| As() const | bio::chemical::Atom | |
| AsAtom() | bio::chemical::Class< Impulse > | inlinevirtual |
| AsAtom() const | bio::chemical::Class< Impulse > | inlinevirtual |
| AsBonded() const | bio::chemical::Atom | |
| AsBondedQuantum() const | bio::chemical::Atom | inline |
| AsLogWriter() const | bio::log::Writer | virtual |
| AsWave() | bio::chemical::Class< Impulse > | inline |
| AsWave() const | bio::chemical::Class< Impulse > | inline |
| Atom() | bio::chemical::Atom | explicit |
| Atom(const Atom &other) | bio::chemical::Atom | explicit |
| Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Impulse > | inlinevirtual |
| 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(Pointer< Impulse > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Impulse > | inline |
| Class(Pointer< Impulse > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Impulse > | inline |
| Class(Pointer< Impulse > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Impulse > | inline |
| Class(const Class &other) | bio::chemical::Class< Impulse > | 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 |
| Identifiable< Id >::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inline |
| Identifiable< Id >::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inline |
| Identifiable< Id >::Class(const Class &other) | bio::physical::Class< T > | inline |
| bio::log::Writer::Class(Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Writer > | inline |
| bio::log::Writer::Class(Pointer< Writer > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Writer > | inline |
| bio::log::Writer::Class(const Class &other) | bio::physical::Class< Writer > | inline |
| bio::log::Writer::Class(Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Filterable > | inline |
| bio::physical::Filterable::Class(Pointer< Filterable > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Filterable > | inline |
| bio::physical::Filterable::Class(const Class &other) | bio::physical::Class< Filterable > | inline |
| bio::chemical::Atom::Class(Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Atom > | inline |
| bio::chemical::Atom::Class(Pointer< Atom > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Atom > | inline |
| bio::chemical::Atom::Class(const Class &other) | bio::physical::Class< Atom > | inline |
| Clone() const | bio::chemical::Class< Impulse > | inlinevirtual |
| CloneBondsFrom(const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy) | bio::chemical::Atom | |
| bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| Identifiable< Id >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| bio::log::Writer::Class< Writer >::Convert(Pointer< Wave > wave) | bio::physical::Class< Writer > | inlinestatic |
| bio::log::Writer::bio::physical::Filterable::Convert(Pointer< Wave > wave) | bio::physical::Class< Filterable > | inlinestatic |
| bio::chemical::Atom::Convert(Pointer< Wave > wave) | bio::physical::Class< Atom > | inlinestatic |
| DefaultBondClonePolicy(const Bond &bond) | bio::chemical::Atom | static |
| Demodulate() | bio::chemical::Class< Impulse > | inlinevirtual |
| Demodulate() const | bio::chemical::Class< Impulse > | inlinevirtual |
| Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Impulse > | inlinevirtual |
| Elementary(const Properties properties) | bio::chemical::Elementary< T > | inlineprotected |
| Elementary() | bio::chemical::Elementary< T > | inlineprotected |
| Filterable() | bio::physical::Filterable | |
| Filterable(Filter filter) | bio::physical::Filterable | |
| 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 | |
| GetAllBonds() | bio::chemical::Atom | |
| GetAllBonds() const | bio::chemical::Atom | |
| 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 |
| GetFilter() const | bio::physical::Filterable | |
| GetId() const | bio::physical::Identifiable< Id > | inlinevirtual |
| GetImpulseProtein() | bio::neural::Impulse | |
| GetName() const | bio::physical::Identifiable< Id > | inlinevirtual |
| GetPerspective() const | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| GetProperties() const | bio::chemical::Class< Impulse > | inlinevirtual |
| bio::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| Identifiable< Id >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Identifiable< Id >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| Identifiable< Id >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::log::Writer::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::log::Writer::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::log::Writer::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::chemical::Atom::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::chemical::Atom::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::chemical::Atom::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::GetSymmetry() const | bio::physical::Wave | |
| Identifiable< Id >::GetSymmetry() const | bio::physical::Wave | |
| bio::log::Writer::Class< Writer >::GetSymmetry() const | bio::physical::Wave | |
| bio::chemical::Atom::GetSymmetry() const | bio::physical::Wave | |
| GetTrigger() const | bio::neural::Impulse | |
| bio::GetTypeId() const | bio::physical::Wave | inline |
| Identifiable< Id >::GetTypeId() const | bio::physical::Wave | inline |
| bio::log::Writer::Class< Writer >::GetTypeId() const | bio::physical::Wave | inline |
| bio::chemical::Atom::GetTypeId() const | bio::physical::Wave | inline |
| bio::GetWaveObject() | bio::physical::Class< T > | inlinevirtual |
| bio::GetWaveObject() const | bio::physical::Class< T > | inlinevirtual |
| bio::log::Writer::Class< Writer >::GetWaveObject() | bio::physical::Class< Writer > | inlinevirtual |
| bio::log::Writer::GetWaveObject() const | bio::physical::Class< Writer > | inlinevirtual |
| bio::log::Writer::bio::physical::Filterable::GetWaveObject() | bio::physical::Class< Filterable > | inlinevirtual |
| 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 |
| 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 > | |
| Impulse(FiringCondition trigger=firing_condition::None(), Name impulseName="", Pointer< Neuron > caller=NULL, bool shouldBeActive=true) | bio::neural::Impulse | |
| 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 |
| Identifiable< Id >::InitializeImplementation(ByteStreams &args) | bio::physical::Identifiable< Id > | inlineprotectedvirtual |
