Cytosim PI Cytoskeleton Simulator

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List of all members | Public Member Functions
Nucleator Class Reference
List of objects | How to create objects » Hand and Derived Activities

## Detailed Description

The Nucleator is a Hand, and thus can bind and unbind from fibers, but in most cases, however you would want `binding_rate=0`.

A free Nucleator can create new fibers with a prescibed rate. The rate, the type of fiber and the characteristics of the fiber are set as three values in property nucleate.

The parameter specificity allow to constrain the direction of the new fiber that is nucleated.

By default the nucleator stays attached at the MINUS_END of the fiber that it has created. This can be changed by setting: track_end

See Examples and the Parameters of Nucleator.

Inheritance diagram for Nucleator:

## Public Member Functions
| Nucleator (NucleatorProp const *p, HandMonitor *h)
| constructor
| ~Nucleator ()
| destructor
void | nucleate (Vector pos)
| create a new Fiber
void | stepFree (const FiberGrid &, Vector const &pos)
| simulate when is not attached More...
void | stepUnloaded ()
| simulate when this is attached but not under load
void | stepLoaded (Vector const &force)
| simulate when this is attached and under load
void | detach ()
| detach from Fiber More...
Public Member Functions inherited from Hand
| Hand (HandProp const *, HandMonitor *h)
| constructor More...
virtual | ~Hand ()
| destructor
virtual bool | attachmentAllowed (FiberBinder &site)
| tell if attachment at given site is possible More...
virtual void | attach (FiberBinder &site)
| attach the hand at the position described by site More...
virtual void | handleOutOfRange (FiberEnd)
| this is called when the attachment point is outside the Fiber's range
void | attachTo (Fiber *, real ab, FiberEnd from)
| attach to the given position on the given Fiber (calls attach(FiberBinder))
void | attachToEnd (Fiber *, FiberEnd end)
| attach to the given end on the given Fiber (calls attach(FiberBinder))
void | read (InputWrapper &, Simul &)
| read
void | write (OutputWrapper &) const
| write
Public Member Functions inherited from FiberBinder
| FiberBinder ()
| construct as unattached
| FiberBinder (Fiber *f, real a)
| construct at the given distance from the origin
void | relocate (Fiber *f)
| move to a different fiber, at same abscissa
void | relocate (Fiber *f, real a)
| move to a different fiber, at given position
void | moveToEnd (FiberEnd end)
| move to the specified FiberEnd (CENTER is also a valid argument)
void | moveTo (real abs)
| move along the Fiber to specified abscissa, or detach
void | moveBy (real dabs)
| move along the Fiber by the abscissa offset dabs, or detach
bool | attached () const
| true if attached
Fiber * | fiber () const
| Fiber to which this is attached, or zero if not attached.
Vector | pos () const
| position in space
Vector | dir () const
| direction of Fiber obtained by normalization
Vector | dirFiber () const
| the direction of the Fiber at the point of attachment
real | abscissa () const
| the abscissa, from the origin of the Fiber
real | abscissaFrom (FiberEnd from) const
| abscissa, counted from the specified FiberEnd (in reversed direction for the PLUS_END)
FiberEnd | nearestEnd () const
| nearest end to the point specified by the abscissa from the origin
bool | withinP () const
| true if abscissa is below abscissaP
bool | withinM () const
| true if abscissa is above abscissaM
bool | within () const
| true if abscissa is within the fiber boundaries
const PointInterpolated & | interpolation () const
| the interpolation
void | updateBinder ()
| set a valid PointInterpolated
void | checkFiberRange ()
| check the abscissa against the edges of the fiber, calling handleOutOfRange() if necessary.
FiberBinder * | next () const
| a static_cast<> of Node::next()
FiberBinder * | prev () const
| a static_cast<> of Node::prev()
void | checkAbscissa () const
| check that fbAbs is within Fiber::abscissaM() and Fiber::abscissaP()
int | bad () const
| check validity of the interpolation (debuging purposes)
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

## Additional Inherited Members
Public Attributes inherited from Hand
HandProp const * | prop
| Property.
Protected Member Functions inherited from Hand
bool | testDetachment ()
| test for detachment with rate prop->unbinding_rate More...
bool | testKramersDetachment (real force)
| test for detachment with Kramers theory More...
Protected Attributes inherited from Hand
HandMonitor * | haMonitor
| the monitor associated with this Hand
real | nextAttach
| Gillespie normalized time for attachment.
real | nextDetach
| Gillespie normalized time for detachment.
Protected Attributes inherited from FiberBinder
Fiber * | fbFiber
| the Fiber on which it is attached, or 0 if not attached
real | fbAbs
| the abscissa from the Fiber origin
Protected Attributes inherited from Node
Node * | nNext
| the next Node in the list
Node * | nPrev
| the previous Node in the list

## Member Function Documentation

void detach | ( |  | ) |
| virtual

If pro->addictive, this gives a poisonous goodbye-kiss to the fiber

Reimplemented from Hand.

void stepFree | ( | const FiberGrid & | ,
|  | Vector const & | pos
| ) |  |
| virtual

Does not attach nearby Fiber, but can nucleate

Reimplemented from Hand.