| Add(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Add(Pointer< T > t) | bio::chemical::UnorderedStructureInterface | inline |
| As() const | bio::chemical::Atom | |
| Class< Mix >::AsAtom() | bio::chemical::Class< Mix > | inlinevirtual |
| Class< Mix >::AsAtom() const | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::AsAtom() | bio::chemical::Class< Reaction > | inlinevirtual |
| bio::chemical::Reaction::AsAtom() const | bio::chemical::Class< Reaction > | inlinevirtual |
| AsBonded() const | bio::chemical::Atom | |
| AsBondedQuantum() const | bio::chemical::Atom | inline |
| AsLogWriter() const | bio::log::Writer | virtual |
| Class< Mix >::AsWave() | bio::chemical::Class< Mix > | inline |
| Class< Mix >::AsWave() const | bio::chemical::Class< Mix > | inline |
| bio::chemical::Reaction::AsWave() | bio::chemical::Class< Reaction > | inline |
| bio::chemical::Reaction::AsWave() const | bio::chemical::Class< Reaction > | inline |
| Atom() | bio::chemical::Atom | explicit |
| Atom(const Atom &other) | bio::chemical::Atom | explicit |
| Attempt(Pointer< Reactants > reactants) | bio::chemical::Reaction | inlinestatic |
| Attempt(Substances &substances) | bio::chemical::Reaction | inlinestatic |
| Attempt(Pointer< Substance > reactant1, Pointer< Substance > reactant2=Pointer< Substance >(), Pointer< Substance > reactant3=Pointer< Substance >()) | bio::chemical::Reaction | inlinestatic |
| Class< Mix >::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Reaction > | inlinevirtual |
| BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical, Reaction, filter::Chemical(), symmetry_type::Operation()) explicit Reaction(const Name &name | bio::chemical::Reaction | |
| BondClonePolicy typedef | bio::chemical::Atom | |
| BondMutator typedef | bio::chemical::Atom | |
| BondVisitor typedef | bio::chemical::Atom | |
| BreakBond(T toDisassociate, BondType type=bond_type::Unknown()) | bio::chemical::Atom | inline |
| BreakBondImplementation(AtomicNumber id, BondType type) | bio::chemical::Atom | virtual |
| BreakBondImplementationLocked(AtomicNumber id, BondType type) | bio::chemical::Atom | |
| Class< Mix >::Class(Pointer< Mix > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Mix > | inline |
| Class< Mix >::Class(Pointer< Mix > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Mix > | inline |
| Class< Mix >::Class(Pointer< Mix > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Mix > | inline |
| Class< Mix >::Class(const Class &other) | bio::chemical::Class< Mix > | inline |
| Class< Mix >::bio::physical::Class::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inline |
| Class< Mix >::bio::physical::Class::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inline |
| Class< Mix >::bio::physical::Class::Class(const Class &other) | bio::physical::Class< T > | inline |
| Class< Mix >::Identifiable< Id >::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inline |
| Class< Mix >::Identifiable< Id >::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inline |
| Class< Mix >::Identifiable< Id >::Class(const Class &other) | bio::physical::Class< T > | inline |
| Class< Mix >::bio::log::Writer::Class(Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Writer > | inline |
| Class< Mix >::bio::log::Writer::Class(Pointer< Writer > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Writer > | inline |
| Class< Mix >::bio::log::Writer::Class(const Class &other) | bio::physical::Class< Writer > | inline |
| Class< Mix >::bio::log::Writer::Class(Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Filterable > | inline |
| Class< Mix >::bio::physical::Filterable::Class(Pointer< Filterable > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Filterable > | inline |
| Class< Mix >::bio::physical::Filterable::Class(const Class &other) | bio::physical::Class< Filterable > | inline |
| Class< Mix >::bio::chemical::Atom::Class(Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Atom > | inline |
| Class< Mix >::bio::chemical::Atom::Class(Pointer< Atom > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Atom > | inline |
| Class< Mix >::bio::chemical::Atom::Class(const Class &other) | bio::physical::Class< Atom > | inline |
| bio::chemical::Reaction::Class(Pointer< Reaction > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Reaction > | inline |
| bio::chemical::Reaction::Class(Pointer< Reaction > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Reaction > | inline |
| bio::chemical::Reaction::Class(Pointer< Reaction > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Reaction > | inline |
