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bio::chemical::Reactants Member List

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

AbstractMotif()bio::chemical::AbstractMotif
Add(const T t)bio::chemical::UnorderedStructureInterfaceinline
AddImplementation(Substance * content)bio::chemical::LinearMotif< Substance * >inlinevirtual
UnorderedMotif< Substance * >::AddImplementation(const Substance * content)bio::chemical::UnorderedMotif< Substance * >inlinevirtual
As()bio::chemical::Atominline
As() constbio::chemical::Atominline
AsAtom()bio::physical::Waveinlinevirtual
AsAtom() constbio::physical::Waveinlinevirtual
AsBonded()bio::chemical::Atominline
AsBonded() constbio::chemical::Atominline
AsBondedQuantum()bio::chemical::Atominline
AsBondedQuantum() constbio::chemical::Atominline
bio::AsWave()bio::physical::Class< Atom >inlinevirtual
bio::AsWave() constbio::physical::Class< Atom >inlinevirtual
Class< Reactants >::bio::AsWave()bio::physical::Class< T >inlinevirtual
Class< Reactants >::AsWave() constbio::physical::Class< T >inlinevirtual
Class< Reactants >::Identifiable< StandardDimension >::AsWave()bio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< Reactants >::Identifiable< StandardDimension >::AsWave() constbio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< Reactants >::bio::log::Writer::bio::AsWave()bio::physical::Class< Filterable >inlinevirtual
Class< Reactants >::bio::log::Writer::AsWave() constbio::physical::Class< Filterable >inlinevirtual
Class< Reactants >::bio::log::Writer::Class< Writer >::AsWave()bio::physical::Class< Writer >inlinevirtual
Class< Writer >::AsWave() constbio::physical::Class< Writer >inlinevirtual
Atom(const Atom &other)bio::chemical::Atomexplicit
bio::Attenuate(const Wave *other)bio::chemical::Atomvirtual
bio::Class< Atom >::Attenuate(const Wave *other)bio::physical::Wavevirtual
LinearMotif< Substance * >::Attenuate(const physical::Wave *other)bio::chemical::LinearMotif< Substance * >inlinevirtual
BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, Reactants) Reactants()bio::chemical::Reactants
bio::chemical::Structure::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Atom) explicit Atom()bio::chemical::Atom
Class< Reactants >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Reactants) Class(Reactants *objectbio::chemical::Class< Reactants >
Class< Reactants >::Identifiable< StandardDimension >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspectivebio::physical::Identifiable< StandardDimension >
Class< Reactants >::bio::log::Writer::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Writer) Writer()bio::log::Writer
Class< Reactants >::bio::physical::Filterable::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Filterable) Filterable()bio::physical::Filterable
LinearMotif< Substance * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, LinearMotif< Substance * >) Class(LinearMotif< Substance * > *objectbio::chemical::Class< LinearMotif< Substance * > >
LinearMotif< Substance * >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, UnorderedMotif< Substance * >) UnorderedMotif()bio::chemical::UnorderedMotif< Substance * >inline
Class< UnorderedMotif< Substance * > >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, UnorderedMotif< Substance * >) Class(UnorderedMotif< Substance * > *objectbio::chemical::Class< UnorderedMotif< Substance * > >
BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS(chemical, LinearMotif< Substance * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physicalbio::chemical::LinearMotif< Substance * >
BreakBond(T toDisassociate, BondType type=bond_type::Unknown())bio::chemical::Atominline
BreakBondImplementation(Wave *toDisassociate, AtomicNumber id, BondType type)bio::chemical::Atomprotectedvirtual
bio::Class(Atom *object, Symmetry *symmetry=NULL)bio::physical::Class< Atom >inline
Class< Reactants >::bio::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
Class< Reactants >::Identifiable< StandardDimension >::Class(Identifiable< StandardDimension > *object, Symmetry *symmetry=NULL)bio::physical::Class< Identifiable< StandardDimension > >inline
