tfAngle.h>
#include <tfBond.h>
#include <tfForce.h>
#include <tfParticleTypeList.h>
#include <tfPotential.h>
#include <rendering/tfArrowRenderer.h>
#include <string>
#include <unordered_map>

Include dependency graph for tfCellPolarity.h:

Go to the source code of this file.

Classes
struct	TissueForge::models::center::CellPolarity::PersistentForce
	Defines a force due to polarity state. More...

struct	TissueForge::models::center::CellPolarity::PolarityArrowData

struct	TissueForge::models::center::CellPolarity::ContactPotential
	Defines polarity state dynamics and anisotropic adhesion. More...

Namespaces
namespace	TissueForge
	Include Python header, disable linking to pythonX_d.lib on Windows in debug mode.

namespace	TissueForge::models
	Application-specific Tissue Forge models and methods.

Typedefs
typedef enum TissueForge::models::center::CellPolarity::PolarContactType	TissueForge::models::center::CellPolarity::PolarContactType

Enumerations
enum	PolarContactType { REGULAR = 0 , ISOTROPIC = 1 , ANISOTROPIC = 2 }

Functions
FVector3	TissueForge::models::center::CellPolarity::getVectorAB (const int &pId, const bool &current=true)
	Gets the AB polarity vector of a cell.

FVector3	TissueForge::models::center::CellPolarity::getVectorPCP (const int &pId, const bool &current=true)
	Gets the PCP polarity vector of a cell.

void	TissueForge::models::center::CellPolarity::setVectorAB (const int &pId, const FVector3 &pVec, const bool &current=true, const bool &init=false)
	Sets the AB polarity vector of a cell.

void	TissueForge::models::center::CellPolarity::setVectorPCP (const int &pId, const FVector3 &pVec, const bool &current=true, const bool &init=false)
	Sets the PCP polarity vector of a cell.

void	TissueForge::models::center::CellPolarity::update ()
	Updates all running polarity models.

void	TissueForge::models::center::CellPolarity::registerParticle (ParticleHandle *ph)
	Registers a particle as polar.

void	TissueForge::models::center::CellPolarity::unregister (ParticleHandle *ph)
	Unregisters a particle as polar.

void	TissueForge::models::center::CellPolarity::registerType (ParticleType *pType, const std::string &initMode="random", const FVector3 &initPolarAB=FVector3(0.0), const FVector3 &initPolarPCP=FVector3(0.0))
	Registers a particle type as polar.

const std::string	TissueForge::models::center::CellPolarity::getInitMode (ParticleType *pType)
	Gets the name of the initialization mode of a type.

void	TissueForge::models::center::CellPolarity::setInitMode (ParticleType *pType, const std::string &value)
	Sets the name of the initialization mode of a type.

const FVector3	TissueForge::models::center::CellPolarity::getInitPolarAB (ParticleType *pType)
	Gets the initial AB polar vector of a type.

void	TissueForge::models::center::CellPolarity::setInitPolarAB (ParticleType *pType, const FVector3 &value)
	Sets the initial AB polar vector of a type.

const FVector3	TissueForge::models::center::CellPolarity::getInitPolarPCP (ParticleType *pType)
	Gets the initial PCP polar vector of a type.

void	TissueForge::models::center::CellPolarity::setInitPolarPCP (ParticleType *pType, const FVector3 &value)
	Sets the initial PCP polar vector of a type.

PersistentForce *	TissueForge::models::center::CellPolarity::createPersistentForce (const FloatP_t &sensAB=0.0, const FloatP_t &sensPCP=0.0)
	Creates a persistent polarity force.

void	TissueForge::models::center::CellPolarity::setDrawVectors (const bool &_draw)
	Toggles whether polarity vectors are rendered.

void	TissueForge::models::center::CellPolarity::setArrowColors (const std::string &colorAB, const std::string &colorPCP)
	Sets rendered polarity vector colors.

void	TissueForge::models::center::CellPolarity::setArrowScale (const FloatP_t &_scale)
	Sets scale of rendered polarity vectors.

void	TissueForge::models::center::CellPolarity::setArrowLength (const FloatP_t &_length)
	Sets length of rendered polarity vectors.

