bio::chemical::Substance Member List

This is the complete list of members for bio::chemical::Substance, including all inherited members.

UnorderedMotif< Property >::AbstractMotif()	bio::chemical::AbstractMotif
UnorderedMotif< State >::AbstractMotif()	bio::chemical::AbstractMotif
Add(const T t)	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::AddImplementation(const Property content)	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::AddImplementation(const State content)	bio::chemical::UnorderedMotif< State >	inlinevirtual
As()	bio::chemical::Atom	inline
As() const	bio::chemical::Atom	inline
AsAtom()	bio::physical::Wave	inlinevirtual
AsAtom() const	bio::physical::Wave	inlinevirtual
AsBonded()	bio::chemical::Atom	inline
AsBonded() const	bio::chemical::Atom	inline
AsBondedQuantum()	bio::chemical::Atom	inline
AsBondedQuantum() const	bio::chemical::Atom	inline
bio::AsWave()	bio::physical::Class< Atom >	inlinevirtual
bio::AsWave() const	bio::physical::Class< Atom >	inlinevirtual
Class< Substance >::bio::AsWave()	bio::physical::Class< T >	inlinevirtual
Class< Substance >::AsWave() const	bio::physical::Class< T >	inlinevirtual
Class< Substance >::Identifiable< StandardDimension >::AsWave()	bio::physical::Class< Identifiable< StandardDimension > >	inlinevirtual
Class< Substance >::Identifiable< StandardDimension >::AsWave() const	bio::physical::Class< Identifiable< StandardDimension > >	inlinevirtual
Class< Substance >::bio::log::Writer::bio::AsWave()	bio::physical::Class< Filterable >	inlinevirtual
Class< Substance >::bio::log::Writer::AsWave() const	bio::physical::Class< Filterable >	inlinevirtual
Class< Substance >::bio::log::Writer::Class< Writer >::AsWave()	bio::physical::Class< Writer >	inlinevirtual
Class< Writer >::AsWave() const	bio::physical::Class< Writer >	inlinevirtual
Atom(const Atom &other)	bio::chemical::Atom	explicit
Attenuate(const Wave *other)	bio::chemical::Atom	virtual
Class< Atom >::Attenuate(const Wave *other)	bio::physical::Wave	virtual
BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(chemical, Substance, &SubstancePerspective::Instance(), filter::Chemical()) BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical	bio::chemical::Substance
bio::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Atom) explicit Atom()	bio::chemical::Atom
Class< Substance >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Substance) Class(Substance *object	bio::chemical::Class< Substance >
Class< Substance >::Identifiable< StandardDimension >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective	bio::physical::Identifiable< StandardDimension >
Class< Substance >::bio::log::Writer::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Writer) Writer()	bio::log::Writer
Class< Substance >::bio::physical::Filterable::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Filterable) Filterable()	bio::physical::Filterable
UnorderedMotif< Property >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Property >) UnorderedMotif()	bio::chemical::UnorderedMotif< Property >	inline
UnorderedMotif< Property >::Class< UnorderedMotif< Property > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Property >) Class(UnorderedMotif< Property > *object	bio::chemical::Class< UnorderedMotif< Property > >
UnorderedMotif< State >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< State >) UnorderedMotif()	bio::chemical::UnorderedMotif< State >	inline
Class< UnorderedMotif< State > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< State >) Class(UnorderedMotif< State > *object	bio::chemical::Class< UnorderedMotif< State > >
BreakBond(T toDisassociate, BondType type=bond_type::Unknown())	bio::chemical::Atom	inline
BreakBondImplementation(Wave *toDisassociate, AtomicNumber id, BondType type)	bio::chemical::Atom	protectedvirtual
bio::Class(Atom *object, Symmetry *symmetry=NULL)	bio::physical::Class< Atom >	inline
Class< Substance >::bio::Class(T *object, Symmetry *symmetry=NULL)	bio::physical::Class< T >	inline
