|
Cytosim
PI
Cytoskeleton Simulator
|
|
Cytosim
PI
Cytoskeleton Simulator
|
The ShackleLong adds a non-zero resting length to Duo, using Meca:interSideSlidingLink()
For zero-resting length, use Shackle
ShackleLong is automatically selected if ( prop:length > 0 )
This is highly experimental!
Public Member Functions | |
| ShackleLong (ShackleProp const *, Vector const &w=Vector(0, 0, 0)) | |
| create following the specifications in the CoupleProp | |
| virtual | ~ShackleLong () |
| destructor | |
| Vector | posSide () const |
| position on the side of fiber1 used for sideInteractions | |
| Vector | force1 () const |
| force between hands More... | |
| void | setInteractions (Meca &) const |
| add interactions to the Meca More... | |
 Public Member Functions inherited from Shackle | |
| Shackle (ShackleProp const *p, Vector const &w=Vector(0, 0, 0)) | |
| create following the specifications in the CoupleProp | |
| virtual | ~Shackle () |
| destructor | |
| void | stepAA () |
| simulation step if doubly attached | |
| Public Member Functions inherited from Couple | |
| 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 | 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 | |
| real | cosAngle () const |
| cosine of the angle between the two Fibers attached by the hands | |
| 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... | |
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... | |
| Public Attributes inherited from Couple | |
| Hand * | cHand1 |
| first Hand | |
| Hand * | cHand2 |
| second Hand | |
| Static Public Attributes inherited from Couple | |
| 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 inherited from Couple | |
| 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 inherited from Shackle | |
| ShackleProp const * | prop |
| property | |
| Protected Attributes inherited from Couple | |
| 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() | |
|
virtual |
When ( prop->length > 0 ), we calculate the force for the interSideLink()
Reimplemented from Couple.
1.8.9.1 
