Couple Class Reference

Detailed Description

A Couple contains two pointers to Hand:

• cHand1
• cHand2

There are 4 possible states for a Couple:

• state FF [0]: cHand1 and cHand2 are free,
• state AF [1]: cHand1 is bound, cHand2 is free,
• state FA [2]: cHand1 is free, cHand2 is bound,
• state AA [3]: both hands are attached

The method state() return the state of the Couple in 0-3, but it is usually not necessary, since there are separate lists in CoupleSet.

Generally the Couple behaves according to its state:

• FF : the Couple is diffusing and both Hands are trying to bind fibers,
• AF, FA : the localization is given by the attachement point on the fiber,
• AA : the Couple is acting as a Hookean spring between the two fibers.

The default Couple has:

• a zero resting length (it uses Meca:interLink())
• no specificity

Inheritance diagram for Couple:

Public Member Functions
	Couple (CoupleProp const *, Vector const &w=Vector(0, 0, 0))
	create following the specifications in the CoupleProp
virtual	~Couple ()
	destructor
Couple &	operator= (Couple const &)
	copy operator
void	setProperty (CoupleProp *)
	change the property and update the two Hands
void	addConfinement (Meca &, const Hand *) const
	add confinement for give Hand if applicable
virtual void	setInteractions (Meca &) const
	add interactions to the Meca
virtual void	setInteractionsAF (Meca &) const
	add interactions to the Meca
virtual void	setInteractionsFA (Meca &) const
	add interactions to the Meca
virtual Vector	position () const
	the position of the complex, calculated from cPos, cHand1 and cHand2 More...
virtual bool	translatable () const
	Couple can be displaced only if it is not attached.
virtual void	translate (Vector const &w)
	translate object's position by the given vector
virtual void	setPosition (Vector const &w)
	move object to specified position
virtual void	foldPosition (const Modulo *s)
	modulo the current position vector in the space
void	randomizePosition ()
	set the position randomly inside the confining Space
real	stiffness () const
	stiffness of the link ( = prop->stiffness )
Hand *	attachedHand () const
	return one Hand that is attached, or zero if both are detached
virtual Vector	force1 () const
	force between hands, essentially: stiffness * ( cHand2->posHand() - cHand1->posHand() )
real	cosAngle () const
	cosine of the angle between the two Fibers attached by the hands
virtual Vector	posSide () const
	position on the side of fiber1 used for sideInteractions
Vector	posFree () const
	the position of the complex if it is unattached
virtual void	stepFF (const FiberGrid &)
	simulation step for a free Couple: diffusion
void	stepAF (const FiberGrid &)
	simulation step for a Couple attached by Hand1
void	stepFA (const FiberGrid &)
	simulation step for a Couple attached by Hand2
void	stepAA ()
	simulation step for a Bridge Couple
Hand const *	hand1 () const
	pointer to Hand1
bool	attached1 () const
	true if Hand1 is attached
Vector	pos1 () const
	position of Hand1 when attached (invalid call otherwise)
Fiber *	fiber1 () const
	Tubule to which Hand1 is attached, or zero if attached to another kind of Fiber.
void	attachTo1 (Fiber *f, real ab, FiberEnd from)
	attach Hand1 at the given position
void	attachToEnd1 (Fiber *f, FiberEnd end)
	attach Hand1 at the given end
void	attach1 (FiberBinder &fb)
	attach Hand1 at the given FiberBinder
Hand const *	hand2 () const
	pointer to Hand2
bool	attached2 () const
	true if Hand2 is attached
Vector	pos2 () const
	position of Hand2 when attached (invalid call otherwise)
Fiber *	fiber2 () const
	Tubule to which Hand2 is attached, or zero if attached to another kind of Fiber.
void	attachTo2 (Fiber *f, real ab, FiberEnd from)
	attach Hand2 at the given position
void	attachToEnd2 (Fiber *f, FiberEnd end)
	attach Hand2 at the given end
void	attach2 (FiberBinder &fb)
	attach Hand2 at the given FiberBinder
Couple *	next () const
	a static_cast<> of Node::next()
Couple *	prev () const
	a static_cast<> of Node::prev()
Tag	tag () const
	return unique character identifying the class
const Property *	property () const
	return Object Property
void	write (OutputWrapper &) const
	write to file
void	read (InputWrapper &, Simul &)
	read from file
Public Member Functions inherited from Object
	Object ()
	constructor
std::string	reference () const
	concatenation of [ tag(), property()->index(), number() ] in plain ascii More...
void	writeReference (OutputWrapper &) const
	write a reference that identifies the Object uniquely More...
void	writeReference (OutputWrapper &, Tag tag) const
	write a reference, but using the provided Tag More...
int	mark () const
	birth mark value
void	mark (int m)
	set birth mark
int	fleck () const
	fleck value (not stored in trajectory files)
void	fleck (int f) const
	set fleck (the value is not stored in trajectory files)
Object *	next () const
	extends Node::next(), with a cast to preserve type
Object *	prev () const
	extends Node::prev(), with a cast to preserve type
Public Member Functions inherited from Node
	Node ()
	constructor set as unlinked
virtual	~Node ()
	destructor More...
bool	linked () const
	true if Node is linked
Node *	next () const
	the next Node in the list, or zero if this is last
Node *	prev () const
	the previous Node in the list, or zero if this is first
NodeList *	list () const
	the list where the object is linked, or zero
ObjectSet *	objset () const
	return associated ObjectSet
Public Member Functions inherited from Inventoried
	Inventoried ()
	initialize (name=0)
	~Inventoried ()
	destructor
void	number (Number n)
	change the serial number
Number	number () const
	serial number : a integer identifier, unique within each class
Public Member Functions inherited from Movable
	Movable ()
	constructor
virtual	~Movable ()
	destructor
virtual bool	rotatable () const
	true if object accepts rotations (default=false)
virtual void	rotate (Rotation const &)
	rotate the object around the origin of coordinates More...
virtual void	rotateP (Rotation const &)
	rotate the object around its current position More...

