bio::chemical Namespace Reference

Classes
class	AbstractMotif
class	Atom
class	Axis
class	Bond
class	Class
class	Element
class	Elementary
class	ExcitationBase
class	ExcitationWithArgument
class	ExcitationWithoutArgument
class	ExcitationWithTwoArguments
class	LinearMotif
class	LinearStructureInterface
class	PeriodicTableImplementation
class	Products
class	Reactant
class	Reactants
class	Reaction
class	Structure
class	Substance
class	Symmetry
class	UnorderedMotif
class	UnorderedStructureInterface

Typedefs
typedef uint16_t	AtomicNumber
typedef physical::Arrangement< Bond * >	Bonds
typedef std::vector< Substance * >	Substances
typedef Index	Valence

Functions
	BIO_PERSPECTIVE_SINGLETON (ReactionPerspective, StandardDimension) class Substance

Typedef Documentation

AtomicNumber

typedef uint16_t bio::chemical::AtomicNumber

The AtomicNumber tracks class definitions. The StandardDimension can be used to track object configurations as well class definitions, so there is some overlap. However, the AtomicNumber should only ever have 1 Perspective: the PeriodicTable. See PeriodicTable.h for more info

Definition at line 72 of file Types.h.

Bonds

typedef physical::Arrangement< Bond* > bio::chemical::Bonds

Definition at line 127 of file Bond.h.

Substances

typedef std::vector< Substance* > bio::chemical::Substances

Definition at line 79 of file Types.h.

Valence

typedef Index bio::chemical::Valence

Valence defines how many Bonds an Atom (e.g. Substance) can have. The max of valence is essentially the max number of parents a child class can have. Valence can be any size up to the size of Index (used by physical::Arrangements). For now, we set Valence to the max possible size and may optimize later.

Definition at line 65 of file Types.h.

Function Documentation

BIO_PERSPECTIVE_SINGLETON()

bio::chemical::BIO_PERSPECTIVE_SINGLETON	(	ReactionPerspective	,
		StandardDimension
	)