| AbstractMotif() | bio::chemical::AbstractMotif | protected |
| AbstractMotif(const AbstractMotif &other) | bio::chemical::AbstractMotif | protected |
| Add(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Add(Pointer< T > t) | bio::chemical::UnorderedStructureInterface | inline |
| AddImplementation(ContentPointer content) | bio::chemical::DependentMotif< Solute, Solution > | inlineprotectedvirtual |
| bio::chemical::LinearMotif::AddImplementation(ContentPointer content) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::AddImplementation(const Pointer< CONTENT_TYPE > content) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| AddSharedImplementation(ContentPointer content) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| AddSharedWaveByContentType(Pointer< physical::Wave > wave) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| AddWaveByContentType(Pointer< physical::Wave > wave) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| AllocateContents enum value | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | protected |
| As() const | bio::chemical::Atom | |
| Class< Solution >::AsAtom() | bio::chemical::Class< Solution > | inlinevirtual |
| Class< Solution >::AsAtom() const | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::AsAtom() | bio::chemical::Class< Substance > | inlinevirtual |
| bio::chemical::Substance::AsAtom() const | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::AsAtom() | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::AsAtom() const | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::AsAtom() | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| bio::chemical::LinearMotif::AsAtom() const | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| AsBonded() const | bio::chemical::Atom | |
| AsBondedQuantum() const | bio::chemical::Atom | inline |
| AsLogWriter() const | bio::log::Writer | virtual |
| Class< Solution >::AsWave() | bio::chemical::Class< Solution > | inline |
| Class< Solution >::AsWave() const | bio::chemical::Class< Solution > | inline |
| bio::chemical::Substance::AsWave() | bio::chemical::Class< Substance > | inline |
| bio::chemical::Substance::AsWave() const | bio::chemical::Class< Substance > | inline |
| DependentMotif< Solute, Solution >::bio::AsWave() | bio::chemical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::AsWave() const | bio::chemical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::AsWave() | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::AsWave() const | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotected |
| bio::chemical::LinearMotif::AsWave() | bio::chemical::Class< T > | inlineprotected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::AsWave() const | bio::chemical::Class< T > | inlineprotected |
| Atom() | bio::chemical::Atom | explicit |
| Atom(const Atom &other) | bio::chemical::Atom | explicit |
| Class< Solution >::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::DependentMotif< Solute, Solution > | inlineprotectedvirtual |
| BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical, Solution, filter::Chemical()) virtual Id Dissolve(Pointer< Substance > toDissolve | bio::chemical::Solution | |
| BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR(chemical, Substance, filter::Chemical()) Substance(const UnorderedMotif< Property > &properties | bio::chemical::Substance | |
| 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< Solution >::Class(Pointer< Solution > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Solution > | inline |
| Class< Solution >::Class(Pointer< Solution > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Solution > | inline |
| Class< Solution >::Class(Pointer< Solution > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Solution > | inline |
| Class< Solution >::Class(const Class &other) | bio::chemical::Class< Solution > | inline |
| Class< Solution >::bio::physical::Class::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inline |
| Class< Solution >::bio::physical::Class::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inline |
| Class< Solution >::bio::physical::Class::Class(const Class &other) | bio::physical::Class< T > | inline |
| Class< Solution >::Identifiable< Id >::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inline |
| Class< Solution >::Identifiable< Id >::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inline |
| Class< Solution >::Identifiable< Id >::Class(const Class &other) | bio::physical::Class< T > | inline |
| Class< Solution >::bio::log::Writer::Class(Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Writer > | inline |
| Class< Solution >::bio::log::Writer::Class(Pointer< Writer > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Writer > | inline |
| Class< Solution >::bio::log::Writer::Class(const Class &other) | bio::physical::Class< Writer > | inline |
| Class< Solution >::bio::log::Writer::Class(Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Filterable > | inline |
| Class< Solution >::bio::physical::Filterable::Class(Pointer< Filterable > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Filterable > | inline |
| Class< Solution >::bio::physical::Filterable::Class(const Class &other) | bio::physical::Class< Filterable > | inline |
| Class< Solution >::bio::chemical::Atom::Class(Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Atom > | inline |
| Class< Solution >::bio::chemical::Atom::Class(Pointer< Atom > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Atom > | inline |