| bio::chemical::Reaction::Class(const Class &other) | bio::chemical::Class< Reaction > | inline |
| bio::physical::Class::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::physical::Class::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inline |
| bio::physical::Class::Class(const Class &other) | bio::physical::Class< T > | inline |
| Clear() | bio::chemical::UnorderedStructureInterface | inline |
| Class< Mix >::Clone() const | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::Clone() const | bio::chemical::Class< Reaction > | inlinevirtual |
| CloneBondsFrom(const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy) | bio::chemical::Atom | |
| Class< Mix >::bio::Class< Mix >::Class< Mix >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| Class< Mix >::Identifiable< Id >::Class< Mix >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| Class< Mix >::bio::log::Writer::Class< Writer >::Convert(Pointer< Wave > wave) | bio::physical::Class< Writer > | inlinestatic |
| Class< Mix >::bio::log::Writer::bio::physical::Filterable::Convert(Pointer< Wave > wave) | bio::physical::Class< Filterable > | inlinestatic |
| Class< Mix >::bio::chemical::Atom::Convert(Pointer< Wave > wave) | bio::physical::Class< Atom > | inlinestatic |
| bio::chemical::Reaction::Class< Reaction >::bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| DefaultBondClonePolicy(const Bond &bond) | bio::chemical::Atom | static |
| Class< Mix >::Demodulate() | bio::chemical::Class< Mix > | inlinevirtual |
| Class< Mix >::Demodulate() const | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::Demodulate() | bio::chemical::Class< Reaction > | inlinevirtual |
| bio::chemical::Reaction::Demodulate() const | bio::chemical::Class< Reaction > | inlinevirtual |
| Class< Mix >::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Reaction > | inlinevirtual |
| Class< Mix >::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inlineprotected |
| Class< Mix >::Elementary() | bio::chemical::Elementary< T > | inlineprotected |
| bio::chemical::Reaction::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inline |
| bio::chemical::Reaction::Elementary() | bio::chemical::Elementary< T > | inline |
| Filterable() | bio::physical::Filterable | |
| Filterable(Filter filter) | bio::physical::Filterable | |
| ForEach(Pointer< ExcitationBase > excitation) | bio::chemical::LinearStructureInterface | inline |
| ForEachBond(BondVisitor visitor, void *context=NULL) const | bio::chemical::Atom | |
| ForEachBondMutable(BondMutator mutator, void *context=NULL) | bio::chemical::Atom | |
| FormBond(T toBond, BondType type=bond_type::Unknown()) | bio::chemical::Atom | inline |
| FormBondImplementation(Pointer< physical::Wave > toBond, AtomicNumber id, BondType type) | bio::chemical::Atom | virtual |
| FormBondImplementation(Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded) | bio::chemical::Atom | |
| FormBondImplementationLocked(Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded) | bio::chemical::Atom | |
| GetAll() | bio::chemical::UnorderedStructureInterface | inline |
| GetAll() const | bio::chemical::UnorderedStructureInterface | inline |
| GetAllBonds() | bio::chemical::Atom | |
| GetAllBonds() const | bio::chemical::Atom | |
| GetAllLike(Pointer< const Affinity > affinity) const | bio::chemical::LinearStructureInterface | inline |
| GetBonded(Valence position) | bio::chemical::Atom | |
| GetBonded(Valence position) const | bio::chemical::Atom | |
| GetBondId() | bio::chemical::Atom | inlinestatic |
| GetBondPosition(AtomicNumber bondedId) const | bio::chemical::Atom | |
| GetBondPosition(const Name &typeName) const | bio::chemical::Atom | |
| GetBondPosition() const | bio::chemical::Atom | inline |
| GetBondPositionLocked(AtomicNumber bondedId) const | bio::chemical::Atom | |
| GetBondType(Valence position) const | bio::chemical::Atom | |
| GetBondType() const | bio::chemical::Atom | inline |
| GetById(const Id &id) | bio::chemical::LinearStructureInterface | inline |
| GetById(const Id &id) const | bio::chemical::LinearStructureInterface | inline |
| GetByName(const Name &name) | bio::chemical::LinearStructureInterface | inline |
| GetByName(const Name &name) const | bio::chemical::LinearStructureInterface | inline |
| GetCount() const | bio::chemical::UnorderedStructureInterface | inline |
| GetFilter() const | bio::physical::Filterable | |
| GetId() const | bio::physical::Identifiable< Id > | inlinevirtual |
| GetName() const | bio::physical::Identifiable< Id > | inlinevirtual |