Class< Reactants >::bio::log::Writer::bio::Class(Filterable *object, Symmetry *symmetry=NULL)bio::physical::Class< Filterable >inline
Class< Reactants >::bio::log::Writer::Class< Writer >::Class(Writer *object, Symmetry *symmetry=NULL)bio::physical::Class< Writer >inline
LinearMotif< Substance * >::Class< LinearMotif< Substance * > >::bio::Class< LinearMotif< Substance * > >::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
LinearMotif< Substance * >::UnorderedMotif< Substance * >::bio::Class(T *object, Symmetry *symmetry=NULL)bio::physical::Class< T >inline
Clear()bio::chemical::UnorderedStructureInterfaceinline
ClearImplementation()bio::chemical::LinearMotif< Substance * >inlinevirtual
bio::Clone() constbio::physical::Class< Atom >inlinevirtual
Class< Reactants >::bio::Clone() constbio::physical::Class< T >inlinevirtual
Class< Reactants >::Identifiable< StandardDimension >::Clone() constbio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< Reactants >::bio::log::Writer::bio::Clone() constbio::physical::Class< Filterable >inlinevirtual
Class< Reactants >::bio::log::Writer::Class< Writer >::Clone() constbio::physical::Class< Writer >inlinevirtual
CloneIntoName(Name name)bio::physical::Identifiable< StandardDimension >inline
Contents typedefbio::chemical::LinearMotif< Substance * >
bio::Convert(Wave *wave)bio::physical::Class< Atom >inline
Class< Reactants >::bio::Convert(Wave *wave)bio::physical::Class< T >inline
Class< Reactants >::Identifiable< StandardDimension >::Convert(Wave *wave)bio::physical::Class< Identifiable< StandardDimension > >inline
Class< Reactants >::bio::log::Writer::bio::Convert(Wave *wave)bio::physical::Class< Filterable >inline
Class< Reactants >::bio::log::Writer::Class< Writer >::Convert(Wave *wave)bio::physical::Class< Writer >inline
LinearMotif< Substance * >::Class< LinearMotif< Substance * > >::bio::Class< LinearMotif< Substance * > >::Convert(Wave *wave)bio::physical::Class< T >inline
LinearMotif< Substance * >::UnorderedMotif< Substance * >::bio::Convert(Wave *wave)bio::physical::Class< T >inline
CreateImplementation(StandardDimension id)bio::chemical::LinearMotif< Substance * >inlinevirtual
Demodulate()bio::physical::Wavevirtual
Demodulate() constbio::physical::Wavevirtual
bio::Disattenuate(const Wave *other)bio::chemical::Atomvirtual
bio::Class< Atom >::Disattenuate(const Wave *other)bio::physical::Wavevirtual
LinearMotif< Substance * >::Disattenuate(const physical::Wave *other)bio::chemical::LinearMotif< Substance * >inlinevirtual
Elementary(const Properties properties)bio::chemical::Elementary< LinearMotif< Substance * > >inline
Elementary()bio::chemical::Elementary< LinearMotif< Substance * > >inline
ExternalLog(Filter logFilter, Level level, const char *format,...) constbio::log::Writer
Class< Reactants >::filterbio::chemical::Class< Reactants >
LinearMotif< Substance * >::Class< LinearMotif< Substance * > >::filterbio::chemical::Class< LinearMotif< Substance * > >
LinearMotif< Substance * >::UnorderedMotif< Substance * >::filterbio::chemical::Class< UnorderedMotif< Substance * > >
Filterable(Filter filter)bio::physical::Filterable
ForEach(ExcitationBase *excitation)bio::chemical::LinearStructureInterfaceinline
ForEachImplementation(ExcitationBase *excitation)bio::chemical::LinearMotif< Substance * >inlinevirtual
FormBond(T toBond, BondType type=bond_type::Unknown())bio::chemical::Atominline
FormBondImplementation(Wave *toBond, AtomicNumber id, BondType type)bio::chemical::Atomprotectedvirtual
GetAll()bio::chemical::UnorderedStructureInterfaceinline
GetAll() constbio::chemical::UnorderedStructureInterfaceinline
GetAllAsVector()bio::chemical::UnorderedStructureInterfaceinline
GetAllAsVector() constbio::chemical::UnorderedStructureInterfaceinline
GetAllBonds()bio::chemical::Atom
GetAllBonds() constbio::chemical::Atom
GetAllImplementation()bio::chemical::AbstractMotifvirtual
GetAllImplementation() constbio::chemical::AbstractMotifvirtual
GetBonded(Valence position)bio::chemical::Atom
GetBonded(Valence position) constbio::chemical::Atom
