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Cytosim
PI
Cytoskeleton Simulator
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Cytosim
PI
Cytoskeleton Simulator
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This code is outdated, and we discourage you to use it.
Public Member Functions | |
| int | dynParamIndex (const FiberEnd which) const |
| returns the index which should be used to get parameters | |
| Tubule (TubuleProp const *) | |
| constructor | |
| virtual | ~Tubule () |
| destructor | |
| int | dynamicState (FiberEnd which) const |
| return assembly/disassembly state of the end which | |
| void | setDynamicState (FiberEnd which, int new_state) |
| set state of FiberEnd which to new_state | |
| real | freshAssembly (FiberEnd which) const |
| the amount of freshly assembled polymer during the last time step | |
| real | givenGrowthRate (FiberEnd which, int alt=0) const |
| the growth rate set for the specified end | |
| real | givenTransitionRate (FiberEnd which, int alt=0) const |
| the transition rate set for the specified end | |
| real | growthRate (real rate0, real rate1, real force) const |
| calculates the growth rate, in units of um/s of added polymer length = speed. More... | |
| real | transitionRate (FiberEnd which, int model) const |
| calculate the transition rate of a MT end, function of the parameter, growth and position More... | |
| Fiber * | severM (real abs) |
| cut fiber at distance abs from MINUS_END More... | |
| void | join (Fiber *fib) |
| join 'other' at the PLUS_END of this fiber | |
| void | stepMinusEnd () |
| simulate dynamic instability at MINUS_END | |
| void | stepPlusEnd () |
| simulate dynamic instability at PLUS_END | |
| void | step () |
| monte-carlo step | |
| void | write (OutputWrapper &) const |
| write Tubule to OutputWrapper | |
| void | read (InputWrapper &, Simul &) |
| read Tubule from InputWrapper | |
 Public Member Functions inherited from Fiber | |
| Fiber (FiberProp const *) | |
| constructor More... | |
| virtual | ~Fiber () |
| destructor | |
| virtual unsigned int | allocatePoints (unsigned int nbp) |
| allocate memory for 'nbp' points | |
| void | setDragCoefficient () |
| calculate viscous drag coefficient More... | |
| void | prepareMecable () |
| prepare for Meca | |
| void | setInteractions (Meca &) const |
| add interactions to a Meca | |
| void | sever (real abs) |
| cut fiber at abscissa abs from the ORIGIN, in the next time step | |
| void | cutAlongPlane (FiberSet *, Vector const &n, real a) |
| Cut all segments intersecting the plane defined by n.x + a = 0 | |
| FiberLocus & | segment (unsigned int p) const |
| FiberLocus representing the segment [p, p+1]. | |
| real | projectPoint (Vector const &w, real &dist) const |
return the abscissa of the closest position to w on this Fiber, and set dist to the square of the distance | |
| bool | isGrowing (FiberEnd which) const |
| true if the tip which has grown in the last time step ( freshAssembly(which) > 0 ) | |
| bool | isShrinking (FiberEnd which) const |
| true if the tip which has shrunk in the last time step ( freshAssembly(which) < 0 ) | |
| void | addBinder (FiberBinder *) |
| register a new Binder | |
| void | removeBinder (FiberBinder *) |
| unregister bound Binder | |
| FiberBinder * | firstBinder () const |
| a FiberBinder bound to this fiber (use ->next() to access all other binders) | |
| void | updateBinders () |
| update all binders | |
| void | detachBinders () |
| detach all binders | |
| int | nbBinders () const |
| number of attached FiberBinders | |
| int | nbBindersInRange (real aMin, real aMax, FiberEnd from) const |
| number of attached FiberBinders in a range of abscissa More... | |
| int | nbBindersNearEnd (real len, FiberEnd which) const |
| number of attached FiberBinders at the specified FiberEnd | |
| int | nbBinders (unsigned int(*count)(FiberBinder const &)) const |
| a function to count binders using custom criteria | |
| void | setGlue1 (Single *glue, FiberEnd which, const Space *space) |
