#include <Symmetry.h>

Inheritance diagram for bio::chemical::Symmetry:

Collaboration diagram for bio::chemical::Symmetry:

Public Member Functions
	Symmetry (Name name, SymmetryType type)

	Symmetry (StandardDimension id, Name type)

	Symmetry (StandardDimension id, SymmetryType type)

virtual	~Symmetry ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, Symmetry) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical

&	physical::SymmetryPerspective::Instance ()) Symmetry(Name name

Public Member Functions inherited from bio::physical::Symmetry
	Symmetry (Name name, Name type)

	Symmetry (Name name, Name type)

	Symmetry (Name name, SymmetryType type)

	Symmetry (Name name, SymmetryType type)

	Symmetry (StandardDimension id, Name type)

	Symmetry (StandardDimension id, SymmetryType type)

virtual	~Symmetry ()

virtual	~Symmetry ()

virtual ByteStream *	AccessValue ()

	AddSymmetry (Symmetry *symmetry)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Symmetry) Symmetry()

Name	GetType () const

const Identifiable< SymmetryType > &	GetType () const

virtual const ByteStream &	GetValue () const

void	SetType (Name type)

void	SetType (SymmetryType type)

	SetValue (const ByteStream &bytes)

virtual void	SetValue (const ByteStream &bytes)

Public Member Functions inherited from bio::physical::Identifiable< SymmetryType >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Identifiable< SymmetryType >) explicit Identifiable(Perspective< SymmetryType > *perspective

void	CloneIntoName (Name name)

Public Member Functions inherited from bio::physical::Observer< Perspective< SymmetryType > >
	Observer (const Observer &other)

	Observer (Perspective *perspective=NULL)

virtual	~Observer ()

virtual Perspective *	GetPerspective () const

virtual void	SetPerspective (Perspective *perspective)

Public Member Functions inherited from bio::physical::Class< Identifiable< SymmetryType > >
	Class (Identifiable< SymmetryType > object, Symmetry symmetry=NULL)

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Identifiable< SymmetryType > *	Convert (Wave *wave)

virtual	operator Identifiable< SymmetryType > * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::physical::Wave
	Wave (Symmetry *symmetry=NULL)

virtual	~Wave ()

virtual chemical::Atom *	AsAtom ()

virtual const chemical::Atom *	AsAtom () const

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Code	Attenuate (const Wave *other)

virtual Wave *	Clone () const

virtual Wave *	Demodulate ()

virtual const Wave *	Demodulate () const

virtual Code	Disattenuate (const Wave *other)

virtual Properties	GetProperties () const

virtual Wave *	Modulate (Wave *signal)

virtual Wave *	operator* ()

virtual const Wave *	operator* () const

virtual Wave *	operator* (Wave *signal)

virtual void	operator+ (const Wave *other)

virtual void	operator- (const Wave *other)

virtual void	operator\| (Symmetry *symmetry)

virtual Code	Reify (Symmetry *symmetry)

virtual Symmetry *	Spin () const

Public Member Functions inherited from bio::physical::Identifiable< StandardDimension >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective

void	CloneIntoName (Name name)

Public Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
	Observer (const Observer &other)

	Observer (Perspective *perspective=NULL)

virtual	~Observer ()

virtual Perspective *	GetPerspective () const

virtual void	SetPerspective (Perspective *perspective)

Public Member Functions inherited from bio::physical::Class< Identifiable< StandardDimension > >
	Class (Identifiable< StandardDimension > object, Symmetry symmetry=NULL)

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Identifiable< StandardDimension > *	Convert (Wave *wave)

virtual	operator Identifiable< StandardDimension > * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::chemical::LinearMotif< Symmetry * >
	LinearMotif (const Contents contents, physical::Perspective< StandardDimension > perspective=NULL)

	LinearMotif (const LinearMotif< Symmetry * > &toCopy)

	LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)

virtual	~LinearMotif ()

virtual Symmetry *	AddImplementation (Symmetry * content)

virtual Code	Attenuate (const physical::Wave *other)

	BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Symmetry * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical

virtual void	ClearImplementation ()

virtual Symmetry *	CreateImplementation (StandardDimension id)

virtual Code	Disattenuate (const physical::Wave *other)

