Cytosim PI Cytoskeleton Simulator

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Aster Class Reference

## Detailed Description

The parameters are defined in AsterProp.

Each Fiber is attached to two points on the Solid:

- a primary point that is tied to the end of the Fiber
- a secondary point that is tied to the Fiber at some distance from the its end.

Together they link the Fiber to the Solid, both in position and direction. Their stiffness is defined in AsterProp::stiffness. To hold N fibers in different directions, the Aster uses multiple anchoring points. How they are distributed on the Solid depends on the dimensionality, and on:

- aster_radius = AsterProp::radius[0] + AsterProp::radius[1]
- inner_radius = AsterProp::radius[1]

In short:

1. If inner_radius == 0:
   - The Solid has one primary point, located in the center.
   - in 1D, only two secondary points are used: left and right,
   - in 2D, N secondary points are distributed on a circle of radius aster_radius.
   - in 3D, N secondary points are distributed on the surface of a sphere of radius aster_radius, using PointsOnSphere.
2. If inner_radius > 0:
   - the secondary points are distributed as if inner_radius==0,
   - an equal number of primary points are obtained by scaling the secondary points, to bring them at distance inner_radius from the center.

The distribution of the points could easily be changed to create non-isotropic fiber arrangements.

Inheritance diagram for Aster:

## Public Member Functions
| Aster (AsterProp const *p)
| constructor
virtual | ~Aster ()
| destructor
ObjectList | build (Glossary &)
| construct all the dependent Objects of the Organizer
Solid * | solid () const
| return the scaffolding Solid
Vector | position () const
| return the center of the Solid
Fiber * | fiber (unsigned int n) const
| return Fiber n
void | step ()
| perform one Monte-Carlo step
void | setInteractions (Meca &) const
| add interactions to the Meca
unsigned int | nbLinks () const
| number of connections between the sphere() and fiber()
Vector | posLink1 (unsigned int ii) const
| the position on the Sphere to which Fiber ii is attached
Vector | posLink2 (unsigned int ii) const
| the position of the Fiber ii which is attached
PointDisp * | pointDisp () const
| display parameters
Tag | tag () const
| return unique character identifying the class
const Property * | property () const
| return Object Property
void | read (InputWrapper &, Simul &)
| read from IO
void | write (OutputWrapper &) const
| write to IO
Public Member Functions inherited from Organizer
| Organizer ()
| default constructor
virtual | ~Organizer ()
| destructor
unsigned int | nbOrganized () const
| number of objects currently organized
Mecable * | organized (unsigned int n) const
| return Mecable at index n
void | grasp (Mecable *)
| add Mecable at end of list
void | grasp (Mecable *, unsigned int)
| add Mecable at index n
void | goodbye (Buddy *)
| handles the disapearance of one of the organized object
virtual Vector | positionP (unsigned int) const
| return the average of object->posP(0)
virtual void | translate (Vector const &T)
| move all associated objects
virtual void | rotate (Rotation const &T)
| transform all associated objects
Organizer * | next () const
| a static_cast<> of Node::next()
Organizer * | prev () const
| a static_cast<> of Node::prev()
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 void | setPosition (Vector const &)
| move object to specified position More...
virtual bool | translatable () const
| true if object accepts translations (default=false)
virtual bool | rotatable () const
| true if object accepts rotations (default=false)
virtual void | rotateP (Rotation const &)
| rotate the object around its current position More...
virtual void | foldPosition (Modulo const *)
| perform modulo for periodic boundary conditions More...

## Public Attributes
AsterProp const * | prop
| Property.

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

## 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...
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()