| CAllocator | Allocates vectors of real |
| CAllot< VAL > | Allot manages a piece of memory |
| CAllot< real > | |
| CArray< VAL > | Dynamic array of VAL |
| CArray< AsterClamp > | |
| CArray< FatLocus > | |
| CArray< FatPoint > | |
| CArray< FiberLocus > | |
| CArray< Mecable * > | |
| CArray< Single * > | |
| CAsterClamp | Defines a connection between Solid and Fiber |
| ►CBuddy | Maintains mutual relationship between objects |
| ►CMecable | Can be simulated using a Meca |
| CBead | A single point with a radius |
| ►CPointSet | Array of points describing a physical object |
| ►CFiberNaked | Mecable with linear geometry |
| ►CRigidFiber | Incompressible FiberNaked with bending elasticity |
| ►CFiber | FiberNaked to which FiberBinder may bind |
| CClassicFiber | A Fiber with a standard two-state model of dynamic instability at the PLUS_END |
| CDynamicFiber | A Fiber with discrete growth and dynamic instability at the PLUS_END |
| CTreadmillingFiber | A Fiber with assembly at both ends |
| CTubule | Adds dynamic instability (growth/shrinkage of the ends) to a Fiber |
| CSolid | Undeformable cloud of points |
| CSphere | Spherical object with a viscous surface |
| ►COrganizer | Assemblage of Object |
| CAster | A radial configuration of Fiber(s) built around a Solid |
| CBundle | Set of Fiber held together using an fixed overlap |
| CFake | Set of two asters held together by a Solid |
| CNucleus | Organizer built around a Sphere |
| CCriteria | Holds a set of criteria to select Objects |
| ►CDisplay | Base class to display Cytosim state using OpenGL |
| CDisplay1 | Cytosim display class - style 1 |
| CDisplay2 | Cytosim display class - style 2 |
| CDisplay3 | Cytosim display class - style 3 |
| ►CException | A mechanism to handle errors (see C++ manual) |
| CInvalidIO | InvalidIO is thrown during file Input/Output |
| CInvalidParameter | This class is thrown if a parameter value is invalid |
| CInvalidSyntax | InvalidSyntax is thrown while parsing config file |
| CFatLocus | Segment of a Fiber for steric interactions |
| CFatPoint | PointExact for steric interactions |
| CFiberGrid | Divide-and-Conquer method to find all FiberLocus located near a given point in space |
| CFiberLocus | Represents the segment between two consecutive points of a Fiber |
| CFieldScalar | Scalar type (real) for a Field |
| CFieldVector< N > | Vector type for a Field containing N real scalars |
| ►CFileWrapper | A wrapper around a C-FILE |
| CInputWrapper | Input with automatic binary/text mode and byte-swapping for cross-platform compatibility |
| CMessages | Control output file with different levels of verbosity |
| COutputWrapper | Output with automatic binary/text mode and byte-swapping for cross-platform compatibility |
| CFrameReader | Class to read a particular frame in a trajectory file |
| Cgle_color_float | RGBA (Red, Green, Blue, Alpha) color, with one float in [0,1] per component |
| Cgle_color_int | RGBA (Red, Green, Blue, Alpha) color, with one byte per component |
| CGlossary | Glossary holds a list of (key, values) where both key and values are strings |
| CGrid< ORD, CELL, INDEX > | Divide a rectangle of dimensionality ORD into regular voxels |
| CGrid< DIM, PointGridCell, unsigned > | |
| CGrid< DIM, SegmentList, unsigned int > | |
| ►CGrid< DIM, VAL, unsigned int > | |
| CFieldBase< VAL > | Value of type VAL defined as a function of position over the simulation Space |
| ►CHandMonitor | Base class to monitor and control Hand's actions |
| ►CCouple | A set of two Hand linked by an elastic element |
| CBridge | A specialized kind of Couple |
| CCoupleLong | A Couple with a non-zero resting length |
| ►CCrosslink | A specialized kind of Couple |