| GetNumMatching(Pointer< const Container > other) const | bio::chemical::UnorderedStructureInterface | inline |
| GetOrCreateById(Id id) | bio::chemical::LinearStructureInterface | inline |
| GetOrCreateByName(const Name &name) | bio::chemical::LinearStructureInterface | inline |
| GetPerspective() const | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| Class< Mix >::GetProperties() const | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::GetProperties() const | bio::chemical::Class< Reaction > | inlinevirtual |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| Identifiable< Id >::Class< Mix >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Identifiable< Id >::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| Identifiable< Id >::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::log::Writer::Class< Mix >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::log::Writer::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::log::Writer::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Mix >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Mix >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::chemical::Reaction::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::chemical::Reaction::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::chemical::Reaction::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| GetStringFrom(std::string separator=", ") | bio::chemical::UnorderedStructureInterface | inline |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::GetSymmetry() const | bio::physical::Wave | |
| Identifiable< Id >::Class< Mix >::GetSymmetry() const | bio::physical::Wave | |
| bio::log::Writer::Class< Writer >::Class< Mix >::GetSymmetry() const | bio::physical::Wave | |
| bio::chemical::Atom::Class< Mix >::GetSymmetry() const | bio::physical::Wave | |
| bio::chemical::Reaction::bio::Class< Reaction >::GetSymmetry() const | bio::physical::Wave | |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::GetTypeId() const | bio::physical::Wave | inline |
| Identifiable< Id >::Class< Mix >::GetTypeId() const | bio::physical::Wave | inline |
| bio::log::Writer::Class< Writer >::Class< Mix >::GetTypeId() const | bio::physical::Wave | inline |
| bio::chemical::Atom::Class< Mix >::GetTypeId() const | bio::physical::Wave | inline |
| bio::chemical::Reaction::bio::Class< Reaction >::GetTypeId() const | bio::physical::Wave | inline |
| Class< Mix >::bio::GetWaveObject() | bio::physical::Class< T > | inlinevirtual |
| Class< Mix >::bio::GetWaveObject() const | bio::physical::Class< T > | inlinevirtual |
| Class< Mix >::bio::log::Writer::Class< Writer >::GetWaveObject() | bio::physical::Class< Writer > | inlinevirtual |
| Class< Mix >::bio::log::Writer::GetWaveObject() const | bio::physical::Class< Writer > | inlinevirtual |
| Class< Mix >::bio::log::Writer::bio::physical::Filterable::GetWaveObject() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Mix >::bio::physical::Filterable::GetWaveObject() const | bio::physical::Class< Filterable > | inlinevirtual |
| bio::chemical::Atom::GetWaveObject() | bio::physical::Class< Atom > | inlinevirtual |
| bio::chemical::Atom::GetWaveObject() const | bio::physical::Class< Atom > | inlinevirtual |
| Has(T content) const | bio::chemical::UnorderedStructureInterface | inline |
| Has(Pointer< T > content) const | bio::chemical::UnorderedStructureInterface | inline |
| HasAll(Pointer< const Container > contents) const | bio::chemical::UnorderedStructureInterface | inline |
| Identifiable(Pointer< Perspective< Id > > perspective=NULL) | bio::physical::Identifiable< Id > | inlineexplicit |
| Identifiable(const Name &name, Pointer< Perspective< Id > > perspective=NULL) | bio::physical::Identifiable< Id > | inlineexplicit |
| Identifiable(Identifier id, Pointer< Perspective< Id > > perspective=NULL) | bio::physical::Identifiable< Id > | inlineexplicit |
| Identifiable(const Identifiable &other) | bio::physical::Identifiable< Id > | inline |
| Identifier typedef | bio::physical::Identifiable< Id > | |
| Ids typedef | bio::physical::Identifiable< Id > | |
| Import(Pointer< const UnorderedMotif< T > > other) | bio::chemical::UnorderedStructureInterface | inline |
| Import(Pointer< const LinearMotif< T > > other) | bio::chemical::UnorderedStructureInterface | inline |
| Import(const ::bio::Arrangement< T > &other) | bio::chemical::UnorderedStructureInterface | inline |
| ImportAll(Pointer< const physical::Wave > other) | bio::chemical::UnorderedStructureInterface | inline |
| ImportAllCollectVisitor(const chemical::Bond &bond, void *ctx) | bio::chemical::UnorderedStructureInterface | inlinestatic |
