This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 12345]

CjLM.JupyterDisplay._Report
CABCMeta
CjLM.BaseTypes.SimObj
Clm::builder::bounding_box	The bounds for a shape represented as a rectangular box
CpySTDLM.CellArranger.CellArranger
CpySTDLM.CellArranger.LooseGridArranger
CpySTDLM.CellArranger.RandomArranger
CpySTDLM.CellArranger.RandomSphericalArranger
CpySTDLM.CellArranger.TightGridArranger
CpySTDLM.Cells.CellShape
CpySTDLM.Cells.BoxCell
CpySTDLM.Cells.CapsuleCell
CpySTDLM.Cells.CapsuleShellCell
CpySTDLM.Cells.SphereCell
CjLM.CME.CMESimulation	A CME simulation that contains reactions and species
CpyLM.CME.CMESimulation	A CME simulation that contains reactions and species
CjLM.ColorGen.ColorGen
Clm::main::ResourceAllocator::ComputeResources	A representation for the resources for a given node
CResourceAllocator::ComputeResources	A representation for the resources for a given node
CjLM.Solvers.ConstBoundaryConc
Clm::CUDA
Clm::main::DataOutputQueue	A queue class that writes out data in the order it is recieved
Clm::main::LocalDataOutputWorker	A class that handles output on a particular core
Clm::main::MPIRemoteDataOutputQueue	A DataOutputQueue that works for MPI jobs across various different nodes that outputs only on the "master" thread
Clm::main::DataOutputQueue::DataSet	A set of data in the form of bytes to be written to disk
Cdoxy2swig.Doxy2SWIG
Cstd::exception
Clm::Exception	Base class for exceptions
Clm::CUDADriverException
Clm::CUDAException
Clm::CommandLineArgumentException	Exception from a command line argument
Clm::IOException	Exception when input or output fails
Clm::InvalidArgException	Exception for an argument to a function
Clm::rdme::InvalidParticleException	InvalidArgException for when a particle is
Clm::rdme::InvalidSiteException	InvalidArgException for when an index into the lattice is out of bound or does not exist
Clm::MPIException	An Exception thrown when an MPI call fails
Clm::io::hdf5::HDF5Exception	Exception due to a failure in writing the HDF5 file
Clm::rdme::ParticleSizeException	Exception thrown when particle size constraints are violated
Clm::thread::PthreadException	An Exception class for handling pthread exceptions
CJD.FileJupyterMixin
CjLM.RDME.File
CjLM.RDMEExtended.FileExtended
CjLM.JupyterDisplay.FileJupyterMixin
CCMESolver::FPTTracking
Clm::cme::CMESolver::FPTTracking
Cgpu_info
Clm::rdme::gpu_worker_thread_int_params
Clm::rdme::gpu_worker_thread_params
CH5Lookup
CH5MetaData
Clogging.Handler
CjLM.LMLogger.NullHandler
CpyLM.LMLogger.NullHandler
CJD.JupyterDisplayMixin
CjLM.RDME.SpatialModel
CjLM.RDME.File
CjLM.RDME.Sim
CjLM.RDMEExtended.SimExtended
CjLM.RDMEExtended.SpatialModelExtended
CjLM.JupyterDisplay.JupyterDisplayMixin
Clm::cme::TwoStateHillSwitch::KHillPropensityArgs
CLattice	Base class for lattice type objects
Clm::rdme::ByteLattice	A Lattice that is based on packed bytes of memory, i.e. one byte per lattice site to hold particles
Clm::rdme::ByteLatticeExtended	Extended ByteLattice with particle size awareness
Clm::rdme::CudaByteLattice
Clm::rdme::CudaByteLatticeExtended	CUDA-accelerated extended ByteLattice with particle size awareness
Clm::rdme::IntLattice	A Lattice that is based on one particle per word, with sites strided per particle
Clm::rdme::CudaIntLattice
Clm::rdme::Lattice	Base class for lattice type objects
Clm::rdme::ByteLattice	A Lattice that is based on packed bytes of memory, i.e. one byte per lattice site to hold particles
Clm::rdme::IntLattice	A Lattice that is based on one particle per word, with sites strided per particle
Clattice_coord_t	Type to store a lattice coordinate
CAN.LatticeAnalysisMixin
CjLM.RDME.SpatialModel
CjLM.Analysis.LatticeAnalysisMixin