| CCrosslinkLong | A Crosslink with a non-zero resting length |
| CFork | A specialized kind of Couple |
| ►CShackle | A specialized kind of Couple |
| CShackleLong | A Shackle with a non-zero resting length |
| ►CSingle | A point-like object containing one Hand |
| ►CPicket | Single attached at a fixed position |
| CPicketLong | Picket with a non-zero resting length |
| ►CWrist | Single anchored to a Mecable |
| CWristLong | Wrist with a non-zero resting length |
| ►CInterface | Cytosim Application Programming Interface |
| ►CParser | Cytosim Parser to read and execute config files |
| CSimThread | SimThread is used to run a simulation in a dedicated thread |
| ►CInventoried | Object that can be entered in a Inventory |
| ►CObject | Parent class for all simulated objects |
| CCouple | A set of two Hand linked by an elastic element |
| CFieldBase< VAL > | Value of type VAL defined as a function of position over the simulation Space |
| CMecable | Can be simulated using a Meca |
| COrganizer | Assemblage of Object |
| CSingle | A point-like object containing one Hand |
| ►CSpace | Defines the spatial constrains in cytosim |
| CSpaceCapsule | Spherocylinder (cylinder capped with hemispheres) |
| CSpaceCylinder | Cylinder of axis X |
| CSpaceCylinderP | Cylinder of axis X that is periodic along X |
| CSpaceCylinderZ | Cylinder of axis Z |
| CSpaceDice | A rectangle ( or a cube ) with rounded edges |
| CSpaceEllipse | Ellipse in 2D, ellipsoid or spheroid in 3D |
| CSpacePeriodic | Rectangular Space with periodic boundary conditions |
| CSpacePolygon | Polygonal convex region in space |
| CSpaceSphere | Sphere centered at the origin |
| CSpaceSquare | Rectangular region |
| CSpaceStrip | Rectangular Space with partial periodic boundary conditions |
| CSpaceTorus | Bent cylinder of constant diameter terminated by hemispheric caps |
| CInventory | Attributes and remember serial-numbers to Inventoried |
| CKeyList< val_type >::key_value | Type for a key-value pair |
| CKeyList< val_type > | Stores a set of pairs ( string, values ). Used by Glossary::set() |
| CLineDisp | Display parameters for a Line |
| CSimThread::Lock | |
| ►CMatrix | The interface for all the large matrices |
| CMatrixSparse | Real (non-symmetric) sparse Matrix |
| CMatrixSparseBandSymmetric | Sparse real symmetric Matrix, with a variable number of full diagonals |
| CMatrixSparseSymmetric | Real symmetric sparse Matrix |
| CMatrixSparseSymmetric1 | Real symmetric sparse Matrix, with optimized multiplication |
| CMatrixSymmetric | A real symmetric Matrix |
| CMatrixBase< SZ > | Fortran-style matrices of small dimensions: 1, 2 and 3 |
| ►CMatrixBase< 1 > | |
| CMatrix1 | |
| ►CMatrixBase< 2 > | |
| CMatrix2 | |
| ►CMatrixBase< 3 > | |
| CMatrix3 | |
| CMeca | A class to calculate the motion of objects in Cytosim |
| ►CModulo | Used to implement periodic boundary conditions |
| CSpaceCylinderP | Cylinder of axis X that is periodic along X |
| CSpacePeriodic | Rectangular Space with periodic boundary conditions |
| CSpaceStrip | Rectangular Space with partial periodic boundary conditions |
| CMonitor | Records the number of iterations, and the convergence |
| ►CMovable | Can be moved and rotated in space |
| CObject | Parent class for all simulated objects |
| Cnamed_color | Holds the name and the RGBA components of a color |
| ►CNode | Can be linked in a NodeList |
| ►CFiberBinder | Location on a Fiber represented by an abscissa |
| ►CHand | Simulates the stochastic binding/unbinding of a FiberBinder |
| CActor | A Hand that can act on a Fiber |
| CCutter | A Hand that can cut a Fiber |
| CMighty | A Hand that can move and do other things to a Fiber |
| CMotor | Hand that can move smoothly on a Fiber |