GetBondPosition(AtomicNumber bondedId) constbio::chemical::Atom
GetBondPosition(Name typeName) constbio::chemical::Atom
GetBondPosition() constbio::chemical::Atominline
GetBondType(Valence position) constbio::chemical::Atom
GetBondType() constbio::chemical::Atominline
GetById(StandardDimension id)bio::chemical::LinearStructureInterfaceinline
GetById(StandardDimension id) constbio::chemical::LinearStructureInterfaceinline
GetByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Substance * >inlinevirtual
GetByIdImplementation(StandardDimension id) constbio::chemical::LinearMotif< Substance * >inlinevirtual
GetByName(Name name)bio::chemical::LinearStructureInterfaceinline
GetByName(Name name) constbio::chemical::LinearStructureInterfaceinline
GetByNameImplementation(Name name)bio::chemical::LinearMotif< Substance * >inlinevirtual
GetByNameImplementation(Name name) constbio::chemical::LinearMotif< Substance * >inlinevirtual
GetClassProperties()bio::chemical::LinearMotif< Substance * >inlinestatic
GetCount() constbio::chemical::UnorderedStructureInterfaceinline
GetCountImplementation() constbio::chemical::UnorderedMotif< Substance * >inlinevirtual
GetFilter() constbio::physical::Filterable
GetLogEngine()bio::log::Writer
GetLogEngine() constbio::log::Writer
GetNumMatching(const Container *other) constbio::chemical::UnorderedStructureInterfaceinline
GetNumMatchingImplementation(const Container *other) constbio::chemical::UnorderedMotif< Substance * >inlinevirtual
GetOrCreateById(StandardDimension id)bio::chemical::LinearStructureInterfaceinline
GetOrCreateByIdImplementation(StandardDimension id)bio::chemical::LinearMotif< Substance * >inlinevirtual
GetOrCreateByName(Name name)bio::chemical::LinearStructureInterfaceinline
GetOrCreateByNameImplementation(Name name)bio::chemical::LinearMotif< Substance * >inlinevirtual
GetPerspective() constbio::physical::Observer< Perspective< StandardDimension > >inlinevirtual
GetProperties() constbio::physical::Wavevirtual
bio::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
bio::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
bio::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
Class< Reactants >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
Class< Reactants >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
Class< Reactants >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
LinearMotif< Substance * >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
LinearMotif< Substance * >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
LinearMotif< Substance * >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
UnorderedMotif< Substance * >::GetResonanceBetween(ConstWaves waves)bio::physical::Wavestatic
UnorderedMotif< Substance * >::GetResonanceBetween(const Wave *wave1, const Wave *wave2)bio::physical::Wavestatic
UnorderedMotif< Substance * >::GetResonanceBetween(const Wave *wave, const Properties &properties)bio::physical::Wavestatic
GetStringFrom(std::string separator=", ")bio::chemical::UnorderedStructureInterfaceinline
GetStringFromImplementation(std::string separator=", ")bio::chemical::LinearMotif< Substance * >inlinevirtual
GetStructuralPerspective()bio::chemical::LinearMotif< Substance * >inline
GetStructuralPerspective() constbio::chemical::LinearMotif< Substance * >inline
Has(T content) constbio::chemical::UnorderedStructureInterfaceinline
HasAll(const Container *contents) constbio::chemical::UnorderedStructureInterfaceinline
HasAllImplementation(const Container *contents) constbio::chemical::UnorderedMotif< Substance * >inlinevirtual
HasImplementation(const Substance * &content) constbio::chemical::LinearMotif< Substance * >inlinevirtual
UnorderedMotif< Substance * >::HasImplementation(const Substance * content) constbio::chemical::UnorderedMotif< Substance * >inlinevirtual
HasLogEngine() constbio::log::Writer
hasRegisteredbio::chemical::Elementary< LinearMotif< Substance * > >static
Id typedefbio::physical::Identifiable< StandardDimension >
Ids typedefbio::physical::Identifiable< StandardDimension >