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual Symmetry *	GetByIdImplementation (StandardDimension id)

virtual const Symmetry *	GetByIdImplementation (StandardDimension id) const

virtual Symmetry *	GetByNameImplementation (Name name)

virtual const Symmetry *	GetByNameImplementation (Name name) const

virtual Symmetry *	GetOrCreateByIdImplementation (StandardDimension id)

virtual Symmetry *	GetOrCreateByNameImplementation (Name name)

virtual std::string	GetStringFromImplementation (std::string separator=", ")

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

const physical::Perspective< StandardDimension > *	GetStructuralPerspective () const

virtual bool	HasImplementation (const Symmetry * &content) const

virtual void	ImportImplementation (const LinearMotif< Symmetry * > *other)

virtual Code	InsertImplementation (Symmetry * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Symmetry * > >
	Elementary ()

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

Public Member Functions inherited from bio::chemical::Class< LinearMotif< Symmetry * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Symmetry * >) Class(LinearMotif< Symmetry * > *object

Public Member Functions inherited from bio::log::Writer
	Writer (Engine *logEngine, Filter logFilter)

virtual	~Writer ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Writer) Writer()

void	ExternalLog (Filter logFilter, Level level, const char *format,...) const

Engine *	GetLogEngine ()

const Engine *	GetLogEngine () const

bool	HasLogEngine () const

virtual void	SetLogEngine (Engine *logEngine)

Public Member Functions inherited from bio::physical::Filterable
	Filterable (Filter filter)

virtual	~Filterable ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Filterable) Filterable()

Filter	GetFilter () const

virtual void	InitializeImplementation (ByteStreams args)

virtual Code	Reify (Symmetry *symmetry)

virtual void	SetFilter (Filter filter)

virtual Symmetry *	Spin () const

Public Member Functions inherited from bio::physical::Class< Filterable >
	Class (Filterable object, Symmetry symmetry=NULL)

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Filterable *	Convert (Wave *wave)

virtual	operator Filterable * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::physical::Class< Writer >
	Class (Writer object, Symmetry symmetry=NULL)

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Writer *	Convert (Wave *wave)

virtual	operator Wave * ()

virtual	operator Writer * ()

Public Member Functions inherited from bio::chemical::Atom
	Atom (const Atom &other)

virtual	~Atom ()

template<typename T >
T	As ()

template<typename T >
const T	As () const

template<typename T >
T	AsBonded ()

template<typename T >
const T	AsBonded () const

template<typename T >
T	AsBondedQuantum ()

template<typename T >
const T	AsBondedQuantum () const

virtual Code	Attenuate (const Wave *other)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Atom) explicit Atom()

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

virtual Code	Disattenuate (const Wave *other)

template<typename T >
bool	FormBond (T toBond, BondType type=bond_type::Unknown())

Bonds *	GetAllBonds ()

const Bonds *	GetAllBonds () const

Wave *	GetBonded (Valence position)

const Wave *	GetBonded (Valence position) const

template<typename T >
Valence	GetBondPosition () const

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (Name typeName) const

template<typename T >
BondType	GetBondType () const

BondType	GetBondType (Valence position) const

template<typename T >
	operator T ()

virtual Code	Reify (physical::Symmetry *symmetry)

virtual physical::Symmetry *	Spin () const

Public Member Functions inherited from bio::physical::Class< Atom >
	Class (Atom object, Symmetry symmetry=NULL)

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Atom *	Convert (Wave *wave)

virtual	operator Atom * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::chemical::UnorderedMotif< Symmetry * >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< Symmetry * > *toCopy)

virtual	~UnorderedMotif ()

virtual Symmetry *	AddImplementation (const Symmetry * content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Symmetry * >) UnorderedMotif()

virtual void	ClearImplementation ()

virtual unsigned long	GetCountImplementation () const

virtual unsigned int	GetNumMatchingImplementation (const Container *other) const

virtual std::string	GetStringFromImplementation (std::string separator=", ")

virtual bool	HasAllImplementation (const Container *contents) const

virtual bool	HasImplementation (const Symmetry * content) const

virtual void	ImportImplementation (const UnorderedMotif< Symmetry * > *other)

virtual Symmetry *	RemoveImplementation (const Symmetry * content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Symmetry * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Symmetry * >) Class(UnorderedMotif< Symmetry * > *object

