Cytosim PI Cytoskeleton Simulator

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Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1 2 3 4 5 6 7]

C Allocator | Allocates vectors of real
C Allot< VAL > | Allot manages a piece of memory
C Allot< real > |
C Array< VAL > | Dynamic array of VAL
C Array< AsterClamp > |
C Array< FatLocus > |
C Array< FatPoint > |
C Array< FiberLocus > |
C Array< Mecable * > |
C Array< Single * > |
C AsterClamp | Defines a connection between Solid and Fiber
►C Buddy | Maintains mutual relationship between objects
►C Mecable | Can be simulated using a Meca
C Bead | A single point with a radius
►C PointSet | Array of points describing a physical object
►C FiberNaked | Mecable with linear geometry
►C RigidFiber | Incompressible FiberNaked with bending elasticity
►C Fiber | FiberNaked to which FiberBinder may bind
C ClassicFiber | A Fiber with a standard two-state model of dynamic instability at the PLUS_END
C DynamicFiber | A Fiber with discrete growth and dynamic instability at the PLUS_END
C TreadmillingFiber | A Fiber with assembly at both ends
C Tubule | Adds dynamic instability (growth/shrinkage of the ends) to a Fiber
C Solid | Undeformable cloud of points
C Sphere | Spherical object with a viscous surface
►C Organizer | Assemblage of Object
C Aster | A radial configuration of Fiber(s) built around a Solid
C Bundle | Set of Fiber held together using an fixed overlap
C Fake | Set of two asters held together by a Solid
C Nucleus | Organizer built around a Sphere
C Criteria | Holds a set of criteria to select Objects
►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 Exception | A mechanism to handle errors (see C++ manual)
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 FatLocus | Segment of a Fiber for steric interactions
C FatPoint | PointExact for steric interactions
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 FieldScalar | Scalar type (real) for a Field
C FieldVector< N > | Vector type for a Field containing N real scalars
►C FileWrapper | A wrapper around a C-FILE
C InputWrapper | Input with automatic binary/text mode and byte-swapping for cross-platform compatibility
C Messages | Control output file with different levels of verbosity
C OutputWrapper | Output with automatic binary/text mode and byte-swapping for cross-platform compatibility
C FrameReader | Class to read a particular frame in a trajectory file
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 Grid< ORD, CELL, INDEX > | Divide a rectangle of dimensionality ORD into regular voxels
C Grid< DIM, PointGridCell, unsigned > |
C Grid< DIM, SegmentList, unsigned int > |
►C Grid< DIM, VAL, unsigned int > |
C FieldBase< VAL > | Value of type VAL defined as a function of position over the simulation Space
►C HandMonitor | Base class to monitor and control Hand's actions
►C Couple | A set of two Hand linked by an elastic element
C Bridge | A specialized kind of Couple
C CoupleLong | A Couple with a non-zero resting length
►C Crosslink | A specialized kind of Couple
C CrosslinkLong | A Crosslink with a non-zero resting length
C Fork | A specialized kind of Couple
►C Shackle | A specialized kind of Couple
C ShackleLong | A Shackle with a non-zero resting length
►C Single | A point-like object containing one Hand
►C Picket | Single attached at a fixed position
C PicketLong | Picket with a non-zero resting length
►C Wrist | Single anchored to a Mecable
C WristLong | Wrist with a non-zero resting length
►C Interface | Cytosim Application Programming Interface
►C Parser | Cytosim Parser to read and execute config files
C SimThread | SimThread is used to run a simulation in a dedicated thread
►C Inventoried | Object that can be entered in a Inventory
►C Object | Parent class for all simulated objects
C Couple | A set of two Hand linked by an elastic element
C FieldBase< VAL > | Value of type VAL defined as a function of position over the simulation Space
C Mecable | Can be simulated using a Meca
C Organizer | Assemblage of Object
C Single | A point-like object containing one Hand
►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 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 Inventory | Attributes and remember serial-numbers to Inventoried
C KeyList< val_type >::key_value | Type for a key-value pair