Class< Substance >::Identifiable< StandardDimension >::Class(Identifiable< StandardDimension > *object, Symmetry *symmetry=NULL)	bio::physical::Class< Identifiable< StandardDimension > >	inline
Class< Substance >::bio::log::Writer::bio::Class(Filterable *object, Symmetry *symmetry=NULL)	bio::physical::Class< Filterable >	inline
Class< Substance >::bio::log::Writer::Class< Writer >::Class(Writer *object, Symmetry *symmetry=NULL)	bio::physical::Class< Writer >	inline
UnorderedMotif< Property >::bio::Class(T *object, Symmetry *symmetry=NULL)	bio::physical::Class< T >	inline
UnorderedMotif< State >::bio::Class(T *object, Symmetry *symmetry=NULL)	bio::physical::Class< T >	inline
Clear()	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::ClearImplementation()	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::ClearImplementation()	bio::chemical::UnorderedMotif< State >	inlinevirtual
bio::Clone() const	bio::physical::Class< Atom >	inlinevirtual
Class< Substance >::bio::Clone() const	bio::physical::Class< T >	inlinevirtual
Class< Substance >::Identifiable< StandardDimension >::Clone() const	bio::physical::Class< Identifiable< StandardDimension > >	inlinevirtual
Class< Substance >::bio::log::Writer::bio::Clone() const	bio::physical::Class< Filterable >	inlinevirtual
Class< Substance >::bio::log::Writer::Class< Writer >::Clone() const	bio::physical::Class< Writer >	inlinevirtual
CloneIntoName(Name name)	bio::physical::Identifiable< StandardDimension >	inline
UnorderedMotif< Property >::Contents typedef	bio::chemical::UnorderedMotif< Property >
UnorderedMotif< State >::Contents typedef	bio::chemical::UnorderedMotif< State >
bio::Convert(Wave *wave)	bio::physical::Class< Atom >	inline
Class< Substance >::bio::Convert(Wave *wave)	bio::physical::Class< T >	inline
Class< Substance >::Identifiable< StandardDimension >::Convert(Wave *wave)	bio::physical::Class< Identifiable< StandardDimension > >	inline
Class< Substance >::bio::log::Writer::bio::Convert(Wave *wave)	bio::physical::Class< Filterable >	inline
Class< Substance >::bio::log::Writer::Class< Writer >::Convert(Wave *wave)	bio::physical::Class< Writer >	inline
UnorderedMotif< Property >::bio::Convert(Wave *wave)	bio::physical::Class< T >	inline
UnorderedMotif< State >::bio::Convert(Wave *wave)	bio::physical::Class< T >	inline
Demodulate()	bio::physical::Wave	virtual
Demodulate() const	bio::physical::Wave	virtual
Disable()	bio::chemical::Substance	virtual
Disattenuate(const Wave *other)	bio::chemical::Atom	virtual
Class< Atom >::Disattenuate(const Wave *other)	bio::physical::Wave	virtual
Enable()	bio::chemical::Substance	virtual
ExternalLog(Filter logFilter, Level level, const char *format,...) const	bio::log::Writer
Class< Substance >::filter	bio::chemical::Class< Substance >
UnorderedMotif< Property >::filter	bio::chemical::Class< UnorderedMotif< Property > >
UnorderedMotif< State >::filter	bio::chemical::Class< UnorderedMotif< State > >
Filterable(Filter filter)	bio::physical::Filterable
ForEach(ExcitationBase *excitation)	bio::chemical::LinearStructureInterface	inline
FormBond(T toBond, BondType type=bond_type::Unknown())	bio::chemical::Atom	inline
FormBondImplementation(Wave *toBond, AtomicNumber id, BondType type)	bio::chemical::Atom	protectedvirtual
GetAll()	bio::chemical::UnorderedStructureInterface	inline
GetAll() const	bio::chemical::UnorderedStructureInterface	inline
GetAllAsVector()	bio::chemical::UnorderedStructureInterface	inline
GetAllAsVector() const	bio::chemical::UnorderedStructureInterface	inline
GetAllBonds()	bio::chemical::Atom
GetAllBonds() const	bio::chemical::Atom
GetAllImplementation()	bio::chemical::AbstractMotif	virtual
GetAllImplementation() const	bio::chemical::AbstractMotif	virtual
GetBonded(Valence position)	bio::chemical::Atom
GetBonded(Valence position) const	bio::chemical::Atom
GetBondPosition(AtomicNumber bondedId) const	bio::chemical::Atom
GetBondPosition(Name typeName) const	bio::chemical::Atom
GetBondPosition() const	bio::chemical::Atom	inline
GetBondType(Valence position) const	bio::chemical::Atom
