#include <Substance.h>

Inheritance diagram for bio::chemical::Substance:

Collaboration diagram for bio::chemical::Substance:

Public Member Functions
Substance	Substance (const typename UnorderedMotif< Property >::Contents properties, const typename UnorderedMotif< State >::Contents states)

virtual	~Substance ()

	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON (chemical, Substance, &SubstancePerspective::Instance(), filter::Chemical()) BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical

virtual void	Disable ()

virtual void	Enable ()

virtual bool	IsEnabled () const

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

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

T *	Convert (Wave *wave)

virtual	operator T* ()

virtual	operator Wave * ()

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::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::UnorderedMotif< Property >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< Property > *toCopy)

virtual	~UnorderedMotif ()

virtual Property	AddImplementation (const Property content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Property >) 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 Property content) const

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

virtual Property	RemoveImplementation (const Property content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Property > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Property >) Class(UnorderedMotif< Property > *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::UnorderedMotif< State >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< State > *toCopy)

virtual	~UnorderedMotif ()

virtual State	AddImplementation (const State content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< State >) 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 State content) const

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

virtual State	RemoveImplementation (const State content)

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

Additional Inherited Members
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::UnorderedMotif< Property >
typedef physical::Arrangement< Property >	Contents

Public Types inherited from bio::chemical::UnorderedMotif< State >
typedef physical::Arrangement< State >	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::AbstractMotif
static Properties	GetClassProperties ()

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

physical::Perspective< StandardDimension > *	perspective

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

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

physical::Perspective< StandardDimension > *	perspective

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

physical::Perspective< StandardDimension > *	perspective

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

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

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::physical::Wave
Wave *	m_signal

Symmetry *	m_symmetry

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

Protected Attributes inherited from bio::VirtualBase
bool	m_hasBeenInitialized

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::AbstractMotif
Container *	m_contents

Detailed Description

A chemical::Substance is just about everything. Substances have Properties and States and that's it. Substances start Enable()d.

Definition at line 41 of file Substance.h.

Constructor & Destructor Documentation

◆ Substance()

bio::chemical::Substance::Substance	(	const typename UnorderedMotif< Property >::Contents *	properties,
		const typename UnorderedMotif< State >::Contents *	states
	)

Parameters

properties
states

Definition at line 27 of file Substance.cpp.

 :
 chemical::Class< Substance >(this),
 UnorderedMotif< Property >(properties),
 UnorderedMotif< State >(states)
{
 CtorCommon();
}

◆ ~Substance()

bio::chemical::Substance::~Substance ( )

virtual

Definition at line 39 of file Substance.cpp.

40{

41}

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON()

bio::chemical::Substance::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON	(	chemical	,
		Substance	,
		&	SubstancePerspective::Instance(),
		filter::Chemical()
	)

Ensure virtual methods point to Class implementations.

◆ Disable()

void bio::chemical::Substance::Disable ( )

virtual

Helper method for removing the Enabled() State. May be overridden to add custom behavior.

Definition at line 48 of file Substance.cpp.

{
 Remove< State >(state::Enabled());
}

References bio::state::Enabled().

◆ Enable()

void bio::chemical::Substance::Enable ( )

virtual

Helper method for setting the Enabled() State. May be overridden to add custom behavior.

Definition at line 43 of file Substance.cpp.

{
 Add< State >(state::Enabled());
}

References bio::state::Enabled().

◆ IsEnabled()

bool bio::chemical::Substance::IsEnabled ( ) const

virtual

Helper method for checking the Enabled() State. May be overridden to add custom checks.

Returns: whether or not *this has the Enabled() State.

Definition at line 53 of file Substance.cpp.

{
 return Has< State >(state::Enabled());
}

References bio::state::Enabled().

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Substance()

◆ ~Substance()

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON()

◆ Disable()

◆ Enable()

◆ IsEnabled()