| Class< Solution >::bio::chemical::Atom::Class(const Class &other) | bio::physical::Class< Atom > | inline |
| bio::chemical::Substance::Class(Pointer< Substance > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Substance > | inline |
| bio::chemical::Substance::Class(Pointer< Substance > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Substance > | inline |
| bio::chemical::Substance::Class(Pointer< Substance > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Substance > | inline |
| bio::chemical::Substance::Class(const Class &other) | bio::chemical::Class< Substance > | 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 |
| DependentMotif< Solute, Solution >::bio::Class(Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::Class(Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::Class(Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::Class(const Class &other) | bio::chemical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::physical::Class::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::physical::Class::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::physical::Class::Class(const Class &other) | bio::physical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::Class(Pointer< LinearMotif< CONTENT_TYPE > > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class(Pointer< LinearMotif< CONTENT_TYPE > > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class(Pointer< LinearMotif< CONTENT_TYPE > > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class(const Class &other) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::physical::Class::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::physical::Class::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::physical::Class::Class(const Class &other) | bio::physical::Class< T > | inlineprotected |
| bio::chemical::LinearMotif::Class(Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< T > | inlineprotected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::Class(Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< T > | inlineprotected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::Class(Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< T > | inlineprotected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::Class(const Class &other) | bio::chemical::Class< T > | inlineprotected |
| bio::physical::Class::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inlineprotected |
| bio::physical::Class::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inlineprotected |
| bio::physical::Class::Class(const Class &other) | bio::physical::Class< T > | inlineprotected |
| Clear() | bio::chemical::UnorderedStructureInterface | inline |
| ClearImplementation() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| Class< Solution >::Clone() const | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::Clone() const | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::Clone() const | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::Clone() const | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| CloneBondsFrom(const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy) | bio::chemical::Atom | |
| Contents typedef | bio::chemical::LinearMotif< CONTENT_TYPE > | protected |
| ContentsAllocation enum name | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | protected |
| Class< Solution >::bio::Class< Solution >::Class< Solution >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| Class< Solution >::Identifiable< Id >::Class< Solution >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| Class< Solution >::bio::log::Writer::Class< Writer >::Convert(Pointer< Wave > wave) | bio::physical::Class< Writer > | inlinestatic |
| Class< Solution >::bio::log::Writer::bio::physical::Filterable::Convert(Pointer< Wave > wave) | bio::physical::Class< Filterable > | inlinestatic |
| Class< Solution >::bio::chemical::Atom::Convert(Pointer< Wave > wave) | bio::physical::Class< Atom > | inlinestatic |
| bio::chemical::Substance::Class< Substance >::bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| DependentMotif< Solute, Solution >::bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlineprotectedstatic |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlineprotectedstatic |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlineprotectedstatic |
| Covalent< UnorderedMotif< Property > >::Covalent() | bio::Covalent< UnorderedMotif< Property > > | inline |
| Covalent< UnorderedMotif< Property > >::Covalent(const Covalent &other) | bio::Covalent< UnorderedMotif< Property > > | inline |
| Covalent< UnorderedMotif< State > >::Covalent() | bio::Covalent< UnorderedMotif< State > > | inline |
| Covalent< UnorderedMotif< State > >::Covalent(const Covalent &other) | bio::Covalent< UnorderedMotif< State > > | inline |
| CreateImplementation() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| CreateWithIdImplementation(const Id &id) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| CreateWithNameImplementation(const Name &name) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| DefaultBondClonePolicy(const Bond &bond) | bio::chemical::Atom | static |
| DeferContents enum value | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | protected |
| Class< Solution >::Demodulate() | bio::chemical::Class< Solution > | inlinevirtual |
| Class< Solution >::Demodulate() const | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::Demodulate() | bio::chemical::Class< Substance > | inlinevirtual |