PolarityArrowData *	TissueForge::models::center::CellPolarity::getVectorArrowAB (const int32_t &pId)
	Gets the rendering info for the AB polarity vector of a cell.

PolarityArrowData *	TissueForge::models::center::CellPolarity::getVectorArrowPCP (const int32_t &pId)
	Gets the rendering info for the PCP polarity vector of a cell.

void	TissueForge::models::center::CellPolarity::load ()
	Runs the polarity model along with a simulation. Must be called before doing any operations with this module.

ContactPotential *	TissueForge::models::center::CellPolarity::createContactPotential (const FloatP_t &cutoff, const FloatP_t &mag=1.0, const FloatP_t &rate=1.0, const FloatP_t &distanceCoeff=1.0, const FloatP_t &couplingFlat=1.0, const FloatP_t &couplingOrtho=0.0, const FloatP_t &couplingLateral=0.0, std::string contactType="regular", const FloatP_t &bendingCoeff=0.0)
	Creates a contact-mediated polarity potential.

Detailed Description

Implements model with additional features defined in Nielsen, Bjarke Frost, et al. "Model to link cell shape and polarity with organogenesis." Iscience 23.2 (2020): 100830.

Function Documentation

◆ createContactPotential()

ContactPotential * TissueForge::models::center::CellPolarity::createContactPotential	(	const FloatP_t &	cutoff,
		const FloatP_t &	mag = 1.0,
		const FloatP_t &	rate = 1.0,
		const FloatP_t &	distanceCoeff = 1.0,
		const FloatP_t &	couplingFlat = 1.0,
		const FloatP_t &	couplingOrtho = 0.0,
		const FloatP_t &	couplingLateral = 0.0,
		std::string	contactType = "regular",
		const FloatP_t &	bendingCoeff = 0.0 )

Creates a contact-mediated polarity potential.

Parameters

cutoff	cutoff distance
mag	magnitude of force
rate	rate of state vector dynamics
distanceCoeff	distance coefficient
couplingFlat	flat coupling coefficient
couplingOrtho	orthogonal coupling coefficient
couplingLateral	lateral coupling coefficient
contactType	type of contact; available are regular, isotropic, anisotropic
bendingCoeff	bending coefficient

Returns: ContactPotential*

◆ createPersistentForce()

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

Creates a persistent polarity force.

Parameters

sensAB	sensitivity to AB vector
sensPCP	sensitivity to PCP vector

Returns: PersistentForce*

◆ getInitMode()

const std::string TissueForge::models::center::CellPolarity::getInitMode ( ParticleType * pType )

Gets the name of the initialization mode of a type.

Parameters

pType a type

Returns: const std::string

◆ getInitPolarAB()

const FVector3 TissueForge::models::center::CellPolarity::getInitPolarAB ( ParticleType * pType )

Gets the initial AB polar vector of a type.

Parameters

pType a type

Returns: const FVector3

◆ getInitPolarPCP()

const FVector3 TissueForge::models::center::CellPolarity::getInitPolarPCP ( ParticleType * pType )

Gets the initial PCP polar vector of a type.

Parameters

pType a type

Returns: const FVector3

◆ getVectorAB()

FVector3 TissueForge::models::center::CellPolarity::getVectorAB	(	const int &	pId,
		const bool &	current = true )

Gets the AB polarity vector of a cell.

Parameters

pId	particle id
current	current value flag; default true

Returns: FVector3

◆ getVectorArrowAB()

PolarityArrowData * TissueForge::models::center::CellPolarity::getVectorArrowAB ( const int32_t & pId )

Gets the rendering info for the AB polarity vector of a cell.

Parameters

pId	particle id

Returns: PolarityArrowData*

◆ getVectorArrowPCP()

PolarityArrowData * TissueForge::models::center::CellPolarity::getVectorArrowPCP ( const int32_t & pId )

Gets the rendering info for the PCP polarity vector of a cell.

Parameters

pId	particle id

Returns: PolarityArrowData*

◆ getVectorPCP()

FVector3 TissueForge::models::center::CellPolarity::getVectorPCP	(	const int &	pId,
		const bool &	current = true )

Gets the PCP polarity vector of a cell.