GetBondType() const	bio::chemical::Atom	inline
GetById(StandardDimension id)	bio::chemical::LinearStructureInterface	inline
GetById(StandardDimension id) const	bio::chemical::LinearStructureInterface	inline
GetByName(Name name)	bio::chemical::LinearStructureInterface	inline
GetByName(Name name) const	bio::chemical::LinearStructureInterface	inline
UnorderedMotif< Property >::GetClassProperties()	bio::chemical::AbstractMotif	static
UnorderedMotif< State >::GetClassProperties()	bio::chemical::AbstractMotif	static
GetCount() const	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::GetCountImplementation() const	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::GetCountImplementation() const	bio::chemical::UnorderedMotif< State >	inlinevirtual
GetFilter() const	bio::physical::Filterable
GetLogEngine()	bio::log::Writer
GetLogEngine() const	bio::log::Writer
GetNumMatching(const Container *other) const	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::GetNumMatchingImplementation(const Container *other) const	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::GetNumMatchingImplementation(const Container *other) const	bio::chemical::UnorderedMotif< State >	inlinevirtual
GetOrCreateById(StandardDimension id)	bio::chemical::LinearStructureInterface	inline
GetOrCreateByName(Name name)	bio::chemical::LinearStructureInterface	inline
GetPerspective() const	bio::physical::Observer< Perspective< StandardDimension > >	inlinevirtual
GetProperties() const	bio::physical::Wave	virtual
bio::GetResonanceBetween(ConstWaves waves)	bio::physical::Wave	static
bio::GetResonanceBetween(const Wave *wave1, const Wave *wave2)	bio::physical::Wave	static
bio::GetResonanceBetween(const Wave *wave, const Properties &properties)	bio::physical::Wave	static
Class< Substance >::GetResonanceBetween(ConstWaves waves)	bio::physical::Wave	static
Class< Substance >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)	bio::physical::Wave	static
Class< Substance >::GetResonanceBetween(const Wave *wave, const Properties &properties)	bio::physical::Wave	static
UnorderedMotif< Property >::GetResonanceBetween(ConstWaves waves)	bio::physical::Wave	static
UnorderedMotif< Property >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)	bio::physical::Wave	static
UnorderedMotif< Property >::GetResonanceBetween(const Wave *wave, const Properties &properties)	bio::physical::Wave	static
UnorderedMotif< State >::GetResonanceBetween(ConstWaves waves)	bio::physical::Wave	static
UnorderedMotif< State >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)	bio::physical::Wave	static
UnorderedMotif< State >::GetResonanceBetween(const Wave *wave, const Properties &properties)	bio::physical::Wave	static
GetStringFrom(std::string separator=", ")	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::GetStringFromImplementation(std::string separator=", ")	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::GetStringFromImplementation(std::string separator=", ")	bio::chemical::UnorderedMotif< State >	inlinevirtual
Has(T content) const	bio::chemical::UnorderedStructureInterface	inline
HasAll(const Container *contents) const	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::HasAllImplementation(const Container *contents) const	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::HasAllImplementation(const Container *contents) const	bio::chemical::UnorderedMotif< State >	inlinevirtual
UnorderedMotif< Property >::HasImplementation(const Property content) const	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::HasImplementation(const State content) const	bio::chemical::UnorderedMotif< State >	inlinevirtual
HasLogEngine() const	bio::log::Writer
Id typedef	bio::physical::Identifiable< StandardDimension >
Ids typedef	bio::physical::Identifiable< StandardDimension >
Import(const UnorderedMotif< T > *other)	bio::chemical::UnorderedStructureInterface	inline
Import(const std::vector< T > &other)	bio::chemical::UnorderedStructureInterface	inline
