Cytosim  PI
Cytoskeleton Simulator
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:
Organizer Object Buddy Node Inventoried Movable

Public Member Functions

 Aster (AsterProp const *p)
 constructor
 
virtual ~Aster ()
 destructor
 
ObjectList build (Glossary &)
 construct all the dependent Objects of the Organizer
 
Solidsolid () const
 return the scaffolding Solid
 
Vector position () const
 return the center of the Solid
 
Fiberfiber (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
 
PointDisppointDisp () const
 display parameters
 
Tag tag () const
 return unique character identifying the class
 
const Propertyproperty () 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
 
Mecableorganized (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
 
Organizernext () const
 a static_cast<> of Node::next()
 
Organizerprev () 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)
 
Objectnext () const
 extends Node::next(), with a cast to preserve type
 
Objectprev () 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
 
Nodenext () const
 the next Node in the list, or zero if this is last
 
Nodeprev () const
 the previous Node in the list, or zero if this is first
 
NodeListlist () const
 the list where the object is linked, or zero
 
ObjectSetobjset () 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
NodenNext
 the next Node in the list
 
NodenPrev
 the previous Node in the list
 
- Protected Attributes inherited from Inventoried
Number nNumber
 object identifier, unique within the class defined by tag()