| bio::chemical::Substance::Demodulate() const | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::Demodulate() | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::Demodulate() const | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::Demodulate() | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| bio::chemical::LinearMotif::Demodulate() const | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| DependentMotif(EnvironmentPointer environment=NULL) | bio::chemical::DependentMotif< Solute, Solution > | inlineexplicitprotected |
| DependentMotif(const typename LinearMotif< Solute >::Contents *contents, EnvironmentPointer environment=NULL) | bio::chemical::DependentMotif< Solute, Solution > | inlineexplicitprotected |
| DependentMotif(const DependentMotif< Solute, Solution > &toCopy) | bio::chemical::DependentMotif< Solute, Solution > | inlineprotected |
| diffusionEffort | bio::chemical::Solution | |
| diffusionTime | bio::chemical::Solution | |
| Disable() | bio::chemical::Substance | virtual |
| Class< Solution >::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::DependentMotif< Solute, Solution > | inlineprotectedvirtual |
| Efflux(const Id &soluteId) | bio::chemical::Solution | virtual |
| Efflux(const Id &soluteId) const | bio::chemical::Solution | virtual |
| Efflux(const Name &substanceName) | bio::chemical::Solution | virtual |
| Efflux(const Name &substanceName) const | bio::chemical::Solution | virtual |
| Class< Solution >::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inlineprotected |
| Class< Solution >::Elementary() | bio::chemical::Elementary< T > | inlineprotected |
| bio::chemical::Substance::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inline |
| bio::chemical::Substance::Elementary() | bio::chemical::Elementary< T > | inline |
| DependentMotif< Solute, Solution >::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inlineprotected |
| DependentMotif< Solute, Solution >::Elementary() | bio::chemical::Elementary< T > | inlineprotected |
| bio::chemical::LinearMotif::DependentMotif< Solute, Solution >::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inlineprotected |
| bio::chemical::LinearMotif::DependentMotif< Solute, Solution >::Elementary() | bio::chemical::Elementary< T > | inlineprotected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inlineprotected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::Elementary() | bio::chemical::Elementary< T > | inlineprotected |
| Enable() | bio::chemical::Substance | virtual |
| EnvironmentDependent(EnvironmentPointer environment=NULL) | bio::chemical::EnvironmentDependent< T > | inlineprotected |
| EnvironmentType typedef | bio::chemical::EnvironmentDependent< T > | protected |
| 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 | |
| ForEachImplementation(Pointer< const ExcitationBase > excitation) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| 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 | |
| GetAllImplementation() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetAllImplementation() const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetAllLike(Pointer< const Affinity > affinity) const | bio::chemical::LinearStructureInterface | inline |
| GetAllLikeImplementation(Pointer< const Affinity > affinity) const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetAllSolutes() | bio::chemical::Solution | virtual |
| GetAllSolutes() const | bio::chemical::Solution | virtual |
| 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 |
| GetByIdImplementation(const Id &id) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetByIdImplementation(const Id &id) const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetByName(const Name &name) | bio::chemical::LinearStructureInterface | inline |
| GetByName(const Name &name) const | bio::chemical::LinearStructureInterface | inline |
| GetByNameImplementation(const Name &name) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetByNameImplementation(const Name &name) const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetClassProperties() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedstatic |
| GetContentTypeId() const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetCount() const | bio::chemical::UnorderedStructureInterface | inline |
| GetCountImplementation() const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| GetEnvironment() | bio::chemical::EnvironmentDependent< T > | inlineprotectedvirtual |
| GetEnvironment() const | bio::chemical::EnvironmentDependent< T > | inlineprotectedvirtual |
| 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 |
| GetNumMatchingImplementation(Pointer< const Container > other) const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| GetOrCreateById(Id id) | bio::chemical::LinearStructureInterface | inline |
| GetOrCreateByIdImplementation(const Id &id) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetOrCreateByName(const Name &name) | bio::chemical::LinearStructureInterface | inline |
