Cytosim PI Cytoskeleton Simulator

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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 1 2]

►N gle | Simple geometrical objects drawn with OpenGL
C named_color | Holds the name and the RGBA components of a color
►N Polygon |
C Point2D | Structure to hold coordinate of point in 2D + misc
►N Rasterizer | 2D and 3D rasterizer
C Vertex | Point in 3D, with information for connectivity
►N Solver | Templated iterative solvers for systems of linear equations
C Allocator | Allocates vectors of real
C Monitor | Records the number of iterations, and the convergence
C Actor | A Hand that can act on a Fiber
C ActorProp | Additional Property for Actor
C Allot | Allot manages a piece of memory
C Array | Dynamic array of VAL
C Aster | A radial configuration of Fiber(s) built around a Solid
C AsterClamp | Defines a connection between Solid and Fiber
C AsterProp | Property for Aster
C Bead | A single point with a radius
C BeadProp | Property for Bead and Solid
C BeadSet | List of Bead
C Bridge | A specialized kind of Couple
C BridgeProp | Additional Property for Bridge
C Buddy | Maintains mutual relationship between objects
C Bundle | Set of Fiber held together using an fixed overlap
C BundleProp | Property for Bundle
C ClassicFiber | A Fiber with a standard two-state model of dynamic instability at the PLUS_END
C ClassicFiberProp | Additional Property for ClassicFiber
C Couple | A set of two Hand linked by an elastic element
C CoupleLong | A Couple with a non-zero resting length
C CoupleProp | Property for Couple
C CoupleSet | Set for Couple
C Criteria | Holds a set of criteria to select Objects
C Crosslink | A specialized kind of Couple
C CrosslinkLong | A Crosslink with a non-zero resting length
C CrosslinkProp | Additional Property for Crosslink and CroslinkLong
C Cutter | A Hand that can cut a Fiber
C CutterProp | Additional Property for Cutter
C Display | Base class to display Cytosim state using OpenGL
C Display1 | Cytosim display class - style 1
C Display2 | Cytosim display class - style 2
C Display3 | Cytosim display class - style 3
C DisplayProp | Property for Play
C DynamicFiber | A Fiber with discrete growth and dynamic instability at the PLUS_END
C DynamicFiberProp | Additional Property for DynamicFiber
C Exception | A mechanism to handle errors (see C++ manual)
C Fake | Set of two asters held together by a Solid
C FakeProp | Property for a Fake
C FatLocus | Segment of a Fiber for steric interactions
C FatPoint | PointExact for steric interactions
C Fiber | FiberNaked to which FiberBinder may bind
C FiberBinder | Location on a Fiber represented by an abscissa
C FiberDisp | Display parameters for a class of Fiber
C FiberGrid | Divide-and-Conquer method to find all FiberLocus located near a given point in space
C FiberLocus | Represents the segment between two consecutive points of a Fiber
C FiberNaked | Mecable with linear geometry
C FiberProp | Property for a Fiber
C FiberSet | List of Fiber
C FieldBase | Value of type VAL defined as a function of position over the simulation Space
C FieldProp | Property for Field
C FieldScalar | Scalar type (real) for a Field
C FieldSet | List of Field
C FieldVector | Vector type for a Field containing N real scalars
C FileWrapper | A wrapper around a C-FILE
C Fork | A specialized kind of Couple
C ForkProp | Additional Property for Fork
C FrameReader | Class to read a particular frame in a trajectory file
C glAppProp | Parameter set for glApp
C gle_color_float | RGBA (Red, Green, Blue, Alpha) color, with one float in [0,1] per component
C gle_color_int | RGBA (Red, Green, Blue, Alpha) color, with one byte per component
►C Glossary | Glossary holds a list of (key, values) where both key and values are strings
C val_type | String-encoded value with a counter
C Grid | Divide a rectangle of dimensionality ORD into regular voxels
C Hand | Simulates the stochastic binding/unbinding of a FiberBinder
C HandMonitor | Base class to monitor and control Hand's actions
C HandProp | Property for Hand
C InputWrapper | Input with automatic binary/text mode and byte-swapping for cross-platform compatibility
C Interface | Cytosim Application Programming Interface
C InvalidIO | InvalidIO is thrown during file Input/Output
C InvalidParameter | This class is thrown if a parameter value is invalid
C InvalidSyntax | InvalidSyntax is thrown while parsing config file
C Inventoried | Object that can be entered in a Inventory
C Inventory | Attributes and remember serial-numbers to Inventoried
►C KeyList | Stores a set of pairs ( string, values ). Used by Glossary::set()
C key_value | Type for a key-value pair
C LineDisp | Display parameters for a Line
C Matrix | The interface for all the large matrices
C Matrix1 |
C Matrix2 |
C Matrix3 |
C MatrixBase | Fortran-style matrices of small dimensions: 1, 2 and 3