| IndexBond(AtomicNumber bondedId, Valence position) | bio::chemical::Atom | protected |
| 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< Mix >::Identifiable< Id >::InitializeImplementation(ByteStreams &args) | bio::physical::Identifiable< Id > | inlineprotectedvirtual |
| bio::log::Writer::InitializeImplementation(ByteStreams &args) | bio::physical::Filterable | virtual |
| Initiate(const AtomicNumber &id) | bio::chemical::Reaction | static |
| Initiate() | bio::chemical::Reaction | inlinestatic |
| Insert(typename LinearStructureRequest< T >::PointerType toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::LinearStructureInterface | inline |
| IsEnabled(LogLevel level) const | bio::log::Writer | |
| IsId(Identifier id) const | bio::physical::Identifiable< Id > | inlinevirtual |
| IsName(const Name &name) const | bio::physical::Identifiable< Id > | inlinevirtual |
| IsNameInsensitive(const Name &name) const | bio::physical::Identifiable< Id > | inlinevirtual |
| LinearStructureInterface() | bio::chemical::LinearStructureInterface | inline |
| LockMutexShared() const | bio::ThreadSafe | |
| LockThread() const | bio::ThreadSafe | |
| Class< Mix >::Log(LogLevel level, const char *format, va_list args) const | bio::log::Writer | virtual |
| Class< Mix >::Log(Pointer< const Writer > writer, LogLevel level, const char *format,...) | bio::log::Writer | static |
| bio::chemical::Reaction::bio::chemical::Structure::Log(const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId()) | bio::chemical::UnorderedStructureInterface | inline |
| mBackflowPreventer | bio::chemical::Atom | protected |
| mBondIndex | bio::chemical::Atom | protected |
| mBonds | bio::chemical::Atom | protected |
| mFilter | bio::physical::Filterable | protected |
| mHasBeenInitialized | bio::VirtualBase | protected |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::mHasSignal | bio::physical::Wave | protected |
| Identifiable< Id >::Class< Mix >::mHasSignal | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::Class< Mix >::mHasSignal | bio::physical::Wave | protected |
| bio::chemical::Atom::Class< Mix >::mHasSignal | bio::physical::Wave | protected |
| bio::chemical::Reaction::bio::Class< Reaction >::mHasSignal | bio::physical::Wave | protected |
| Mix() | bio::chemical::Mix | |
| Class< Mix >::bio::Class< Mix >::Class< Mix >::mObject | bio::physical::Class< T > | mutableprotected |
| Class< Mix >::Identifiable< Id >::Class< Mix >::mObject | bio::physical::Class< T > | mutableprotected |
| Class< Mix >::bio::log::Writer::Class< Writer >::mObject | bio::physical::Class< Writer > | mutableprotected |
| Class< Mix >::bio::log::Writer::bio::physical::Filterable::mObject | bio::physical::Class< Filterable > | mutableprotected |
| Class< Mix >::bio::chemical::Atom::mObject | bio::physical::Class< Atom > | mutableprotected |
| bio::chemical::Reaction::Class< Reaction >::bio::mObject | bio::physical::Class< T > | mutableprotected |
| Class< Mix >::Modulate(Pointer< ::bio::physical::Wave > signal) | bio::chemical::Class< Mix > | inlinevirtual |
| Class< Mix >::bio::physical::Class::Modulate(Pointer< Wave > signal) | bio::physical::Wave | virtual |
| bio::chemical::Reaction::Modulate(Pointer< ::bio::physical::Wave > signal) | bio::chemical::Class< Reaction > | inlinevirtual |
| mRequiredReactants | bio::chemical::Reaction | protected |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::mSymmetry | bio::physical::Wave | mutableprotected |
| Identifiable< Id >::Class< Mix >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::log::Writer::Class< Writer >::Class< Mix >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::chemical::Atom::Class< Mix >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::chemical::Reaction::bio::Class< Reaction >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::mTypeId | bio::physical::Wave | protected |
| Identifiable< Id >::Class< Mix >::mTypeId | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::Class< Mix >::mTypeId | bio::physical::Wave | protected |
| bio::chemical::Atom::Class< Mix >::mTypeId | bio::physical::Wave | protected |
| bio::chemical::Reaction::bio::Class< Reaction >::mTypeId | bio::physical::Wave | protected |
| Observer(Pointer< Perspective > perspective=NULL) | bio::physical::Observer< PERSPECTIVE > | inlineexplicit |
| Observer(const Observer &other) | bio::physical::Observer< PERSPECTIVE > | inline |
| operator Atom &() | bio::physical::Class< Atom > | inlinevirtual |
| operator const Atom &() const | bio::physical::Class< Atom > | inlinevirtual |
