Cytosim PI Cytoskeleton Simulator

- Main Page
- Related Pages
- Modules
- Namespaces
- Classes
- Files

Todo List

Class Bridge
  : change Bridge to use Meca::interLongLink()
Member Bundle::step ()
  : we should orient the new Fiber in bundle direction
Member CoupleSet::write (OutputWrapper &) const
  Write size of uniLists, to export a complete state info
Member Fiber::nbBindersInRange (real aMin, real aMax, FiberEnd from) const
  : Convert aMin and aMax instead of converting each Binder abscissa
Member FiberBinder::read (InputWrapper &, Simul &)
  : we should allow binder to refer to any Mecable
Class FiberGrid
  we could call paintGrid() only if the objects have moved by a certain threshold. This would work if we also extend the painted area around the rod, by the same threshold. we must also redo the paintGrid() when MT points are added or removed.
Member FiberNaked::resegment (unsigned int nb_points)
  2d-order interpolation in FiberNaked::resegment()
Member FiberSet::infoDirection (Vector &G, Vector &D, Vector &N, bool(*func)(Fiber const *, void *)=0, void *=0) const
  better nematic tensor calculation in 3D.
Member FieldBase< VAL >::step (FiberSet &, real time_step)
  implement Crank-Nicholson for diffusion
Member glApp::displayLabel (const char *fmt,...)
  : replace displayLabel(...) by a std::ostream & display text permanently in bottom-left corner of the window
Member glApp::flashText (const char *fmt,...)
  : replace flashText(...) by a std::ostream & display text for 3 sec (to report that something has been done)
Member glApp::processNormalKey (unsigned char, int mouseX=0, int mouseY=0)
  flexible key assignment map to accomodate different keyboard layouts
Namespace gle
  namespace gle should be a class -> we use GL.vertex(v) Problem: the gle prefix is already used by standard OpenGL elements
Class Glossary
  parse and instantiate values like 'random.uniform()' or 'PI*30' or '0.1/60'
Member Glossary::warnings (std::ostream &, pair_type const &, unsigned threshold=1)
  : use color only if the terminal supports it
Class Grid< ORD, CELL, INDEX >

  Derive GridNumeric specialized for numerical values

  add Grid<> copy constructor and copy assignment

Member HandProp::checkStiffness (real stiff, real len, real mul, real kT) const
  the warning may not be relevant for long Links
Class InputWrapper
  : Introduce a set of classes: Inputter (text, base class) InputterText InputterBinary InputterBinarySwap
Class Messages
  build Messages from a OutputStream
Member Movable::readPosition (std::istream &, const Space *)
  : specify a croping plane, eg: "circle 4 if x > 0"
Module NewField
  : read the value of the field from a file, at initialization
Member ObjectSet::placeObjects (ObjectList const &, Glossary &opt, const Space *)
  implement keyword 'transformation'
Member Organizer::read (InputWrapper &, Simul &)
  check that tag corresponds to a Mecable
Member Parser::parse_call (std::istream &)
  : propagate the arguments (do_set, do_new) to the custom commands
Member Parser::parse_include (std::istream &)
  : able to specify do_set and do_new for command 'include'
Member Parser::parse_run (std::istream &)
  : add code executed at each time-step
Member PointExact::read (InputWrapper &, Simul &)
  : check that tag corresponds to a Mecable
Class PointInterpolated
  : PointInterpolated could be extended to refer to a Mecable, by using virtual functions
Class PointsOnSphere
  we could replace here the Coulomb repulsive interaction by a linear force
Namespace Rasterizer
  implement a rasterizer in variable precision, keeping arguments as 'real'
Member Solid::build (Glossary &)
  Solid: 3D clustered distribution
Member Solid::getPoints (const real *x)
  : store the rotation and translation calculated by reshapeReally()
Member Space::project (const real point[], real proj[], real rad) const
  problem in project() with radius if point is exactly on the box (n==0)
Member SpacePolygon::setInteraction (Vector const &pos, PointExact const &, Meca &, real stiff) const
  Also project re-entrant polygon corners on the segments of the Fiber.
Class TreadmillingFiber

  Document TreadmillingFiber