| set the box glue for pure pushing More... | |
| void | setGlue2 (Single *glue, FiberEnd which, const Space *space) |
| set the box glue for pure pulling More... | |
| void | setGlue3 (Single *glue, FiberEnd which, const Space *space) |
| set the box glue for pushing and pulling More... | |
| void | setGlue (Single *&glue, FiberEnd which, const Space *space, int glue_type) |
| a setGlue to rule them all | |
| Fiber * | next () const |
| a static_cast<> of Node::next() | |
| Fiber * | prev () const |
| a static_cast<> of Node::prev() | |
| Tag | tag () const |
| return unique character identifying the class | |
| const Property * | property () const |
| return Object Property | |
| Public Member Functions inherited from RigidFiber | |
| RigidFiber () | |
| Constructor. | |
| RigidFiber (RigidFiber const &) | |
| copy constructor | |
| RigidFiber & | operator= (RigidFiber const &) |
| copy assignment | |
| virtual | ~RigidFiber () |
| Destructor. | |
| virtual unsigned | allocatePoints (unsigned nbp) |
| sets the number of points in the Fiber | |
| real | lagrange (unsigned p) const |
| Lagrange multiplier for segment p. | |
| real | tension (unsigned p) const |
| longitudinal force along segment p (positive=extension, negative=compression) | |
| real | dragCoefficient () const |
| total drag-coefficient of object (force = drag * speed) | |
| real | pointMobility () const |
| mobility of one point | |
| void | makeProjection () |
| prepare for projection | |
| void | projectForces (const real *X, real *Y, real s, real *work) const |
| apply the projection: Y <- s * P * X More... | |
| void | makeProjectionDiff (const real *) |
| prepare the correction to the projection | |
| void | addProjectionDiff (const real *, real *) const |
| add the contribution from the projection correction | |
| real | addBrownianForces (real *rhs, real sc) const |
| add displacements due to the Brownian motion to rhs[] More... | |
| void | setSpeedsFromForces (const real *X, real *Y, real, bool) const |
| calculate the speeds from the forces, including projection More... | |
| void | addRigidity (const real *X, real *Y) const |
| add the rigidity force corresponding to configuration X into vector Y More... | |
| void | addRigidityMatUp (Matrix &, int offset) const |
| add rigidity terms into the matrix | |
| Public Member Functions inherited from FiberNaked | |
| FiberNaked () | |
| Constructor. | |
| ~FiberNaked () | |
| Destructor. | |
| void | setStraight (Vector const &pos, Vector const &dir) |
| set position of MINUS_END and direction (length and Nb of points are not modified) More... | |
| void | setStraight (Vector const &pos, Vector const &dir, FiberEnd ref) |
| set position of 'ref' and direction of Fiber | |
| void | setStraight (Vector const &pos, Vector const &dir, real len, FiberEnd ref) |
| set position of 'ref', direction and length of Fiber | |
| void | setShape (const real pts[], unsigned n_pts, unsigned np) |
| import shape from the given array of size DIM*n_pts, and create a shape with np points More... | |
| PointExact | exactEnd (FiberEnd) const |
| exact representation of given end | |
| PointInterpolated | interpolateEnd (FiberEnd) const |
| interpolation representing a given end (CENTER is also a valid argument) | |
| PointInterpolated | interpolateCenter () const |
| interpolation representing a given end | |
| PointInterpolated | interpolateMinusEnd () const |
| interpolation representing the MINUS_END | |
| PointInterpolated | interpolatePlusEnd () const |
| interpolation representing the PLUS_END | |
| PointInterpolated | interpolate (real ab) const |
| interpolation of the site specified by its distance from the ORIGIN More... | |
| PointInterpolated | interpolateM (real ab) const |
| interpolation of the site specified from the MINUS_END More... | |
| PointInterpolated | interpolate (real ab, FiberEnd from) const |
| interpolation of a site specified by its distance from a FiberEnd | |