| operator const Filterable &() const | bio::physical::Class< Filterable > | inlinevirtual |
| operator const T &() const | bio::physical::Class< T > | inlinevirtual |
| operator const Writer &() const | bio::physical::Class< Writer > | inlinevirtual |
| operator Filterable &() | bio::physical::Class< Filterable > | inlinevirtual |
| operator Id() const | bio::physical::Identifiable< Id > | inlinevirtual |
| Class< Mix >::operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< Mix > | inline |
| bio::chemical::Reaction::operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< Reaction > | inline |
| Class< Mix >::bio::operator Pointer< Wave >() | bio::physical::Class< T > | inlinevirtual |
| Class< Mix >::bio::log::Writer::Class< Writer >::operator Pointer< Wave >() | bio::physical::Class< Writer > | inlinevirtual |
| Class< Mix >::bio::log::Writer::bio::physical::Filterable::operator Pointer< Wave >() | bio::physical::Class< Filterable > | inlinevirtual |
| bio::chemical::Atom::operator Pointer< Wave >() | bio::physical::Class< Atom > | inlinevirtual |
| operator T() const | bio::chemical::Atom | |
| operator T&() | bio::physical::Class< T > | inlinevirtual |
| operator Writer &() | bio::physical::Class< Writer > | inlinevirtual |
| operator()(Pointer< Reactants > reactants) const | bio::chemical::Reaction | virtual |
| operator*(Pointer< Wave > signal) | bio::physical::Wave | virtual |
| operator*() | bio::physical::Wave | virtual |
| operator*() const | bio::physical::Wave | virtual |
| operator+(Pointer< const Wave > other) | bio::physical::Wave | virtual |
| operator-(Pointer< const Wave > other) | bio::physical::Wave | virtual |
| operator<<(std::ostream &out, const Identifiable< Id > &t) | bio::physical::Identifiable< Id > | inlineprotected |
| Class< Mix >::bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Mix >::Identifiable< Id >::Class< Mix >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Mix >::bio::log::Writer::Class< Writer >::Class< Mix >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Mix >::bio::chemical::Atom::Class< Atom >::Class< Mix >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Mix >::bio::chemical::Atom::bio::ThreadSafe::operator=(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| bio::chemical::Reaction::Class< Reaction >::bio::operator=(const Wave &other) | bio::physical::Wave | |
| operator==(const Identifier id) const | bio::physical::Identifiable< Id > | inlinevirtual |
| operator==(const Name &name) const | bio::physical::Identifiable< Id > | inlinevirtual |
| operator==(const Identifiable< Id > &other) const | bio::physical::Identifiable< Id > | inlinevirtual |
| operator|(Pointer< Symmetry > symmetry) | bio::physical::Wave | virtual |
| Perspective typedef | bio::physical::Observer< PERSPECTIVE > | |
| Process(Pointer< Reactants > reactants) const | bio::chemical::Mix | virtual |
| reactants | bio::chemical::Reaction | |
| ReactantsMeetRequirements(Pointer< const Reactants > toCheck) const | bio::chemical::Mix | virtual |
| Class< Mix >::RegisterProperties(const Properties &properties) | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::RegisterProperties(const Properties &properties) | bio::chemical::Class< Reaction > | inlinevirtual |
| Class< Mix >::RegisterType() | bio::chemical::Elementary< T > | inlineprotected |
| bio::chemical::Reaction::RegisterType() | bio::chemical::Elementary< T > | inline |
| Class< Mix >::bio::Reify(Pointer< const Symmetry > symmetry) | bio::physical::Wave | virtual |
| Class< Mix >::bio::log::Writer::bio::physical::Filterable::Reify(Pointer< const Symmetry > symmetry) | bio::physical::Filterable | virtual |
| bio::chemical::Atom::Reify(Pointer< const physical::Symmetry > symmetry) | bio::chemical::Atom | virtual |
| Remove(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Remove(Pointer< T > t) | bio::chemical::UnorderedStructureInterface | inline |
| RemoveById(const Id &id) | bio::chemical::LinearStructureInterface | inline |
| RemoveByName(const Name &name) | bio::chemical::LinearStructureInterface | inline |
| Require(Pointer< Reactant > reactant) | bio::chemical::Reaction | virtual |
| Require(const Name &typeName, Pointer< const Substance > substance) | bio::chemical::Reaction | |
| Require(const Name &typeName, const UnorderedMotif< Property > &properties, const UnorderedMotif< State > &states) | bio::chemical::Reaction | |
| Require() | bio::chemical::Reaction | inline |
| Require(Pointer< const T > substance) | bio::chemical::Reaction | inline |