Import(const UnorderedMotif< T > *other)bio::chemical::UnorderedStructureInterfaceinline
Import(const std::vector< T > &other)bio::chemical::UnorderedStructureInterfaceinline
ImportAll(const physical::Wave *other)bio::chemical::UnorderedStructureInterfaceinline
ImportImplementation(const LinearMotif< Substance * > *other)bio::chemical::LinearMotif< Substance * >inlinevirtual
UnorderedMotif< Substance * >::ImportImplementation(const UnorderedMotif< Substance * > *other)bio::chemical::UnorderedMotif< Substance * >inlinevirtual
bio::chemical::AbstractMotif::ImportImplementation(const void *other)bio::chemical::AbstractMotifinlinevirtual
Initialize(ByteStreams args)bio::VirtualBaseprotected
Initialize(ByteStream arg1)bio::VirtualBaseprotected
Initialize(ByteStream arg1, ByteStream arg2)bio::VirtualBaseprotected
Initialize(ByteStream arg1, ByteStream arg2, ByteStream arg3)bio::VirtualBaseprotected
Class< Reactants >::Identifiable< StandardDimension >::InitializeImplementation(ByteStreams args)bio::physical::Observer< Perspective< StandardDimension > >inlineprotectedvirtual
bio::log::Writer::InitializeImplementation(ByteStreams args)bio::log::Writerprotectedvirtual
Insert(T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)bio::chemical::LinearStructureInterfaceinline
InsertImplementation(Substance * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)bio::chemical::LinearMotif< Substance * >inlinevirtual
LinearMotif(physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Substance * >inlineexplicit
LinearMotif(const Contents *contents, physical::Perspective< StandardDimension > *perspective=NULL)bio::chemical::LinearMotif< Substance * >inlineexplicit
LinearMotif(const LinearMotif< Substance * > &toCopy)bio::chemical::LinearMotif< Substance * >inline
LinearStructureInterface()bio::chemical::LinearStructureInterfaceinline
LockThread() constbio::ThreadSafe
Log(Level level, const char *format,...) constbio::log::Writerprotected
m_bondsbio::chemical::Atomprotected
m_contentsbio::chemical::AbstractMotifmutableprotected
m_filterbio::physical::Filterableprotected
m_hasBeenInitializedbio::VirtualBaseprotected
m_idbio::physical::Identifiable< StandardDimension >
bio::m_objectbio::physical::Class< Atom >protected
Class< Reactants >::bio::m_objectbio::physical::Class< T >protected
Class< Reactants >::Identifiable< StandardDimension >::m_objectbio::physical::Class< Identifiable< StandardDimension > >protected
Class< Reactants >::bio::log::Writer::bio::m_objectbio::physical::Class< Filterable >protected
Class< Reactants >::bio::log::Writer::Class< Writer >::m_objectbio::physical::Class< Writer >protected
LinearMotif< Substance * >::Class< LinearMotif< Substance * > >::bio::Class< LinearMotif< Substance * > >::m_objectbio::physical::Class< T >protected
LinearMotif< Substance * >::UnorderedMotif< Substance * >::bio::m_objectbio::physical::Class< T >protected
m_perspectivebio::chemical::LinearMotif< Substance * >
bio::m_signalbio::physical::Waveprotected
Class< Reactants >::bio::m_signalbio::physical::Waveprotected
LinearMotif< Substance * >::bio::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::m_signalbio::physical::Waveprotected
LinearMotif< Substance * >::UnorderedMotif< Substance * >::bio::m_signalbio::physical::Waveprotected
bio::m_symmetrybio::physical::Waveprotected
Class< Reactants >::bio::m_symmetrybio::physical::Waveprotected
LinearMotif< Substance * >::bio::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::m_symmetrybio::physical::Waveprotected
LinearMotif< Substance * >::UnorderedMotif< Substance * >::bio::m_symmetrybio::physical::Waveprotected
Modulate(Wave *signal)bio::physical::Wavevirtual
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 Substances()bio::chemical::Reactants
operator T()bio::chemical::Atominline
operator T*()bio::physical::Class< T >inlinevirtual
bio::operator Wave *()bio::physical::Class< Atom >inlinevirtual
Class< Reactants >::bio::operator Wave *()bio::physical::Class< T >inlinevirtual
Class< Reactants >::Identifiable< StandardDimension >::operator Wave *()bio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< Reactants >::bio::log::Writer::bio::operator Wave *()bio::physical::Class< Filterable >inlinevirtual