| real | abscissaM () const |
| signed distance from ORIGIN to MINUS_END (abscissa of MINUS_END) | |
| real | abscissaP () const |
| signed distance from ORIGIN to PLUS_END (abscissa of PLUS_END) | |
| real | abscissaP (const real n) const |
| signed distance from ORIGIN to given point or intermediate position | |
| real | abscissa (FiberEnd end) const |
| signed distance from the ORIGIN to the specified FiberEnd More... | |
| real | abscissa (real ab, FiberEnd from) const |
| converts abscissa from the specified FiberEnd, to abscissa from the ORIGIN More... | |
| real | length () const |
| the total length of the Fiber | |
| bool | within (const real ab) const |
| true if ( abscissaM() < ab < abscissaP() ) | |
| bool | withinP (const real ab) const |
| true if abscissa is below abscissaP | |
| bool | withinM (const real ab) const |
| true if abscissa is above abscissaM | |
| unsigned int | signature () const |
| a random number which is used in speckle display | |
| void | signature (unsigned int s) |
| set signature | |
| FiberEnd | whichEndDomain (real ab, real lambda) const |
| calculate the domain in which ab is located (near a FiberEnd, or central) More... | |
| Vector | pos (real ab) const |
| position of a point specified by abscissa from the origin | |
| Vector | posM (real ab) const |
| position of a point specified by abscissa from the MINUS_END | |
| Vector | pos (real ab, FiberEnd from) const |
| position of a point specified by abscissa on the Fiber | |
| Vector | posEnd (FiberEnd which) const |
| position of a FiberEnd (CENTER is also a valid argument) | |
| Vector | dirP (unsigned p) const |
| normalized tangent vector to the fiber at given model point More... | |
| Vector | dir (real ab) const |
| normalized tangent vector to the fiber at given abscissa from the origin | |
| Vector | dir (real ab, FiberEnd from) const |
| normalized tangent vector to the fiber at given abscissa from given reference | |
| Vector | dirEnd (FiberEnd which) const |
| normalized tangent vector to the fiber at given end | |
| real | projectedForceOnEnd (FiberEnd which) const |
| dot-product (force/km on the end of the Fiber).(direction of Fiber growth) More... | |
| void | segmentation (real c) |
| set desired segmentation (the actual segmentation might be different) | |
| real | segmentation () const |
| the current segment length (distance between successive model-points) | |
| real | segmentationCub () const |
| returns segmentation() ^ 3 | |
| void | resegment (unsigned int nb_points) |
| recalculate fiber to have nb_points model points More... | |
| void | adjustSegmentation () |
| set the number of points to minimize abs( fnCut - fnCutWished ) More... | |
| void | reshape () |
| re-establish the distance between successive model-points | |
| void | getPoints (const real *x) |
| set position | |
| void | minMaxSegments (real &, real &) const |
| calculate the minimum and maximum segment length More... | |
| void | infoSegments (real &, real &) const |
| calculate average and variance of the segment length More... | |
| real | minCosinus () const |
| the cosine of the maximum segment angle: indicate the errors due to curvature | |
| unsigned | nbKinks (real threshold=0) const |
| number of joints at which ( cosine(angle) < threshold ) More... | |
| void | join (FiberNaked const *fib) |
| merge two fibers by joining the PLUS_END of fib with the MINUS_END of this More... | |
| void | growM (real dlen) |
| increase/decrease length of Fiber by dlen, at the MINUS_END More... | |
| void | addSegmentM () |
| add a segment of length segmentation() at the MINUS_END More... | |
| void | cutM (real dlen) |
| remove a piece of length dlen >= 0 at the MINUS_END More... | |
| void | growP (real dlen) |
| increase/decrease length of Fiber by dlen, at the PLUS_END More... | |
| void | addSegmentP () |
| add a segment of length segmentation() at the MINUS_END More... | |
| void | cutP (real dlen) |
| remove a piece of length dlen >= 0 at the PLUS_END More... | |