| GetOrCreateByNameImplementation(const Name &name) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| GetPerspective() const | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| Class< Solution >::GetProperties() const | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::GetProperties() const | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::GetProperties() const | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::GetProperties() const | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::log::Writer::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::log::Writer::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::log::Writer::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::chemical::Substance::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::chemical::Substance::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::chemical::Substance::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| DependentMotif< Solute, Solution >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | protectedstatic |
| DependentMotif< Solute, Solution >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | protectedstatic |
| DependentMotif< Solute, Solution >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | protectedstatic |
| bio::chemical::LinearMotif::DependentMotif< Solute, Solution >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | protectedstatic |
| bio::chemical::LinearMotif::DependentMotif< Solute, Solution >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | protectedstatic |
| bio::chemical::LinearMotif::DependentMotif< Solute, Solution >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | protectedstatic |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | protectedstatic |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | protectedstatic |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | protectedstatic |
| GetStringFrom(std::string separator=", ") | bio::chemical::UnorderedStructureInterface | inline |
| GetStringFromImplementation(std::string separator=", ") | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::GetStringFromImplementation(String separator=", ") | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetSymmetry() const | bio::physical::Wave | |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetSymmetry() const | bio::physical::Wave | |
| bio::log::Writer::Class< Writer >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetSymmetry() const | bio::physical::Wave | |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetSymmetry() const | bio::physical::Wave | |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::GetSymmetry() const | bio::physical::Wave | |
| DependentMotif< Solute, Solution >::bio::GetSymmetry() const | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::GetSymmetry() const | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::GetSymmetry() const | bio::physical::Wave | protected |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetTypeId() const | bio::physical::Wave | inline |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetTypeId() const | bio::physical::Wave | inline |
| bio::log::Writer::Class< Writer >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetTypeId() const | bio::physical::Wave | inline |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::GetTypeId() const | bio::physical::Wave | inline |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::GetTypeId() const | bio::physical::Wave | inline |
| DependentMotif< Solute, Solution >::bio::GetTypeId() const | bio::physical::Wave | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::GetTypeId() const | bio::physical::Wave | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::GetTypeId() const | bio::physical::Wave | inlineprotected |
| Class< Solution >::bio::GetWaveObject() | bio::physical::Class< T > | inlinevirtual |
| Class< Solution >::bio::GetWaveObject() const | bio::physical::Class< T > | inlinevirtual |
| Class< Solution >::bio::log::Writer::Class< Writer >::GetWaveObject() | bio::physical::Class< Writer > | inlinevirtual |
| Class< Solution >::bio::log::Writer::GetWaveObject() const | bio::physical::Class< Writer > | inlinevirtual |
| Class< Solution >::bio::log::Writer::bio::physical::Filterable::GetWaveObject() | bio::physical::Class< Filterable > | inlinevirtual |
| Class< Solution >::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 |
| HasAllImplementation(Pointer< const Container > contents) const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| HasImplementation(const ContentPointer &content) const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::HasImplementation(const Pointer< CONTENT_TYPE > content) const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| 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 |
| ImportImplementation(Pointer< const LinearMotif< CONTENT_TYPE > > other) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| ImportImplementation(const void *other) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::ImportImplementation(Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > other) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| IndexBond(AtomicNumber bondedId, Valence position) | bio::chemical::Atom | protected |
| Influx(const Solute &toInflux) | bio::chemical::Solution | virtual |
| 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< Solution >::Identifiable< Id >::InitializeImplementation(ByteStreams &args) | bio::physical::Identifiable< Id > | inlineprotectedvirtual |
| bio::log::Writer::InitializeImplementation(ByteStreams &args) | bio::physical::Filterable | virtual |
| Insert(typename LinearStructureRequest< T >::PointerType toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::LinearStructureInterface | inline |
| InsertImplementation(ContentPointer toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::DependentMotif< Solute, Solution > | inlineprotectedvirtual |