Public Attributes
Hand *	cHand1
	first Hand
Hand *	cHand2
	second Hand

Static Public Attributes
static const Tag	TAG = 'c'
	a unique character identifying the class
Static Public Attributes inherited from Object
static const Tag	TAG = 'v'
	Object::TAG = 'v' represents the 'void' pointer.

Protected Member Functions
bool	allowAttachment (const FiberBinder &)
	specialization of HandMonitor More...
void	afterAttachment ()
	specialization of HandMonitor
void	beforeDetachment ()
	specialization of HandMonitor
void	afterDetachment ()
	specialization of HandMonitor
Number	objNumber () const
	specialization of HandMonitor
Hand *	otherHand (Hand *) const
	specialization of HandMonitor
Vector	otherDirection (Hand *) const
	specialization of HandMonitor
real	interactionLength () const
	specialization of HandMonitor

Protected Attributes
CoupleProp const *	prop
	property
Vector	cPos
	position and position in previous step of complex
Protected Attributes inherited from Node
Node *	nNext
	the next Node in the list
Node *	nPrev
	the previous Node in the list
Protected Attributes inherited from Inventoried
Number	nNumber
	object identifier, unique within the class defined by tag()

Additional Inherited Members
Static Public Member Functions inherited from Object
static std::string	strReference (char, int, Number, int)
	build a string reference by concatenating (tag, property_index, number, mark) More...
static void	readReference (InputWrapper &, int &, Number &, int &, char pretag)
	read a reference (property_index, number, mark) from input More...
static void	writeNullReference (OutputWrapper &)
	write a reference that does not refer to any Object
Static Public Member Functions inherited from Movable
static Vector	readPrimitive (std::istream &, const Space *)
	read a position specified with primitives, such as 'circle 5', etc. More...
static Vector	readPosition (std::istream &, const Space *)
	read a position in space More...
static Vector	readDirection (std::istream &, const Vector &, const Space *)
	read an orientation, and return a normalized vector More...
static Rotation	readRotation (std::istream &, const Vector &, const Space *)
	read a rotation specified in is, at position pos More...

Member Function Documentation

bool allowAttachment ( const FiberBinder &  fb )

protectedvirtual

If ( prop->stiff == true ): Check if binding is directly adjacent to the place where the other Hand of the complex is already attached. Such 'degenerate' link are allowed if the parameter prop->stiff is false. They cannot produce forces but change the cooperativity of Couple binding.

Reimplemented from HandMonitor.

Reimplemented in Bridge, and Crosslink.

Vector position ( ) const

virtual

The position is:

• cPos if the Couple is free,
• the position of the attached Hand if only one is attached
• the average position of the two hands if they are both attached

Reimplemented from Movable.