| void | setLength (real len, FiberEnd ref) |
| adjust length without changing the position of ref | |
| void | truncateM (unsigned int p) |
| Remove all model points in [ 0, P-1 ], keep [ P, nbPoints() ]. | |
| void | truncateP (unsigned int p) |
| Keep model points [ 0, p ], remove other points. | |
| Public Member Functions inherited from PointSet | |
| PointSet () | |
| Constructor. | |
| PointSet (const PointSet &) | |
| Copy constructor. | |
| PointSet & | operator= (const PointSet &) |
| Assignement operator. | |
| virtual | ~PointSet () |
| Destructor. | |
| virtual void | deallocatePoints () |
| free memory allocated by allocatePoints() | |
| unsigned int | nbPoints () const |
| Number of points. | |
| unsigned int | lastPoint () const |
| Index of the last point = nbPoints - 1. | |
| unsigned int | nbSegments () const |
| Number of segments = nbPoints - 1. | |
| unsigned int | lastSegment () const |
| Index of the last segment = nbPoints - 2. | |
| Vector | posP (const unsigned p) const |
| Position of point 'p' of the object. | |
| real const * | addr () const |
| Address of point p. | |
| real const * | addrPoint (const unsigned p) const |
| Address of point p. | |
| void | setPoint (unsigned p, Vector const &w) |
| Set position of point p to w. | |
| void | nbPoints (const unsigned n) |
| Set the number of points in the array. | |
| unsigned int | addPoint (Vector const &w) |
| Add a point, returning the array index that was used. | |
| void | removePoint (unsigned int p) |
| Remove a point from the array psPos, returns number of points remaining. | |
| void | clearPoints () |
| Remove all points. | |
| void | resetPoints () |
| Set all coordinates to zero (nicer for debug/testing) | |
| void | addNoise (real amount) |
| Add random noise uniformly to all coordinate (used for testing purposes) | |
| virtual void | putPoints (real *) const |
| copy current coordinates to argument | |
| virtual void | getForces (const real *ptr) |
| replace current forces by the ones provided | |
| Vector | netForceP (const unsigned p) const |
| Force on point p calculate by Brownian dynamics. | |
| void | movePoint (const unsigned int p, Vector const &w) |
| Shift point at index p by vector w. | |
| Vector | diffPoints (const unsigned p) const |
| Difference of two points = Q - P = vector PQ. | |
| Vector | diffPoints (const unsigned int p, const unsigned int q) const |
| Difference of two points = Q - P = vector PQ. | |
| Vector | interpolatePoints (const unsigned int p, const unsigned int q, const real a) const |
| Calculate intermediate position = P + a ( Q - P ) | |
| void | calculateMomentum (real[], bool divide=false) |
| calculate first momentum of point coordinates More... | |
| void | calculateMomentum (real[], real[], bool divide=false) |
| calculate first and second momentum of point coordinates More... | |
| virtual Vector | position () const |
| Position of center of gravity. More... | |
| virtual bool | translatable () const |
| true if object accepts translations | |
| virtual void | translate (Vector const &) |
| Translate object (moves all the points by w) | |
| virtual bool | rotatable () const |
| true if object accepts translations | |
| virtual void | rotate (Rotation const &) |
| Rotate object by given rotation. | |
| virtual void | foldPosition (const Modulo *) |
| Modulo around the first point. | |
| virtual void | foldPositionG (const Modulo *) |
| Call modulo around the center of gravity. | |
| void | write (OutputWrapper &) const |
| Write to file. | |
| void | read (InputWrapper &, Simul &) |
| Read from file. | |
| Public Member Functions inherited from Mecable | |
| Mecable () | |
| The constructor resets the pointers. | |
| virtual | ~Mecable () |
| Destructor de-allocates memory. | |
| virtual Vector | posP (unsigned int P) const =0 |
| return position of point P | |
| virtual void | putPoints (real[]) const =0 |
| copy current coordinates to provided array | |