ImportAll(const physical::Wave *other)	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::ImportImplementation(const UnorderedMotif< Property > *other)	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< Property >::bio::chemical::AbstractMotif::ImportImplementation(const void *other)	bio::chemical::AbstractMotif	inlinevirtual
UnorderedMotif< State >::ImportImplementation(const UnorderedMotif< State > *other)	bio::chemical::UnorderedMotif< State >	inlinevirtual
Initialize(ByteStreams args)	bio::VirtualBase	protected
Initialize(ByteStream arg1)	bio::VirtualBase	protected
Initialize(ByteStream arg1, ByteStream arg2)	bio::VirtualBase	protected
Initialize(ByteStream arg1, ByteStream arg2, ByteStream arg3)	bio::VirtualBase	protected
Class< Substance >::Identifiable< StandardDimension >::InitializeImplementation(ByteStreams args)	bio::physical::Observer< Perspective< StandardDimension > >	inlineprotectedvirtual
bio::log::Writer::InitializeImplementation(ByteStreams args)	bio::log::Writer	protectedvirtual
Insert(T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)	bio::chemical::LinearStructureInterface	inline
IsEnabled() const	bio::chemical::Substance	virtual
LinearStructureInterface()	bio::chemical::LinearStructureInterface	inline
LockThread() const	bio::ThreadSafe
Log(Level level, const char *format,...) const	bio::log::Writer	protected
m_bonds	bio::chemical::Atom	protected
UnorderedMotif< Property >::m_contents	bio::chemical::AbstractMotif	mutableprotected
UnorderedMotif< State >::m_contents	bio::chemical::AbstractMotif	mutableprotected
m_filter	bio::physical::Filterable	protected
m_hasBeenInitialized	bio::VirtualBase	protected
m_id	bio::physical::Identifiable< StandardDimension >
bio::m_object	bio::physical::Class< Atom >	protected
Class< Substance >::bio::m_object	bio::physical::Class< T >	protected
Class< Substance >::Identifiable< StandardDimension >::m_object	bio::physical::Class< Identifiable< StandardDimension > >	protected
Class< Substance >::bio::log::Writer::bio::m_object	bio::physical::Class< Filterable >	protected
Class< Substance >::bio::log::Writer::Class< Writer >::m_object	bio::physical::Class< Writer >	protected
UnorderedMotif< Property >::bio::m_object	bio::physical::Class< T >	protected
UnorderedMotif< State >::bio::m_object	bio::physical::Class< T >	protected
bio::m_signal	bio::physical::Wave	protected
Class< Substance >::bio::m_signal	bio::physical::Wave	protected
UnorderedMotif< Property >::bio::m_signal	bio::physical::Wave	protected
UnorderedMotif< State >::bio::m_signal	bio::physical::Wave	protected
bio::m_symmetry	bio::physical::Wave	protected
Class< Substance >::bio::m_symmetry	bio::physical::Wave	protected
UnorderedMotif< Property >::bio::m_symmetry	bio::physical::Wave	protected
UnorderedMotif< State >::bio::m_symmetry	bio::physical::Wave	protected
Modulate(Wave *signal)	bio::physical::Wave	virtual
Observer(Perspective *perspective=NULL)	bio::physical::Observer< Perspective< StandardDimension > >	inlineexplicit
Observer(const Observer &other)	bio::physical::Observer< Perspective< StandardDimension > >	inline
operator Atom *()	bio::physical::Class< Atom >	inlinevirtual
operator Filterable *()	bio::physical::Class< Filterable >	inlinevirtual
operator Identifiable< StandardDimension > *()	bio::physical::Class< Identifiable< StandardDimension > >	inlinevirtual
operator T()	bio::chemical::Atom	inline
operator T*()	bio::physical::Class< T >	inlinevirtual
bio::operator Wave *()	bio::physical::Class< Atom >	inlinevirtual
Class< Substance >::bio::operator Wave *()	bio::physical::Class< T >	inlinevirtual
Class< Substance >::Identifiable< StandardDimension >::operator Wave *()	bio::physical::Class< Identifiable< StandardDimension > >	inlinevirtual
Class< Substance >::bio::log::Writer::bio::operator Wave *()	bio::physical::Class< Filterable >	inlinevirtual
Class< Substance >::bio::log::Writer::Class< Writer >::operator Wave *()	bio::physical::Class< Writer >	inlinevirtual
operator Writer *()	bio::physical::Class< Writer >	inlinevirtual
operator*(Wave *signal)	bio::physical::Wave	virtual
