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Cytosim
PI
Cytoskeleton Simulator
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The parameters are defined in AsterProp.
Each Fiber is attached to two points on the Solid:
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:
In short:
The distribution of the points could easily be changed to create non-isotropic fiber arrangements.
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() | |