C MatrixSparse | Real (non-symmetric) sparse Matrix
C MatrixSparseBandSymmetric | Sparse real symmetric Matrix, with a variable number of full diagonals
C MatrixSparseSymmetric | Real symmetric sparse Matrix
C MatrixSparseSymmetric1 | Real symmetric sparse Matrix, with optimized multiplication
C MatrixSymmetric | A real symmetric Matrix
C Meca | A class to calculate the motion of objects in Cytosim
C Mecable | Can be simulated using a Meca
C Messages | Control output file with different levels of verbosity
C Mighty | A Hand that can move and do other things to a Fiber
C MightyProp | Additional Property for Mighty
C Modulo | Used to implement periodic boundary conditions
C Motor | Hand that can move smoothly on a Fiber
C MotorProp | Additional Property for Motor
C Movable | Can be moved and rotated in space
C Node | Can be linked in a NodeList
C NodeList | Doubly linked list of Nodes
C Nucleator | A Hand that can nucleate a Fiber
C NucleatorProp | Additional Property for Nucleator
C Nucleus | Organizer built around a Sphere
C NucleusProp | Property for Nucleus
C Object | Parent class for all simulated objects
C ObjectSet | A set of Object
C Organizer | Assemblage of Object
C OrganizerSet | List of Organizer (Aster, Nucleus, Bundle)
C OutputWrapper | Output with automatic binary/text mode and byte-swapping for cross-platform compatibility
C Parser | Cytosim Parser to read and execute config files
C Picket | Single attached at a fixed position
C PicketLong | Picket with a non-zero resting length
C PlayProp | Property for Play
C PointDisp | Parameters necessary to display a point-like object
C PointExact | Indicates a point of interest in a Mecable
C PointGrid | Divide-and-Conquer to implement steric interactions
C PointGridCell | Few lists associated with the same location
C PointGridParam | Contains the stiffness parameters for the steric engine
C PointInterpolated | Indicates an intermediate position between two points of a PointSet
C PointSet | Array of points describing a physical object
C PointsOnSphere | Distribute points on the unit sphere, minimizing the 'electrostatic' energy
C Property | A Property holds the parameters for a particular kind of objects
C PropertyList | List of Property
C Quaternion | Quaternion is similar to a complex number, but of dimension four
C Random | Random Number Generator
C Rescuer | A Hand that may rescue a shrinking fiber
C RescuerProp | Additional Property for Rescuer
C RigidFiber | Incompressible FiberNaked with bending elasticity
C Shackle | A specialized kind of Couple
C ShackleLong | A Shackle with a non-zero resting length
C ShackleProp | Additional Property for Shackle
►C SimThread | SimThread is used to run a simulation in a dedicated thread
C Lock |
C TryLock |
C Simul | Simulator class
C SimulProp | Property for Simul
C Single | A point-like object containing one Hand
C SingleProp | Property for Single
C SingleSet | Set for Single
C Slider | A Hand that will move on a Fiber passively with viscous resistance
C SliderProp | Additional Property for Slider
C Solid | Undeformable cloud of points
C SolidSet | List of Solid
C Space | Defines the spatial constrains in cytosim
C SpaceCapsule | Spherocylinder (cylinder capped with hemispheres)
C SpaceCylinder | Cylinder of axis X
C SpaceCylinderP | Cylinder of axis X that is periodic along X
C SpaceCylinderZ | Cylinder of axis Z
C SpaceDice | A rectangle ( or a cube ) with rounded edges
C SpaceEllipse | Ellipse in 2D, ellipsoid or spheroid in 3D
C SpacePeriodic | Rectangular Space with periodic boundary conditions
C SpacePolygon | Polygonal convex region in space
C SpaceProp | Property for Space
C SpaceSet | List of Space
C SpaceSphere | Sphere centered at the origin
C SpaceSquare | Rectangular region
C SpaceStrip | Rectangular Space with partial periodic boundary conditions
C SpaceTorus | Bent cylinder of constant diameter terminated by hemispheric caps
C Sphere | Spherical object with a viscous surface
C SphereProp | Property for Sphere
C SphereSet | List of Sphere
C Tracker | A Hand that only binds near the end of a Fiber
C TrackerProp | Additional Property for Tracker
C TreadmillingFiber | A Fiber with assembly at both ends
C TreadmillingFiberProp | Additional Property for TreadmillingFiber
C Tubule | Adds dynamic instability (growth/shrinkage of the ends) to a Fiber
C TubuleBundle | Bundle of dynamic Microtubules
C TubuleProp | Additional Property for Tubule
C Vector1 | Vector1 is a vector with 1 `real` component
C Vector2 | Vector2 is a vector with 2 `real` components
C Vector3 | Vector3 is a vector with 3 `real` components
C View | Handles the viewing angle, projection and other aspects of an OpenGL display
C ViewProp | Properties needed to define a view
C Wrist | Single anchored to a Mecable
C WristLong | Wrist with a non-zero resting length
C zObject | A display element with a depth coordinate