operator*()	bio::physical::Wave	virtual
operator*() const	bio::physical::Wave	virtual
operator+(const Wave *other)	bio::physical::Wave	virtual
operator-(const Wave *other)	bio::physical::Wave	virtual
operator|(Symmetry *symmetry)	bio::physical::Wave	virtual
Class< Substance >::perspective	bio::chemical::Class< Substance >
UnorderedMotif< Property >::perspective	bio::chemical::Class< UnorderedMotif< Property > >
UnorderedMotif< State >::perspective	bio::chemical::Class< UnorderedMotif< State > >
Perspective typedef	bio::physical::Observer< Perspective< StandardDimension > >
bio::Reify(physical::Symmetry *symmetry)	bio::chemical::Atom	virtual
Class< Substance >::bio::log::Writer::Reify(Symmetry *symmetry)	bio::physical::Filterable	virtual
Remove(const T t)	bio::chemical::UnorderedStructureInterface	inline
UnorderedMotif< Property >::RemoveImplementation(const Property content)	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::RemoveImplementation(const State content)	bio::chemical::UnorderedMotif< State >	inlinevirtual
SetFilter(Filter filter)	bio::physical::Filterable	virtual
SetLogEngine(Engine *logEngine)	bio::log::Writer	virtual
SetPerspective(Perspective *perspective)	bio::physical::Observer< Perspective< StandardDimension > >	inlinevirtual
bio::Spin() const	bio::chemical::Atom	virtual
Class< Substance >::bio::log::Writer::Spin() const	bio::physical::Filterable	virtual
Structure()	bio::chemical::Structure
Substance(const typename UnorderedMotif< Property >::Contents *properties, const typename UnorderedMotif< State >::Contents *states)	bio::chemical::Substance
ThreadSafe()	bio::ThreadSafe
ThreadSafe(const ThreadSafe &toCopy)	bio::ThreadSafe
UnlockThread() const	bio::ThreadSafe
UnorderedMotif< Property >::UnorderedMotif(const Contents *contents)	bio::chemical::UnorderedMotif< Property >	inline
UnorderedMotif< Property >::UnorderedMotif(const UnorderedMotif< Property > *toCopy)	bio::chemical::UnorderedMotif< Property >	inline
UnorderedMotif< State >::UnorderedMotif(const Contents *contents)	bio::chemical::UnorderedMotif< State >	inline
UnorderedMotif< State >::UnorderedMotif(const UnorderedMotif< State > *toCopy)	bio::chemical::UnorderedMotif< State >	inline
UnorderedStructureInterface()	bio::chemical::UnorderedStructureInterface	inline
VirtualBase()	bio::VirtualBase	protected
bio::Wave(Symmetry *symmetry=NULL)	bio::physical::Wave
Class< Substance >::bio::Wave(Symmetry *symmetry=NULL)	bio::physical::Wave
UnorderedMotif< Property >::bio::Wave(Symmetry *symmetry=NULL)	bio::physical::Wave
UnorderedMotif< State >::bio::Wave(Symmetry *symmetry=NULL)	bio::physical::Wave
Writer(Engine *logEngine, Filter logFilter)	bio::log::Writer
~AbstractMotif()	bio::chemical::AbstractMotif	virtual
~Atom()	bio::chemical::Atom	virtual
bio::~Class()	bio::physical::Class< Atom >	inlinevirtual
Class< Substance >::bio::~Class()	bio::physical::Class< T >	inlinevirtual
Class< Substance >::Identifiable< StandardDimension >::~Class()	bio::physical::Class< Identifiable< StandardDimension > >	inlinevirtual
Class< Substance >::bio::log::Writer::bio::~Class()	bio::physical::Class< Filterable >	inlinevirtual
Class< Substance >::bio::log::Writer::Class< Writer >::~Class()	bio::physical::Class< Writer >	inlinevirtual
~Filterable()	bio::physical::Filterable	virtual
~LinearStructureInterface()	bio::chemical::LinearStructureInterface	inlinevirtual
~Observer()	bio::physical::Observer< Perspective< StandardDimension > >	inlinevirtual
~Structure()	bio::chemical::Structure	virtual
~Substance()	bio::chemical::Substance	virtual
~ThreadSafe()	bio::ThreadSafe	virtual
UnorderedMotif< Property >::~UnorderedMotif()	bio::chemical::UnorderedMotif< Property >	inlinevirtual
UnorderedMotif< State >::~UnorderedMotif()	bio::chemical::UnorderedMotif< State >	inlinevirtual
~UnorderedStructureInterface()	bio::chemical::UnorderedStructureInterface	inlinevirtual
~VirtualBase()	bio::VirtualBase	protectedvirtual
~Wave()	bio::physical::Wave	virtual
~Writer()	bio::log::Writer	virtual