Parameters

pId	particle id
current	current value flag; default true

Returns: FVector3

◆ registerParticle()

void TissueForge::models::center::CellPolarity::registerParticle ( ParticleHandle * 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	handle of particle

◆ registerType()

void TissueForge::models::center::CellPolarity::registerType	(	ParticleType *	pType,
		const std::string &	initMode = "random",
		const FVector3 &	initPolarAB = FVector3(0.0),
		const FVector3 &	initPolarPCP = FVector3(0.0) )

Registers a particle type as polar.

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

Parameters

pType	particle type
initMode	initialization mode for particles of this type
initPolarAB	initial value of AB polarity vector; only used when initMode="value"
initPolarPCP	initial value of PCP polarity vector; only used when initMode="value"

◆ setArrowColors()

void TissueForge::models::center::CellPolarity::setArrowColors	(	const std::string &	colorAB,
		const std::string &	colorPCP )

Sets rendered polarity vector colors.

Applies to subsequently created vectors and all current vectors.

Parameters

colorAB	name of AB vector color
colorPCP	name of PCP vector color

◆ setArrowLength()

void TissueForge::models::center::CellPolarity::setArrowLength ( const FloatP_t & _length )

Sets length of rendered polarity vectors.

Applies to subsequently created vectors and all current vectors.

Parameters

_length length of rendered vectors

◆ setArrowScale()

void TissueForge::models::center::CellPolarity::setArrowScale ( const FloatP_t & _scale )

Sets scale of rendered polarity vectors.

Applies to subsequently created vectors and all current vectors.

Parameters

_scale scale of rendered vectors

◆ setDrawVectors()

void TissueForge::models::center::CellPolarity::setDrawVectors ( const bool & _draw )

Toggles whether polarity vectors are rendered.

Parameters

_draw rendering flag; vectors are rendered when true

◆ setInitMode()

void TissueForge::models::center::CellPolarity::setInitMode	(	ParticleType *	pType,
		const std::string &	value )

Sets the name of the initialization mode of a type.

Parameters

pType	a type
value	initialization mode

◆ setInitPolarAB()

void TissueForge::models::center::CellPolarity::setInitPolarAB	(	ParticleType *	pType,
		const FVector3 &	value )

Sets the initial AB polar vector of a type.

Parameters

pType	a type
value	initial AB polar vector

◆ setInitPolarPCP()

void TissueForge::models::center::CellPolarity::setInitPolarPCP	(	ParticleType *	pType,
		const FVector3 &	value )

Sets the initial PCP polar vector of a type.

Parameters

pType	a type
value	initial PCP polar vector

◆ setVectorAB()

void TissueForge::models::center::CellPolarity::setVectorAB	(	const int &	pId,
		const FVector3 &	pVec,
		const bool &	current = true,
		const bool &	init = false )

Sets the AB polarity vector of a cell.

Parameters

pId	particle id
pVec	vector value
current	current value flag; default true
init	initialization flag; default false

◆ setVectorPCP()

void TissueForge::models::center::CellPolarity::setVectorPCP	(	const int &	pId,
		const FVector3 &	pVec,
		const bool &	current = true,
		const bool &	init = false )

Sets the PCP polarity vector of a cell.

Parameters

pId	particle id
pVec	vector value
current	current value flag; default true
init	initialization flag; default false

◆ unregister()

void TissueForge::models::center::CellPolarity::unregister ( ParticleHandle * ph )

Unregisters a particle as polar.

This must be called before destroying a registered particle.

Parameters

ph	handle of particle

Classes

Namespaces

Typedefs

Enumerations

Functions

Detailed Description

Function Documentation

◆ createContactPotential()

◆ createPersistentForce()

◆ getInitMode()

◆ getInitPolarAB()

◆ getInitPolarPCP()

◆ getVectorAB()

◆ getVectorArrowAB()

◆ getVectorArrowPCP()

◆ getVectorPCP()

◆ registerParticle()

◆ registerType()

◆ setArrowColors()

◆ setArrowLength()

◆ setArrowScale()

◆ setDrawVectors()

◆ setInitMode()

◆ setInitPolarAB()

◆ setInitPolarPCP()

◆ setVectorAB()

◆ setVectorPCP()

◆ unregister()