Clm::builder::LatticeBuilder	A class that defines regions of a lattice based on a set of geometries defined by shapes. It also allows packing different types of particles into different regions
CjLM.LmInteract.LmReadMixin
CLM.LmReadMixin
CjLM.RDME.File
CjLM.LmInteract.LmWriteMixin
CLM.LmWriteMixin
CjLM.RDME.Sim
Clm::builder::matrix	A matrix used for rotations
Clm::me::MESolver	An abstract base class for all Master Equation solvers, this is essentially a representation of "the simulation instance"
Clm::cme::CMESolver
Clm::cme::GillespieDSolver
Clm::cme::HillSwitch
Clm::cme::TwoStateExpression
Clm::cme::TwoStateHillLoopSwitch
Clm::cme::TwoStateHillSwitch
Clm::cme::NextReactionSolver
Clm::cme::FluctuatingNRSolver
Clm::cme::LacHillSwitch
Clm::cme::SelfRegulatingGeneSwitch
Clm::rdme::RDMESolver
Clm::rdme::IntMpdRdmeSolver
Clm::rdme::IntMpdRdmeSolverExtended
Clm::rdme::MGPUIntMpdRdmeSolver
Clm::rdme::MGPUMpdRdmeSolver
Clm::rdme::MPIMpdRdmeSolver
Clm::rdme::MpdRdmeSolver
Clm::MpdRdmeSolverExtended
Clm::rdme::MpdTestHarness
Clm::rdme::NextSubvolumeSolver
CMESolver	An abstract base class for all Master Equation solvers, this is essentially a representation of "the simulation instance"
Clm::cme::CMESolver
Clm::me::MESolverFactory	A factory object used to create Master Equation simulation instances
CMESolverFactory	A factory object used to create Master Equation simulation instances
Cmetaclass
CjLM.BaseTypes.SimObj
Clm::MPI	Handles the MPI capabilities and properties of the simulation
CMultiGPUMapper
CZDivMultiGPUMapper
CjLM.BaseTypes.Namespace
Cneighbor_buffer
Clm::cme::SelfRegulatingGeneSwitch::OUKHillPropensityArgs
Cparticle_loc_t	Type to store a particle and position
CpySTDLM.Distributions.ParticleGenerator
Clm::builder::LatticeBuilder::ParticlePlacement	A representation of a placement operation that needs to occur (i.e. where to place (siteType), what to place (particleType) and how many (count))
CjLM.ParticleSizeSupport.ParticleSizeError
Clm::rdme::ParticleSizeManager	Manages particle sizes and validates site occupancy constraints
CjLM.ParticleSizeSupport.ParticleSizeMixin
CjLM.RDMEExtended.FileExtended
CjLM.RDMEExtended.SimExtended
CjLM.RDMEExtended.SpatialModelExtended
CjLM.ParticleSizeSupport.ParticleSizeValidator
Clm::builder::point	Type to store a position in space
Clm::Print	Print messages to the console at varying levels of verbosity
CPrint	Print messages to the console at varying levels of verbosity
CCMESolver::PropensityArgs
Clm::cme::CMESolver::CompetitiveMMPropensityArgs
Clm::cme::CMESolver::FirstOrderPropensityArgs
Clm::cme::CMESolver::KHillPropensityArgs
Clm::cme::CMESolver::KHillTransportPropensityArgs
Clm::cme::CMESolver::MichaelisMentenPropensityArgs
Clm::cme::CMESolver::NoncompetitiveMMPropensityArgs
Clm::cme::CMESolver::SecondOrderPropensityArgs
Clm::cme::CMESolver::SecondOrderSelfPropensityArgs
Clm::cme::CMESolver::UncompetitiveMMPropensityArgs
Clm::cme::CMESolver::ZerothOrderHeavisidePropensityArgs
Clm::cme::CMESolver::ZerothOrderPropensityArgs
Clm::cme::CMESolver::PropensityArgs
Clm::cme::CMESolver::CompetitiveMMPropensityArgs
Clm::cme::CMESolver::FirstOrderPropensityArgs
Clm::cme::CMESolver::KHillPropensityArgs
Clm::cme::CMESolver::KHillTransportPropensityArgs
Clm::cme::CMESolver::MichaelisMentenPropensityArgs
Clm::cme::CMESolver::NoncompetitiveMMPropensityArgs
Clm::cme::CMESolver::SecondOrderPropensityArgs
Clm::cme::CMESolver::SecondOrderSelfPropensityArgs
Clm::cme::CMESolver::UncompetitiveMMPropensityArgs
Clm::cme::CMESolver::ZerothOrderHeavisidePropensityArgs
Clm::cme::CMESolver::ZerothOrderPropensityArgs
CPropensityArgs
Clm::cme::FluctuatingNRSolver::OUPropensityArgs
Clm::rng::RandomGenerator	Base class for random number generators in Lattice Microbes