| bio::log::Writer::InitializeImplementation(ByteStreams &args) | bio::physical::Filterable | virtual |
| 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 |
| LockMutexShared() const | bio::ThreadSafe | |
| LockThread() const | bio::ThreadSafe | |
| Log(LogLevel level, const char *format, va_list args) const | bio::log::Writer | virtual |
| Log(Pointer< const Writer > writer, LogLevel level, const char *format,...) | bio::log::Writer | static |
| mBackflowPreventer | bio::chemical::Atom | protected |
| mBondIndex | bio::chemical::Atom | protected |
| mBonds | bio::chemical::Atom | protected |
| mCaller | bio::neural::Impulse | protected |
| mFilter | bio::physical::Filterable | protected |
| mHasBeenInitialized | bio::VirtualBase | protected |
| bio::mHasSignal | bio::physical::Wave | protected |
| Identifiable< Id >::mHasSignal | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::mHasSignal | bio::physical::Wave | protected |
| bio::chemical::Atom::mHasSignal | bio::physical::Wave | protected |
| mImpulse | bio::neural::Impulse | protected |
| bio::mObject | bio::physical::Class< T > | mutableprotected |
| Identifiable< Id >::mObject | bio::physical::Class< T > | mutableprotected |
| bio::log::Writer::Class< Writer >::mObject | bio::physical::Class< Writer > | mutableprotected |
| bio::log::Writer::bio::physical::Filterable::mObject | bio::physical::Class< Filterable > | mutableprotected |
| bio::chemical::Atom::mObject | bio::physical::Class< Atom > | mutableprotected |
| Modulate(Pointer< ::bio::physical::Wave > signal) | bio::chemical::Class< Impulse > | inlinevirtual |
| bio::physical::Class::Modulate(Pointer< Wave > signal) | bio::physical::Wave | virtual |
| mShouldBeActive | bio::neural::Impulse | protected |
| bio::mSymmetry | bio::physical::Wave | mutableprotected |
| Identifiable< Id >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::log::Writer::Class< Writer >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::chemical::Atom::mSymmetry | bio::physical::Wave | mutableprotected |
| mTrigger | bio::neural::Impulse | protected |
| bio::mTypeId | bio::physical::Wave | protected |
| Identifiable< Id >::mTypeId | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::mTypeId | bio::physical::Wave | protected |
| bio::chemical::Atom::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 |
| operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< Impulse > | inline |
| bio::operator Pointer< Wave >() | bio::physical::Class< T > | inlinevirtual |
| bio::log::Writer::Class< Writer >::operator Pointer< Wave >() | bio::physical::Class< Writer > | inlinevirtual |
| 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< 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 |
| bio::operator=(const Wave &other) | bio::physical::Wave | |
| Identifiable< Id >::operator=(const Wave &other) | bio::physical::Wave | |
| bio::log::Writer::Class< Writer >::operator=(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Atom::Class< Atom >::operator=(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Atom::bio::ThreadSafe::operator=(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| 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 > | |
| RegisterProperties(const Properties &properties) | bio::chemical::Class< Impulse > | inlinevirtual |
| RegisterType() | bio::chemical::Elementary< T > | inlineprotected |
| bio::Reify(Pointer< const Symmetry > symmetry) | bio::physical::Wave | virtual |
| 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 |
| ResolveBondedForReadById(AtomicNumber bondId) const | bio::chemical::Atom | |
| ResolveBondedForWriteById(AtomicNumber bondId) | bio::chemical::Atom | |
| Send() | bio::neural::Impulse | |
| SetCaller(Pointer< Neuron > caller) | bio::neural::Impulse | |
| 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::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| Identifiable< Id >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::log::Writer::Class< Writer >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::chemical::Atom::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| ShouldLog(Pointer< const Writer > writer, LogLevel level) | bio::log::Writer | static |
| bio::Spin() const | bio::physical::Wave | virtual |
| bio::log::Writer::bio::physical::Filterable::Spin() const | bio::physical::Filterable | virtual |
| bio::chemical::Atom::Spin() const | bio::chemical::Atom | virtual |
| Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Impulse > | inlinevirtual |
| Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Impulse > | inlinevirtual |
| bio::physical::Class::Superpose(Pointer< const Wave > displacement, Pointer< Interference > pattern) | bio::physical::Wave | virtual |
| bio::physical::Class::Superpose(const ConstWaves &displacement, Pointer< Interference > pattern) | bio::physical::Wave | virtual |
| ThreadSafe() | bio::ThreadSafe | |
| ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| UnindexBond(AtomicNumber bondedId) | bio::chemical::Atom | protected |
| UnlockMutexShared() const | bio::ThreadSafe | |
| UnlockThread() const | bio::ThreadSafe | |
| VirtualBase() | bio::VirtualBase | protected |
| bio::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::Wave(const Wave &other) | bio::physical::Wave | |
| Identifiable< Id >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| Identifiable< Id >::Wave(const Wave &other) | bio::physical::Wave | |
| bio::log::Writer::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::log::Writer::Wave(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Atom::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Atom::Wave(const Wave &other) | bio::physical::Wave | |
| Writer() | bio::log::Writer | |
| Writer(Filter logFilter) | bio::log::Writer | |
| ~Atom() | bio::chemical::Atom | virtual |
| ~Class() | bio::chemical::Class< Impulse > | inlinevirtual |
| ~Elementary() | bio::chemical::Elementary< T > | inlineprotectedvirtual |
| ~Filterable() | bio::physical::Filterable | virtual |
| ~Identifiable() | bio::physical::Identifiable< Id > | inlinevirtual |
| ~Impulse() | bio::neural::Impulse | virtual |
| ~Observer() | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| ~ThreadSafe() | bio::ThreadSafe | |
| ~VirtualBase() | bio::VirtualBase | protectedvirtual |
| ~Wave() | bio::physical::Wave | virtual |
| ~Writer() | bio::log::Writer | virtual |
