| Add(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| 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 |
| Class< Reaction >::bio::AsWave() | bio::physical::Class< T > | inlinevirtual |
| Class< Reaction >::bio::AsWave() const | bio::physical::Class< T > | inlinevirtual |
| Class< Reaction >::Identifiable< StandardDimension >::AsWave() | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Reaction >::Identifiable< StandardDimension >::AsWave() const | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::bio::AsWave() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::AsWave() const | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::Class< Writer >::AsWave() | bio::physical::Class< Writer > | inlinevirtual |
| Class< Reaction >::bio::Class< Writer >::AsWave() const | bio::physical::Class< Writer > | inlinevirtual |
| bio::chemical::Atom::AsWave() | bio::physical::Class< Atom > | inlinevirtual |
| bio::chemical::Atom::AsWave() const | bio::physical::Class< Atom > | inlinevirtual |
| Atom(const Atom &other) | bio::chemical::Atom | explicit |
| Attempt(Reactants *reactants) | bio::chemical::Reaction | inlinestatic |
| Attempt(Substances &substances) | bio::chemical::Reaction | inlinestatic |
| Attempt(Substance *reactant1, Substance *reactant2=NULL, Substance *reactant3=NULL) | bio::chemical::Reaction | inlinestatic |
| Class< Reaction >::bio::Attenuate(const Wave *other) | bio::physical::Wave | virtual |
| bio::chemical::Atom::Attenuate(const Wave *other) | bio::chemical::Atom | virtual |
| BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical, Reaction) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical | bio::chemical::Reaction | |
| Class< Reaction >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Reaction) Class(Reaction *object | bio::chemical::Class< Reaction > | |
| Class< Reaction >::Identifiable< StandardDimension >::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective | bio::physical::Identifiable< StandardDimension > | |
| Class< Reaction >::bio::log::Writer::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Writer) Writer() | bio::log::Writer | |
| Class< Reaction >::bio::physical::Filterable::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Filterable) Filterable() | bio::physical::Filterable | |
| bio::chemical::Atom::BIO_DISAMBIGUATE_ALL_CLASS_METHODS(physical, Atom) explicit Atom() | bio::chemical::Atom | |
| BreakBond(T toDisassociate, BondType type=bond_type::Unknown()) | bio::chemical::Atom | inline |
| BreakBondImplementation(Wave *toDisassociate, AtomicNumber id, BondType type) | bio::chemical::Atom | protectedvirtual |
| Class< Reaction >::bio::Class(T *object, Symmetry *symmetry=NULL) | bio::physical::Class< T > | inline |
| Class< Reaction >::Identifiable< StandardDimension >::Class(Identifiable< StandardDimension > *object, Symmetry *symmetry=NULL) | bio::physical::Class< Identifiable< StandardDimension > > | inline |
| Class< Reaction >::bio::log::Writer::bio::Class(Filterable *object, Symmetry *symmetry=NULL) | bio::physical::Class< Filterable > | inline |
| Class< Reaction >::bio::log::Writer::Class< Writer >::Class(Writer *object, Symmetry *symmetry=NULL) | bio::physical::Class< Writer > | inline |
| bio::chemical::Atom::Class(Atom *object, Symmetry *symmetry=NULL) | bio::physical::Class< Atom > | inline |
| Clear() | bio::chemical::UnorderedStructureInterface | inline |
| Class< Reaction >::bio::Clone() const | bio::physical::Class< T > | inlinevirtual |
| Class< Reaction >::Identifiable< StandardDimension >::Clone() const | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::bio::Clone() const | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::Class< Writer >::Clone() const | bio::physical::Class< Writer > | inlinevirtual |
| bio::chemical::Atom::Clone() const | bio::physical::Class< Atom > | inlinevirtual |
| CloneIntoName(Name name) | bio::physical::Identifiable< StandardDimension > | inline |
| Class< Reaction >::bio::Convert(Wave *wave) | bio::physical::Class< T > | inline |
| Class< Reaction >::Identifiable< StandardDimension >::Convert(Wave *wave) | bio::physical::Class< Identifiable< StandardDimension > > | inline |
| Class< Reaction >::bio::log::Writer::bio::Convert(Wave *wave) | bio::physical::Class< Filterable > | inline |
| Class< Reaction >::bio::log::Writer::Class< Writer >::Convert(Wave *wave) | bio::physical::Class< Writer > | inline |