| Require(Pointer< const typename UnorderedMotif< Property >::Contents > properties, Pointer< const typename UnorderedMotif< State >::Contents > states) | bio::chemical::Reaction | inline |
| ResolveBondedForReadById(AtomicNumber bondId) const | bio::chemical::Atom | |
| ResolveBondedForWriteById(AtomicNumber bondId) | bio::chemical::Atom | |
| ResolveLinearMotif() | bio::chemical::LinearStructureInterface | inlineprotected |
| ResolveLinearMotif() const | bio::chemical::LinearStructureInterface | inlineprotected |
| SetFilter(Filter filter) | bio::physical::Filterable | virtual |
| SetId(Identifier id) | bio::physical::Identifiable< Id > | inlinevirtual |
| SetName(const Name &name) | bio::physical::Identifiable< Id > | inlinevirtual |
| SetPerspective(Pointer< Perspective< Id > > perspective) | bio::physical::Identifiable< Id > | inlinevirtual |
| bio::physical::Observer::SetPerspective(Pointer< Perspective > perspective) | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| Identifiable< Id >::Class< Mix >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::log::Writer::Class< Writer >::Class< Mix >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::chemical::Atom::Class< Mix >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::chemical::Reaction::bio::Class< Reaction >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| ShouldLog(Pointer< const Writer > writer, LogLevel level) | bio::log::Writer | static |
| Class< Mix >::bio::Spin() const | bio::physical::Wave | virtual |
| Class< Mix >::bio::log::Writer::bio::physical::Filterable::Spin() const | bio::physical::Filterable | virtual |
| bio::chemical::Atom::Spin() const | bio::chemical::Atom | virtual |
| Structure() | bio::chemical::Structure | |
| Class< Mix >::Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Mix > | inlinevirtual |
| Class< Mix >::Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Mix > | inlinevirtual |
| Class< Mix >::bio::physical::Class::Superpose(Pointer< const Wave > displacement, Pointer< Interference > pattern) | bio::physical::Wave | virtual |
| Class< Mix >::bio::physical::Class::Superpose(const ConstWaves &displacement, Pointer< Interference > pattern) | bio::physical::Wave | virtual |
| bio::chemical::Reaction::Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Reaction > | inlinevirtual |
| bio::chemical::Reaction::Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Reaction > | inlinevirtual |
| ThreadSafe() | bio::ThreadSafe | |
| ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| UnindexBond(AtomicNumber bondedId) | bio::chemical::Atom | protected |
| UnlockMutexShared() const | bio::ThreadSafe | |
| UnlockThread() const | bio::ThreadSafe | |
| UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inline |
| VirtualBase() | bio::VirtualBase | protected |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::Class< Mix >::Class< Mix >::Class< Mix >::Class< Mix >::Wave(const Wave &other) | bio::physical::Wave | |
| Identifiable< Id >::Class< Mix >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| Identifiable< Id >::Class< Mix >::Wave(const Wave &other) | bio::physical::Wave | |
| bio::log::Writer::Class< Mix >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::log::Writer::Class< Mix >::Wave(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Atom::Class< Mix >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Atom::Class< Mix >::Wave(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Reaction::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Reaction::Wave(const Wave &other) | bio::physical::Wave | |
| Writer() | bio::log::Writer | |
| Writer(Filter logFilter) | bio::log::Writer | |
| ~Atom() | bio::chemical::Atom | virtual |
| Class< Mix >::~Class() | bio::chemical::Class< Mix > | inlinevirtual |
| bio::chemical::Reaction::~Class() | bio::chemical::Class< Reaction > | inlinevirtual |
| ~Elementary() | bio::chemical::Elementary< T > | inlineprotectedvirtual |
| ~Filterable() | bio::physical::Filterable | virtual |
| ~Identifiable() | bio::physical::Identifiable< Id > | inlinevirtual |
| ~LinearStructureInterface() | bio::chemical::LinearStructureInterface | inlinevirtual |
| ~Mix() | bio::chemical::Mix | virtual |
| ~Observer() | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| ~Structure() | bio::chemical::Structure | virtual |
| ~ThreadSafe() | bio::ThreadSafe | |
| ~UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inlinevirtual |
| ~VirtualBase() | bio::VirtualBase | protectedvirtual |
| ~Wave() | bio::physical::Wave | virtual |
| ~Writer() | bio::log::Writer | virtual |
