pyLM  v1.1
A Python Problem Solving Environment for the simulation of stochastic biological systems
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123]
oNpeekFile
oNpyLMThe problem solving environement which interfaces to Lattice Microbes simulation software
|oNCME
||\CCMESimulationA CME simulation that contains reactions and species
|oNipyInterface
|oNLMLogger
||\CNullHandler
|oNRDME
||oCCMESimulationA CME simulation that contains reactions and species
||oCRDMERegionA class that represents a type region of an RDME simulation
||\CRDMESimulationA class that contains all regions, reactions, diffusions and rules for a RDME simulation
|\Nunits
\NpySTDLMA standard library of functionality that is commonly used in biological simulations
 oNCellArranger
 |oCCellArrangerA base class for laying out cells in a 3D space
 |oCRandomArrangerAn arranger that randomly orients a number of cells in a regin until either a count or a volume fraction target is met
 |oCRandomSphericalArrangerAn arranger that randomly orients a number of cells in a sphere inside a regin until either a count or a volume fraction target is met
 |oCTightGridArrangerAn arranger that orients cells in square grid
 |\CLooseGridArrangerAn arranger that orients cells in square grid with padding in between
 oNCells
 |oCCellShapeBase class for a particular cell type for use in CellArranger (and later more)
 |oCSphereCellA representation for a spherical cell
 |oCBoxCellA representation for a spherical cell
 |oCCapsuleCellA representation for a spherical cell
 |\CCapsuleShellCellA representation for a spherical cell
 oNDistributions
 |\CParticleGeneratorA particle generator that adds particles to a particular region of a simulation
 oNFitting
 |oCComparator
 |oCMomentComparator
 |oCTraceComparator
 |oCFitter
 |oCSweepFitter
 |\CSimulatedAnnealingFitter
 oNNetworkVisualization
 oNOnTheFly
 oNPostProcessing
 oNSBMLReader
 oNStandardCells
 oNStandardReactions
 \NStandardReactionSystems