Public Member Functions inherited from bio::chemical::AbstractMotif
	AbstractMotif ()

virtual	~AbstractMotif ()

virtual void	ClearImplementation ()

virtual Container *	GetAllImplementation ()

virtual const Container *	GetAllImplementation () const

virtual unsigned long	GetCountImplementation () const

virtual std::string	GetStringFromImplementation (std::string separator=", ")

virtual void	ImportImplementation (const void *other)

Public Member Functions inherited from bio::chemical::Class< Symmetry >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Symmetry) Class(Symmetry *object

Public Member Functions inherited from bio::chemical::Structure
	Structure ()

virtual	~Structure ()

Public Member Functions inherited from bio::chemical::UnorderedStructureInterface
	UnorderedStructureInterface ()

virtual	~UnorderedStructureInterface ()

template<typename T >
T	Add (const T t)

template<typename T >
void	Clear ()

template<typename T >
Container *	GetAll ()

template<typename T >
const Container *	GetAll () const

template<typename T >
std::vector< T >	GetAllAsVector ()

template<typename T >
const std::vector< T >	GetAllAsVector () const

template<typename T >
unsigned long	GetCount () const

template<typename T >
unsigned int	GetNumMatching (const Container *other) const

template<typename T >
std::string	GetStringFrom (std::string separator=", ")

template<typename T >
bool	Has (T content) const

template<typename T >
bool	HasAll (const Container *contents) const

template<typename T >
void	Import (const std::vector< T > &other)

template<typename T >
void	Import (const UnorderedMotif< T > *other)

Code	ImportAll (const physical::Wave *other)

template<typename T >
T	Remove (const T t)

Public Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

virtual	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

Public Member Functions inherited from bio::chemical::LinearStructureInterface
	LinearStructureInterface ()

virtual	~LinearStructureInterface ()

template<typename T >
Emission	ForEach (ExcitationBase *excitation)

template<typename T >
T	GetById (StandardDimension id)

template<typename T >
const T	GetById (StandardDimension id) const

template<typename T >
T	GetByName (Name name)

template<typename T >
const T	GetByName (Name name) const

template<typename T >
T	GetOrCreateById (StandardDimension id)

template<typename T >
T	GetOrCreateByName (Name name)

template<typename T >
Code	Insert (T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

Public Attributes
	Symmetry

Name	type

Public Attributes inherited from bio::physical::Identifiable< SymmetryType >
Id	m_id

Public Attributes inherited from bio::physical::Identifiable< StandardDimension >
Id	m_id

Public Attributes inherited from bio::chemical::LinearMotif< Symmetry * >
physical::Perspective< StandardDimension > *	m_perspective

Public Attributes inherited from bio::chemical::Class< LinearMotif< Symmetry * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Symmetry * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< Symmetry >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Additional Inherited Members
Public Types inherited from bio::physical::Identifiable< SymmetryType >
typedef SymmetryType	Id

typedef std::vector< Id >	Ids

Public Types inherited from bio::physical::Observer< Perspective< SymmetryType > >
typedef Perspective< SymmetryType >	Perspective

Public Types inherited from bio::physical::Identifiable< StandardDimension >
typedef StandardDimension	Id

typedef std::vector< Id >	Ids

Public Types inherited from bio::physical::Observer< Perspective< StandardDimension > >
typedef Perspective< StandardDimension >	Perspective

Public Types inherited from bio::chemical::LinearMotif< Symmetry * >
typedef physical::Line	Contents

Public Types inherited from bio::chemical::UnorderedMotif< Symmetry * >
typedef physical::Arrangement< Symmetry * >	Contents

Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (const Wave *wave, const Properties &properties)

static Properties	GetResonanceBetween (const Wave wave1, const Wave wave2)

static Properties	GetResonanceBetween (ConstWaves waves)

Static Public Member Functions inherited from bio::chemical::LinearMotif< Symmetry * >
static LinearMotif< Symmetry * > Properties	GetClassProperties ()

Static Public Member Functions inherited from bio::chemical::AbstractMotif
static Properties	GetClassProperties ()

Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Symmetry * > >
static bool	hasRegistered

