NFcore Namespace Reference

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Detailed Description

Contains the primary classes and functions of NFsim.

This namespace contains all the basic components needed for a typical simulation in NFsim. The main classes are defined in the NFcore.hh header file for convenience, but the actual definitions are in the appropriately named cpp files. Additional classes in the NFcore namespace for handling reactions, functions, modules, and other features are spread throughout the code. When developing NFsim, it is advisable to work in this namespace if you are working on core NFsim functionality. If, instead, you are merely putting in an add on or manipulating a System, you should create a new namespace.

Author:

Michael Sneddon

Classes
class	MoleculeList
	Keeps a set of molecules neatly for a MoleculeType. More...
class	ComplexList
	Container to organize all system complexes. More...
class	System
	The main class that begins and runs simulations. More...
class	MoleculeType
	Keeps track of the types of molecules that can exist. More...
class	Molecule
	Each molecule in the system is represented by an instance of this. More...
class	ReactionClass
	Abstract Base Class that defines the interface for all reaction rules. More...
class	Complex
	Container to dynamically keep track of all system complexes. More...
class	Observable
	Tracks the counts of predefined observables in the simulation. More...
class	MoleculesObservable
class	SpeciesObservable
class	ReactionSelector
class	DirectSelector
class	LogClassSelector
class	TemplateMolecule
	Used for matching Molecule objects to the given pattern. More...
class	FuncFactory
	Parses mathmatical functions that can be easily used anywhere. More...
class	GlobalFunction
	Defines functions to be used globally in a simulation. More...
class	FunctionReference
class	StateCounter
class	LocalFunction
class	CompositeFunction
class	Outputter
class	DumpSystem
	Class for outputting the state of the system. More...
class	Mapping
	Keeps a pointer to a molecule and remembers a single component to act on. More...
class	MapGenerator
	Knows how to assign mappings in a MappingSet to a particular Molecule. More...
class	MappingSet
	Keeps a list of mappings needed by a particular list of reactants. More...
class	ReactantContainer
	Interface for all containers of Reactants (MappingSets) needed by ReactionClasses. More...
class	ReactantList
	Maintains a list of MappingSets needed by ReactionClass. More...
class	ReactantTree
	Maintains a tree of MappingSets needed by Distribution of Rates Reactions. More...
class	BasicRxnClass
class	FunctionalRxnClass
class	MMRxnClass
class	DORRxnClass
class	SpeciesCreator
class	TransformationFactory
class	Transformation
class	LocalFunctionReference
class	EmptyTransform
class	StateChangeTransform
class	BindingTransform
class	BindingSeparateComplexTransform
class	UnbindingTransform
class	AddMoleculeTransform
class	RemoveMoleculeTransform
class	IncrementStateTransform
class	DecrementStateTransform
class	TransformationSet
	Maintains a set of Transformation objects for a ReactionClass. More...
Functions
void	test ()
void	test_tree ()
void	test_simple ()

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Function Documentation

void NFcore::test

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Function used for initial testing of the entire "mapping" construct including MappingSets, TransformationSets, ReactantLists, etc.

Author:

Michael Sneddon

void NFcore::test_simple

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Some very simple initial testing and debugging of ReactantLists and the rest of the mapping functions unter NFreactions

Author:

Michael Sneddon

void NFcore::test_tree

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