C KeyList< val_type > | Stores a set of pairs ( string, values ). Used by Glossary::set()
C LineDisp | Display parameters for a Line
C SimThread::Lock |
►C Matrix | The interface for all the large matrices
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 MatrixBase< SZ > | Fortran-style matrices of small dimensions: 1, 2 and 3
►C MatrixBase< 1 > |
C Matrix1 |
►C MatrixBase< 2 > |
C Matrix2 |
►C MatrixBase< 3 > |
C Matrix3 |
C Meca | A class to calculate the motion of objects in Cytosim
►C Modulo | Used to implement periodic boundary conditions
C SpaceCylinderP | Cylinder of axis X that is periodic along X
C SpacePeriodic | Rectangular Space with periodic boundary conditions
C SpaceStrip | Rectangular Space with partial periodic boundary conditions
C Monitor | Records the number of iterations, and the convergence
►C Movable | Can be moved and rotated in space
C Object | Parent class for all simulated objects
C named_color | Holds the name and the RGBA components of a color
►C Node | Can be linked in a NodeList
►C FiberBinder | Location on a Fiber represented by an abscissa
►C Hand | Simulates the stochastic binding/unbinding of a FiberBinder
C Actor | A Hand that can act on a Fiber
C Cutter | A Hand that can cut a Fiber
C Mighty | A Hand that can move and do other things to a Fiber
C Motor | Hand that can move smoothly on a Fiber
C Nucleator | A Hand that can nucleate a Fiber
C Rescuer | A Hand that may rescue a shrinking fiber
C Slider | A Hand that will move on a Fiber passively with viscous resistance
C Tracker | A Hand that only binds near the end of a Fiber
C Object | Parent class for all simulated objects
C NodeList | Doubly linked list of Nodes
►C ObjectSet | A set of Object
C BeadSet | List of Bead
C CoupleSet | Set for Couple
C FiberSet | List of Fiber
C FieldSet | List of Field
C OrganizerSet | List of Organizer (Aster, Nucleus, Bundle)
C SingleSet | Set for Single
C SolidSet | List of Solid
C SpaceSet | List of Space
C SphereSet | List of Sphere
C Point2D | Structure to hold coordinate of point in 2D + misc
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 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 AsterProp | Property for Aster
C BeadProp | Property for Bead and Solid
C BundleProp | Property for Bundle
►C CoupleProp | Property for Couple
C BridgeProp | Additional Property for Bridge
C CrosslinkProp | Additional Property for Crosslink and CroslinkLong
C ForkProp | Additional Property for Fork
C ShackleProp | Additional Property for Shackle
C DisplayProp | Property for Play
C FakeProp | Property for a Fake
C FiberDisp | Display parameters for a class of Fiber
►C FiberProp | Property for a Fiber
C ClassicFiberProp | Additional Property for ClassicFiber
C DynamicFiberProp | Additional Property for DynamicFiber
C TreadmillingFiberProp | Additional Property for TreadmillingFiber
C TubuleProp | Additional Property for Tubule
C FieldProp | Property for Field
C glAppProp | Parameter set for glApp
►C HandProp | Property for Hand
C ActorProp | Additional Property for Actor
C CutterProp | Additional Property for Cutter
C MightyProp | Additional Property for Mighty
C MotorProp | Additional Property for Motor
C NucleatorProp | Additional Property for Nucleator
C RescuerProp | Additional Property for Rescuer
C SliderProp | Additional Property for Slider
C TrackerProp | Additional Property for Tracker
C NucleusProp | Property for Nucleus
C PlayProp | Property for Play
C PointDisp | Parameters necessary to display a point-like object
C SimulProp | Property for Simul
C SingleProp | Property for Single
C SpaceProp | Property for Space
C SphereProp | Property for Sphere
►C ViewProp | Properties needed to define a view
C View | Handles the viewing angle, projection and other aspects of an OpenGL display
C PropertyList | List of Property
C Quaternion< R > | Quaternion is similar to a complex number, but of dimension four
C Quaternion< real > |
C Random | Random Number Generator
C Simul | Simulator class
C SimThread::TryLock |
C TubuleBundle | Bundle of dynamic Microtubules
C Glossary::val_type | String-encoded value with a counter
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 Vertex | Point in 3D, with information for connectivity
C zObject | A display element with a depth coordinate