Clm::rng::XORShift	A random number generator that works for a grid based on the index
Clm::rng::XORWow
CRandomGenerator	Base class for random number generators in Lattice Microbes
Clm::rng::XORShift	A random number generator that works for a grid based on the index
Clm::rng::XORWow
CpyLM.RDME.RDMERegion
CpyLM.RDME.RDMESimulation
CpyLM.RDME.IntRDMESimulation
Clm::reaction::ReactionQueue::ReactionEvent	Definition of a reaction event with the time to reaction and the propensity for the reaction to occur
CReactionQueue::ReactionEvent	Definition of a reaction event with the time to reaction and the propensity for the reaction to occur
Clm::reaction::ReactionQueue	A queue that contains information on reaction events
CReactionQueue	A queue that contains information on reaction events
CjLM.RegionBuilder.RegionBuilder
Clm::io::hdf5::SimulationFile::ReplicateHandles	A handle for the different replicates that may be stored in the HDF5 file
CSimulationFile::ReplicateHandles	A handle for the different replicates that may be stored in the HDF5 file
Clm::main::ResourceAllocator	An object that tracks the available resources for the main simulation runner
CResourceAllocator	An object that tracks the available resources for the main simulation runner
CsegmentDescriptor
Clm::builder::Shape	Abstract base class for all the shapes in Lattice Microbes simulation builder
Clm::builder::Capsule	A Shape representing a cylinder with hemispherical ends
Clm::builder::CapsuleShell	A capsule shell Shape with a hollow inside
Clm::builder::Cone	A Shape that represents a Cone
Clm::builder::Cuboid	A cube-like Shape
Clm::builder::Cylinder	A Shape representing a cylinder
Clm::builder::Difference	A Shape that represents a Difference between the first and second object
Clm::builder::Ellipse
Clm::builder::Hemisphere	A hemisphere Shape
Clm::builder::Intersection	A Shape that represents a Intersection of two shapes
Clm::builder::Mesh	A Shape that represents a mesh
Clm::builder::Sphere	A Shape that represents a Sphere
Clm::builder::Torus	A Shape that represents a Torus
Clm::builder::Union	A Shape that represents a Union between two shapes
Clm::builder::UnionSet	A Shape that represents a Union of many shapes
CBT.SimObj
CjLM.Types.DiffusionConst
CjLM.Types.RateConst
CjLM.Types.Reaction
CjLM.Types.BuilderReaction
CjLM.Types.Region
CjLM.Types.BuilderRegion
CjLM.Types.TrajRegion
CjLM.Types.Species
CjLM.Types.BuilderSpecies
CjLM.Types.TrajSpecies
CjLM.BaseTypes.SimObjs
Clm::io::hdf5::SimulationFile	A representation of the simulation that is used to input or output from an HDF5 file
CSimulationFile	A representation of the simulation that is used to input or output from an HDF5 file
Clm::io::SimulationParameters
CCMESolver::SpeciesLimit
Clm::cme::CMESolver::SpeciesLimit
CjLM.ImageAnalysis.SvgContext
Clm::thread::Thread	A base class wrapping pthreads
Clm::thread::Worker	An actual worker Thread that runs a simulation replicate
Clm::main::CheckpointSignaler	A type of worker thread that checkpoints at a specified interval
Clm::main::LocalDataOutputWorker	A class that handles output on a particular core
Clm::main::ReplicateRunner	A thread that launches all the various replicates requested
Clm::main::SignalHandler	A thread safe Worker thread type that captures SIG* type signals over the various threads
CCMESolver::TrackedParameter
Clm::cme::CMESolver::TrackedParameter
CAN.TrajAnalysisMixin
CjLM.RDME.File
CjLM.Analysis.TrajAnalysisMixin
Clm::builder::vector	A vector which points in a direction
Clm::thread::WorkerManager	A singleton manager that creates and manages workers that run on a processing node
CWorkerManager	A singleton manager that creates and manages workers that run on a processing node
CZDivMPIGPUMapper