| bio::chemical::Atom::Convert(Wave *wave) | bio::physical::Class< Atom > | inline |
| Demodulate() | bio::physical::Wave | virtual |
| Demodulate() const | bio::physical::Wave | virtual |
| Class< Reaction >::bio::Disattenuate(const Wave *other) | bio::physical::Wave | virtual |
| bio::chemical::Atom::Disattenuate(const Wave *other) | bio::chemical::Atom | virtual |
| ExternalLog(Filter logFilter, Level level, const char *format,...) const | bio::log::Writer | |
| filter | bio::chemical::Class< Reaction > | |
| filter::Chemical() | bio::chemical::Reaction | |
| 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 | |
| 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 |
| GetCount() const | bio::chemical::UnorderedStructureInterface | inline |
| GetFilter() const | bio::physical::Filterable | |
| GetLogEngine() | bio::log::Writer | |
| GetLogEngine() const | bio::log::Writer | |
| GetNumMatching(const Container *other) const | bio::chemical::UnorderedStructureInterface | inline |
| 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::Class< Reaction >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::Class< Reaction >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| bio::Class< Reaction >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| Identifiable< StandardDimension >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Identifiable< StandardDimension >::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| Identifiable< StandardDimension >::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| Class< Writer >::bio::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Class< Writer >::bio::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| Class< Writer >::bio::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| bio::chemical::Atom::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::chemical::Atom::GetResonanceBetween(const Wave *wave1, const Wave *wave2) | bio::physical::Wave | static |
| bio::chemical::Atom::GetResonanceBetween(const Wave *wave, const Properties &properties) | bio::physical::Wave | static |
| GetStringFrom(std::string separator=", ") | bio::chemical::UnorderedStructureInterface | inline |
| Has(T content) const | bio::chemical::UnorderedStructureInterface | inline |
| HasAll(const Container *contents) const | bio::chemical::UnorderedStructureInterface | inline |
| 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 |
| 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 |
| Identifiable< StandardDimension >::InitializeImplementation(ByteStreams args) | bio::physical::Observer< Perspective< StandardDimension > > | inlineprotectedvirtual |
| bio::log::Writer::InitializeImplementation(ByteStreams args) | bio::log::Writer | protectedvirtual |
| Initiate(StandardDimension id) | bio::chemical::Reaction | static |
| Initiate() | bio::chemical::Reaction | inlinestatic |
| Insert(T toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::LinearStructureInterface | inline |
| 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 |
| m_filter | bio::physical::Filterable | protected |
| m_hasBeenInitialized | bio::VirtualBase | protected |
| m_id | bio::physical::Identifiable< StandardDimension > | |
| Class< Reaction >::bio::m_object | bio::physical::Class< T > | protected |
| Class< Reaction >::Identifiable< StandardDimension >::m_object | bio::physical::Class< Identifiable< StandardDimension > > | protected |
| Class< Reaction >::bio::log::Writer::bio::m_object | bio::physical::Class< Filterable > | protected |
| Class< Reaction >::bio::log::Writer::Class< Writer >::m_object | bio::physical::Class< Writer > | protected |
| bio::chemical::Atom::m_object | bio::physical::Class< Atom > | protected |
| m_requiredReactants | bio::chemical::Reaction | protected |
| bio::Class< Reaction >::m_signal | bio::physical::Wave | protected |
| Identifiable< StandardDimension >::m_signal | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::m_signal | bio::physical::Wave | protected |
| bio::chemical::Atom::m_signal | bio::physical::Wave | protected |
| bio::Class< Reaction >::m_symmetry | bio::physical::Wave | protected |
| Identifiable< StandardDimension >::m_symmetry | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::m_symmetry | bio::physical::Wave | protected |
| bio::chemical::Atom::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 |
| Class< Reaction >::bio::operator Wave *() | bio::physical::Class< T > | inlinevirtual |