Protected Member Functions inherited from bio::physical::Observer< Perspective< SymmetryType > >
virtual void	InitializeImplementation (ByteStreams args)

Protected Member Functions inherited from bio::VirtualBase
	VirtualBase ()

virtual	~VirtualBase ()

void	Initialize (ByteStream arg1)

void	Initialize (ByteStream arg1, ByteStream arg2)

void	Initialize (ByteStream arg1, ByteStream arg2, ByteStream arg3)

void	Initialize (ByteStreams args)

virtual void	InitializeImplementation (ByteStreams args)=0

Protected Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
virtual void	InitializeImplementation (ByteStreams args)

Protected Member Functions inherited from bio::log::Writer
virtual void	InitializeImplementation (ByteStreams args)

void	Log (Level level, const char *format,...) const

Protected Member Functions inherited from bio::chemical::Atom
virtual bool	BreakBondImplementation (Wave *toDisassociate, AtomicNumber id, BondType type)

virtual bool	FormBondImplementation (Wave *toBond, AtomicNumber id, BondType type)

Protected Attributes inherited from bio::physical::Symmetry
Name	m_name

Identifiable< SymmetryType >	m_type

ByteStream	m_value

Protected Attributes inherited from bio::VirtualBase
bool	m_hasBeenInitialized

Protected Attributes inherited from bio::physical::Class< Identifiable< SymmetryType > >
Identifiable< SymmetryType > *	m_object

Protected Attributes inherited from bio::physical::Wave
Wave *	m_signal

Symmetry *	m_symmetry

Protected Attributes inherited from bio::physical::Class< Identifiable< StandardDimension > >
Identifiable< StandardDimension > *	m_object

Protected Attributes inherited from bio::physical::Filterable
Filter	m_filter

Protected Attributes inherited from bio::physical::Class< Filterable >
Filterable *	m_object

Protected Attributes inherited from bio::physical::Class< Writer >
Writer *	m_object

Protected Attributes inherited from bio::chemical::Atom
Bonds	m_bonds

Protected Attributes inherited from bio::physical::Class< Atom >
Atom *	m_object

Protected Attributes inherited from bio::chemical::AbstractMotif
Container *	m_contents

Detailed Description

chemical::Symmetry adds a recursive structure to physical::Symmetry. This enables nesting and complex structures to form. Primarily, chemical::Symmetry allows for lists (chemical::Structures) and basic operations (chemical::Reactions) to be Rotated.

Definition at line 37 of file Symmetry.h.

Constructor & Destructor Documentation

◆ Symmetry() [1/3]

bio::chemical::Symmetry::Symmetry	(	Name	name,
		SymmetryType	type
	)

Parameters

name
type

◆ Symmetry() [2/3]

bio::chemical::Symmetry::Symmetry	(	StandardDimension	id,
		Name	type
	)

Parameters

id
type

◆ Symmetry() [3/3]

bio::chemical::Symmetry::Symmetry	(	StandardDimension	id,
		SymmetryType	type
	)

Parameters

id
type

◆ ~Symmetry()

bio::chemical::Symmetry::~Symmetry ( )

virtual

Reimplemented from bio::physical::Symmetry.

Definition at line 83 of file Symmetry.cpp.

{
 
}

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::chemical::Symmetry::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	chemical	,
		Symmetry
	)

Ensure virtual methods point to Class implementations.

◆ physical::SymmetryPerspective::Instance()

& bio::chemical::Symmetry::physical::SymmetryPerspective::Instance ( )

Parameters

name
type

Member Data Documentation

◆ Symmetry

bio::chemical::Symmetry::Symmetry

Definition at line 52 of file Symmetry.h.

◆ type

Name bio::chemical::Symmetry::type

Definition at line 61 of file Symmetry.h.

The documentation for this class was generated from the following files:

/home/eons/git/biology/lib_bio/inc/bio/chemical/Symmetry.h
/home/eons/git/biology/lib_bio/src/chemical/Symmetry.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Symmetry() [1/3]

◆ Symmetry() [2/3]

◆ Symmetry() [3/3]

◆ ~Symmetry()

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

◆ physical::SymmetryPerspective::Instance()

Member Data Documentation

◆ Symmetry

◆ type