| CNucleator | A Hand that can nucleate a Fiber |
| CRescuer | A Hand that may rescue a shrinking fiber |
| CSlider | A Hand that will move on a Fiber passively with viscous resistance |
| CTracker | A Hand that only binds near the end of a Fiber |
| CObject | Parent class for all simulated objects |
| CNodeList | Doubly linked list of Nodes |
| ►CObjectSet | A set of Object |
| CBeadSet | List of Bead |
| CCoupleSet | Set for Couple |
| CFiberSet | List of Fiber |
| CFieldSet | List of Field |
| COrganizerSet | List of Organizer (Aster, Nucleus, Bundle) |
| CSingleSet | Set for Single |
| CSolidSet | List of Solid |
| CSpaceSet | List of Space |
| CSphereSet | List of Sphere |
| CPoint2D | Structure to hold coordinate of point in 2D + misc |
| CPointExact | Indicates a point of interest in a Mecable |
| CPointGrid | Divide-and-Conquer to implement steric interactions |
| CPointGridCell | Few lists associated with the same location |
| CPointGridParam | Contains the stiffness parameters for the steric engine |
| CPointInterpolated | Indicates an intermediate position between two points of a PointSet |
| CPointsOnSphere | Distribute points on the unit sphere, minimizing the 'electrostatic' energy |
| ►CProperty | A Property holds the parameters for a particular kind of objects |
| CAsterProp | Property for Aster |
| CBeadProp | Property for Bead and Solid |
| CBundleProp | Property for Bundle |
| ►CCoupleProp | Property for Couple |
| CBridgeProp | Additional Property for Bridge |
| CCrosslinkProp | Additional Property for Crosslink and CroslinkLong |
| CForkProp | Additional Property for Fork |
| CShackleProp | Additional Property for Shackle |
| CDisplayProp | Property for Play |
| CFakeProp | Property for a Fake |
| CFiberDisp | Display parameters for a class of Fiber |
| ►CFiberProp | Property for a Fiber |
| CClassicFiberProp | Additional Property for ClassicFiber |
| CDynamicFiberProp | Additional Property for DynamicFiber |
| CTreadmillingFiberProp | Additional Property for TreadmillingFiber |
| CTubuleProp | Additional Property for Tubule |
| CFieldProp | Property for Field |
| CglAppProp | Parameter set for glApp |
| ►CHandProp | Property for Hand |
| CActorProp | Additional Property for Actor |
| CCutterProp | Additional Property for Cutter |
| CMightyProp | Additional Property for Mighty |
| CMotorProp | Additional Property for Motor |
| CNucleatorProp | Additional Property for Nucleator |
| CRescuerProp | Additional Property for Rescuer |
| CSliderProp | Additional Property for Slider |
| CTrackerProp | Additional Property for Tracker |
| CNucleusProp | Property for Nucleus |
| CPlayProp | Property for Play |
| CPointDisp | Parameters necessary to display a point-like object |
| CSimulProp | Property for Simul |
| CSingleProp | Property for Single |
| CSpaceProp | Property for Space |
| CSphereProp | Property for Sphere |
| ►CViewProp | Properties needed to define a view |
| CView | Handles the viewing angle, projection and other aspects of an OpenGL display |
| CPropertyList | List of Property |
| CQuaternion< R > | Quaternion is similar to a complex number, but of dimension four |
| CQuaternion< real > | |
| CRandom | Random Number Generator |
| CSimul | Simulator class |
| CSimThread::TryLock | |
| CTubuleBundle | Bundle of dynamic Microtubules |
| CGlossary::val_type | String-encoded value with a counter |
| CVector1 | Vector1 is a vector with 1 real component |
| CVector2 | Vector2 is a vector with 2 real components |
| CVector3 | Vector3 is a vector with 3 real components |
| CVertex | Point in 3D, with information for connectivity |
| CzObject | A display element with a depth coordinate |
1.8.9.1 