Class< Reactants >::bio::log::Writer::Class< Writer >::operator Wave *()bio::physical::Class< Writer >inlinevirtual
operator Writer *()bio::physical::Class< Writer >inlinevirtual
operator*(Wave *signal)bio::physical::Wavevirtual
operator*()bio::physical::Wavevirtual
operator*() constbio::physical::Wavevirtual
operator+(const Wave *other)bio::physical::Wavevirtual
operator-(const Wave *other)bio::physical::Wavevirtual
operator|(Symmetry *symmetry)bio::physical::Wavevirtual
Class< Reactants >::perspectivebio::chemical::Class< Reactants >
LinearMotif< Substance * >::Class< LinearMotif< Substance * > >::perspectivebio::chemical::Class< LinearMotif< Substance * > >
LinearMotif< Substance * >::UnorderedMotif< Substance * >::perspectivebio::chemical::Class< UnorderedMotif< Substance * > >
Perspective typedefbio::physical::Observer< Perspective< StandardDimension > >
Reactants(Substances &substances)bio::chemical::Reactants
RegisterProperties(const Properties properties)bio::chemical::Elementary< LinearMotif< Substance * > >inline
bio::Reify(physical::Symmetry *symmetry)bio::chemical::Atomvirtual
Class< Reactants >::bio::log::Writer::Reify(Symmetry *symmetry)bio::physical::Filterablevirtual
Remove(const T t)bio::chemical::UnorderedStructureInterfaceinline
RemoveImplementation(const Substance * content)bio::chemical::UnorderedMotif< Substance * >inlinevirtual
SetFilter(Filter filter)bio::physical::Filterablevirtual
SetLogEngine(Engine *logEngine)bio::log::Writervirtual
SetPerspective(Perspective *perspective)bio::physical::Observer< Perspective< StandardDimension > >inlinevirtual
bio::Spin() constbio::chemical::Atomvirtual
Class< Reactants >::bio::log::Writer::Spin() constbio::physical::Filterablevirtual
Structure()bio::chemical::Structure
ThreadSafe()bio::ThreadSafe
ThreadSafe(const ThreadSafe &toCopy)bio::ThreadSafe
UnlockThread() constbio::ThreadSafe
UnorderedMotif(const Contents *contents)bio::chemical::UnorderedMotif< Substance * >inline
UnorderedMotif(const UnorderedMotif< Substance * > *toCopy)bio::chemical::UnorderedMotif< Substance * >inline
UnorderedStructureInterface()bio::chemical::UnorderedStructureInterfaceinline
VirtualBase()bio::VirtualBaseprotected
bio::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
Class< Reactants >::bio::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
LinearMotif< Substance * >::bio::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::Class< LinearMotif< Substance * > >::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
LinearMotif< Substance * >::UnorderedMotif< Substance * >::bio::Wave(Symmetry *symmetry=NULL)bio::physical::Wave
Writer(Engine *logEngine, Filter logFilter)bio::log::Writer
~AbstractMotif()bio::chemical::AbstractMotifvirtual
~Atom()bio::chemical::Atomvirtual
bio::~Class()bio::physical::Class< Atom >inlinevirtual
Class< Reactants >::bio::~Class()bio::physical::Class< T >inlinevirtual
Class< Reactants >::Identifiable< StandardDimension >::~Class()bio::physical::Class< Identifiable< StandardDimension > >inlinevirtual
Class< Reactants >::bio::log::Writer::bio::~Class()bio::physical::Class< Filterable >inlinevirtual
Class< Reactants >::bio::log::Writer::Class< Writer >::~Class()bio::physical::Class< Writer >inlinevirtual
~Elementary()bio::chemical::Elementary< LinearMotif< Substance * > >inlinevirtual
~Filterable()bio::physical::Filterablevirtual
~LinearMotif()bio::chemical::LinearMotif< Substance * >inlinevirtual
~LinearStructureInterface()bio::chemical::LinearStructureInterfaceinlinevirtual
~Observer()bio::physical::Observer< Perspective< StandardDimension > >inlinevirtual
~Reactants()bio::chemical::Reactantsvirtual
~Structure()bio::chemical::Structurevirtual
~ThreadSafe()bio::ThreadSafevirtual
~UnorderedMotif()bio::chemical::UnorderedMotif< Substance * >inlinevirtual
~UnorderedStructureInterface()bio::chemical::UnorderedStructureInterfaceinlinevirtual
~VirtualBase()bio::VirtualBaseprotectedvirtual
~Wave()bio::physical::Wavevirtual
~Writer()bio::log::Writervirtual