| virtual void | getPoints (const real[])=0 |
| replace current coordinates of points by values from the provided array | |
| virtual Vector | netForceP (unsigned int p) const =0 |
| return Force on point p calculated at previous step by Brownian dynamics | |
| virtual void | getForces (const real[])=0 |
| replace current forces by the ones provided | |
| void | matIndex (Matrix::index_type index) |
| Store the index where coordinates are located in Meca. | |
| Matrix::index_type | matIndex () const |
| Index in mB of the first point. the index in the vectors is DIM*matIndex() More... | |
| bool | useBlock () const |
| Tell Meca to use preconditionning on this object or not. | |
| void | useBlock (bool b) |
| change preconditionning flag | |
| real * | allocateBlock (unsigned) |
| Allocate a block of the requested size. | |
| real * | block () const |
| return allocated block | |
| 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 void | rotateP (Rotation const &) |
| rotate the object around its current position More... | |
| Public Member Functions inherited from Buddy | |
| virtual | ~Buddy () |
| upon destruction, goodbye is called for all buddies | |
| void | hello (Buddy *b) |
| will make this and b mutual buddies | |
| virtual void | goodbye (Buddy *) |
| this is called everytime a known buddy is destroyed | |
| Buddy * | buddy (unsigned int ix) const |
| return buddy at index ix | |
| void | buddy (Buddy *b, unsigned int ix) |
| replace the buddy that may have been at index ix | |
Public Attributes | |
| TubuleProp const * | prop |
| the Property of this object | |
| Public Attributes inherited from Fiber | |
| FiberProp const * | prop |
| the Property of this object | |
| LineDisp mutable * | disp |
| the display parameters | |
Additional Inherited Members | |
| Static Public Member Functions inherited from PointSet | |
| static Vector | diffPoints (const real *src, const unsigned p) |
| Difference of two points = P+1 - P. | |
| 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... | |
| Static Public Attributes inherited from Fiber | |
| static const Tag | TAG = 'f' |
| 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 Fiber | |
| Fiber * | severNow (real abs) |
| cut fiber at abscissa abs from the ORIGIN; returns section [ abs - PLUS_END ] | |
| void | delayedSevering () |
| cut fiber at absicca given to sever() More... | |
| virtual Fiber * | severPoint (unsigned int pti) |
| cut Fiber at point pti, return section [ pti - PLUS_END ] More... | |
| void | severKinkedFibers (FiberSet *set) |
| cut fiber at points where consecutive segments make a kink More... | |
| real | dragCoefficientSurface () |
| viscous drag coefficient for a cylinder moving close to a surface More... | |
| real | dragCoefficientVolume () |
| viscous drag coefficient for a cylinder moving close to a surface More... | |
| Protected Member Functions inherited from RigidFiber | |
| void | storeDifferences () |
| calculate the average difference of successive model-point in rfDiff[] More... | |
| Protected Attributes inherited from RigidFiber | |
| real | rfMobility |
| mobility of the points More... | |
| real | rfRigidity |
| rigidity scaling factor used in addRigidity() | |
| Protected Attributes inherited from PointSet | |
| real * | psPos |
| psPos[] of size DIM*psAllocated contains DIM*psSize point-coordinates | |
| real const * | psFor |
| psFor[] of size DIM*psAllocated contains DIM*psSize force-coordinates | |
| Vector | psCenter |
| Center of gravity calculed in calculatePosition() | |
| 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() | |
growthRate() returns the average assembly rate, in um/s
Calls Fiber::severM(abs) Set the dynamic state of newly created fiber tips:
Reimplemented from Fiber.
Dynamic instability of MTs is regulated by force M.Janson, M. de Dood, M. Dogterom. JCB 2003, Figure 2 C. the position of the plus-end in the Space determines its dynamics: transitions are trans1[] inside the box and trans2[] outside
1.8.9.1