| Class< Reaction >::Identifiable< StandardDimension >::operator Wave *() | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::bio::operator Wave *() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::Class< Writer >::operator Wave *() | bio::physical::Class< Writer > | inlinevirtual |
| bio::chemical::Atom::operator Wave *() | bio::physical::Class< Atom > | inlinevirtual |
| operator Writer *() | bio::physical::Class< Writer > | inlinevirtual |
| operator()(Reactants *reactants) const | bio::chemical::Reaction | virtual |
| 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 |
| perspective | bio::chemical::Class< Reaction > | |
| Perspective typedef | bio::physical::Observer< Perspective< StandardDimension > > | |
| Process(Reactants *reactants) const | bio::chemical::Reaction | inlinevirtual |
| reactants | bio::chemical::Reaction | |
| ReactantsMeetRequirements(const Reactants *toCheck) const | bio::chemical::Reaction | virtual |
| Reaction | bio::chemical::Reaction | |
| ReactionPerspective::Instance() | bio::chemical::Reaction | |
| Class< Reaction >::bio::Reify(Symmetry *symmetry) | bio::physical::Wave | virtual |
| Class< Reaction >::bio::log::Writer::Reify(Symmetry *symmetry) | bio::physical::Filterable | virtual |
| bio::chemical::Atom::Reify(physical::Symmetry *symmetry) | bio::chemical::Atom | virtual |
| Remove(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Require(Reactant *reactant) | bio::chemical::Reaction | virtual |
| Require(Name typeName, const Substance *substance) | bio::chemical::Reaction | |
| Require(Name typeName, const typename UnorderedMotif< Property >::Contents *properties, const typename UnorderedMotif< State >::Contents *states) | bio::chemical::Reaction | |
| Require() | bio::chemical::Reaction | inline |
| Require(const T *substance) | bio::chemical::Reaction | inline |
| Require(const typename UnorderedMotif< Property >::Contents *properties, const typename UnorderedMotif< State >::Contents *states) | bio::chemical::Reaction | inline |
| SetFilter(Filter filter) | bio::physical::Filterable | virtual |
| SetLogEngine(Engine *logEngine) | bio::log::Writer | virtual |
| SetPerspective(Perspective *perspective) | bio::physical::Observer< Perspective< StandardDimension > > | inlinevirtual |
| Class< Reaction >::bio::Spin() const | bio::physical::Wave | virtual |
| Class< Reaction >::bio::log::Writer::Spin() const | bio::physical::Filterable | virtual |
| bio::chemical::Atom::Spin() const | bio::chemical::Atom | virtual |
| Structure() | bio::chemical::Structure | |
| symmetry_type::Operation()) explicit Reaction(Name name | bio::chemical::Reaction | |
| ThreadSafe() | bio::ThreadSafe | |
| ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| UnlockThread() const | bio::ThreadSafe | |
| UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inline |
| VirtualBase() | bio::VirtualBase | protected |
| bio::Class< Reaction >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| Identifiable< StandardDimension >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::log::Writer::Class< Writer >::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Atom::Wave(Symmetry *symmetry=NULL) | bio::physical::Wave | |
| Writer(Engine *logEngine, Filter logFilter) | bio::log::Writer | |
| ~Atom() | bio::chemical::Atom | virtual |
| Class< Reaction >::bio::~Class() | bio::physical::Class< T > | inlinevirtual |
| Class< Reaction >::Identifiable< StandardDimension >::~Class() | bio::physical::Class< Identifiable< StandardDimension > > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::bio::~Class() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Reaction >::bio::log::Writer::Class< Writer >::~Class() | bio::physical::Class< Writer > | inlinevirtual |
| bio::chemical::Atom::~Class() | bio::physical::Class< Atom > | inlinevirtual |
| ~Filterable() | bio::physical::Filterable | virtual |
| ~LinearStructureInterface() | bio::chemical::LinearStructureInterface | inlinevirtual |
| ~Observer() | bio::physical::Observer< Perspective< StandardDimension > > | inlinevirtual |
| ~Structure() | bio::chemical::Structure | virtual |
| ~ThreadSafe() | bio::ThreadSafe | virtual |
| ~UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inlinevirtual |
| ~VirtualBase() | bio::VirtualBase | protectedvirtual |
| ~Wave() | bio::physical::Wave | virtual |
| ~Writer() | bio::log::Writer | virtual |
1.9.4