| bio::chemical::LinearMotif::InsertImplementation(ContentPointer toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| Class< Solution >::IsEnabled(LogLevel level) const | bio::log::Writer | |
| bio::chemical::Substance::IsEnabled() const | bio::chemical::Substance | virtual |
| 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 |
| LinearMotif() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineexplicitprotected |
| LinearMotif(const Contents *contents) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineexplicitprotected |
| LinearMotif(const LinearMotif< CONTENT_TYPE > &toCopy) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotected |
| LinearStructureInterface() | bio::chemical::LinearStructureInterface | inline |
| LockMutexShared() const | bio::ThreadSafe | |
| LockThread() const | bio::ThreadSafe | |
| Class< Solution >::Log(LogLevel level, const char *format, va_list args) const | bio::log::Writer | virtual |
| Class< Solution >::Log(Pointer< const Writer > writer, LogLevel level, const char *format,...) | bio::log::Writer | static |
| bio::chemical::Substance::bio::chemical::Structure::Log(const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId()) | bio::chemical::UnorderedStructureInterface | inline |
| LogImplementation(const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId()) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| mBackflowPreventer | bio::chemical::Atom | protected |
| mBondIndex | bio::chemical::Atom | protected |
| mBonds | bio::chemical::Atom | protected |
| mContentId | bio::chemical::LinearMotif< CONTENT_TYPE > | mutableprotected |
| mContents | bio::chemical::AbstractMotif | mutableprotected |
| mEnvironment | bio::chemical::EnvironmentDependent< T > | protected |
| mFilter | bio::physical::Filterable | protected |
| mHasBeenInitialized | bio::VirtualBase | protected |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mHasSignal | bio::physical::Wave | protected |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mHasSignal | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mHasSignal | bio::physical::Wave | protected |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mHasSignal | bio::physical::Wave | protected |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::mHasSignal | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::mHasSignal | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::mHasSignal | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::mHasSignal | bio::physical::Wave | protected |
| Class< Solution >::bio::Class< Solution >::Class< Solution >::mObject | bio::physical::Class< T > | mutableprotected |
| Class< Solution >::Identifiable< Id >::Class< Solution >::mObject | bio::physical::Class< T > | mutableprotected |
| Class< Solution >::bio::log::Writer::Class< Writer >::mObject | bio::physical::Class< Writer > | mutableprotected |
| Class< Solution >::bio::log::Writer::bio::physical::Filterable::mObject | bio::physical::Class< Filterable > | mutableprotected |
| Class< Solution >::bio::chemical::Atom::mObject | bio::physical::Class< Atom > | mutableprotected |
| bio::chemical::Substance::Class< Substance >::bio::mObject | bio::physical::Class< T > | mutableprotected |
| DependentMotif< Solute, Solution >::bio::mObject | bio::physical::Class< T > | mutableprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::mObject | bio::physical::Class< T > | mutableprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::mObject | bio::physical::Class< T > | mutableprotected |
| Class< Solution >::Modulate(Pointer< ::bio::physical::Wave > signal) | bio::chemical::Class< Solution > | inlinevirtual |
| Class< Solution >::bio::physical::Class::Modulate(Pointer< Wave > signal) | bio::physical::Wave | virtual |
| bio::chemical::Substance::Modulate(Pointer< ::bio::physical::Wave > signal) | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::Modulate(Pointer< ::bio::physical::Wave > signal) | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::Modulate(Pointer< ::bio::physical::Wave > signal) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mSymmetry | bio::physical::Wave | mutableprotected |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::log::Writer::Class< Writer >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::mSymmetry | bio::physical::Wave | mutableprotected |
| DependentMotif< Solute, Solution >::bio::mSymmetry | bio::physical::Wave | mutableprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::mSymmetry | bio::physical::Wave | mutableprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::mSymmetry | bio::physical::Wave | mutableprotected |
| Covalent< UnorderedMotif< Property > >::mT | bio::Covalent< UnorderedMotif< Property > > | protected |
| Covalent< UnorderedMotif< State > >::mT | bio::Covalent< UnorderedMotif< State > > | protected |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mTypeId | bio::physical::Wave | protected |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mTypeId | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mTypeId | bio::physical::Wave | protected |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::mTypeId | bio::physical::Wave | protected |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::mTypeId | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::mTypeId | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::mTypeId | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::mTypeId | bio::physical::Wave | protected |
| NewContents(Index expectedSize) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedstatic |
| NewContents(const Contents &contents) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedstatic |
| NewContents(Pointer< const Container > contents) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedstatic |
| Covalent< UnorderedMotif< Property > >::Object() | bio::Covalent< UnorderedMotif< Property > > | inline |
| Covalent< UnorderedMotif< Property > >::Object() const | bio::Covalent< UnorderedMotif< Property > > | inline |
| Covalent< UnorderedMotif< State > >::Object() | bio::Covalent< UnorderedMotif< State > > | inline |
| Covalent< UnorderedMotif< State > >::Object() const | bio::Covalent< UnorderedMotif< State > > | inline |
| 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< Solution >::operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< Solution > | inline |
| bio::chemical::Substance::operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< Substance > | inline |
| DependentMotif< Solute, Solution >::bio::operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::operator Pointer< ::bio::physical::Wave >() | bio::chemical::Class< T > | inlineprotected |
| Class< Solution >::bio::operator Pointer< Wave >() | bio::physical::Class< T > | inlinevirtual |
| Class< Solution >::bio::log::Writer::Class< Writer >::operator Pointer< Wave >() | bio::physical::Class< Writer > | inlinevirtual |
| Class< Solution >::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 |
| Class< Solution >::bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Solution >::Identifiable< Id >::Class< Solution >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Solution >::bio::log::Writer::Class< Writer >::Class< Solution >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Solution >::bio::chemical::Atom::Class< Atom >::Class< Solution >::operator=(const Wave &other) | bio::physical::Wave | |
| Class< Solution >::bio::chemical::Atom::bio::ThreadSafe::operator=(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| bio::chemical::Substance::Class< Substance >::bio::operator=(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Substance::Covalent< UnorderedMotif< Property > >::operator=(const Covalent &other) | bio::Covalent< UnorderedMotif< Property > > | inline |
| bio::chemical::Substance::Covalent< UnorderedMotif< State > >::operator=(const Covalent &other) | bio::Covalent< UnorderedMotif< State > > | inline |
| DependentMotif< Solute, Solution >::operator=(const Wave &other) | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::operator=(const Wave &other) | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::operator=(const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::Class::operator=(const Wave &other) | bio::physical::Wave | protected |
| bio::chemical::AbstractMotif::operator=(const AbstractMotif &other) | bio::chemical::AbstractMotif | protected |
| 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 > | |
| Class< Solution >::RegisterProperties(const Properties &properties) | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::RegisterProperties(const Properties &properties) | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::RegisterProperties(const Properties &properties) | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::RegisterProperties(const Properties &properties) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| Class< Solution >::RegisterType() | bio::chemical::Elementary< T > | inlineprotected |
| bio::chemical::Substance::RegisterType() | bio::chemical::Elementary< T > | inline |
| DependentMotif< Solute, Solution >::bio::RegisterType() | bio::chemical::Elementary< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::RegisterType() | bio::chemical::Elementary< T > | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::RegisterType() | bio::chemical::Elementary< T > | inlineprotected |
| Class< Solution >::bio::Reify(Pointer< const Symmetry > symmetry) | bio::physical::Wave | virtual |
| Class< Solution >::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 |
| ReleaseContentOwnership() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotected |
| ReleaseImplementation(const ContentPointer content) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotected |
| Remove(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Remove(Pointer< T > t) | bio::chemical::UnorderedStructureInterface | inline |
| RemoveById(const Id &id) | bio::chemical::LinearStructureInterface | inline |
| RemoveByIdImplementation(const Id &id) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| RemoveByName(const Name &name) | bio::chemical::LinearStructureInterface | inline |
| RemoveByNameImplementation(const Name &name) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| RemoveImplementation(const ContentPointer content) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::RemoveImplementation(const Pointer< CONTENT_TYPE > content) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| ResolveBondedForReadById(AtomicNumber bondId) const | bio::chemical::Atom | |
| ResolveBondedForWriteById(AtomicNumber bondId) | bio::chemical::Atom | |
| ResolveLinearMotif() | bio::chemical::LinearStructureInterface | inlineprotected |
| ResolveLinearMotif() const | bio::chemical::LinearStructureInterface | inlineprotected |
| Separate(const Id &id) | bio::chemical::Solution | virtual |
| SetEnvironment(EnvironmentPointer environment) | bio::chemical::DependentMotif< Solute, Solution > | inlineprotectedvirtual |
| bio::chemical::EnvironmentDependent::SetEnvironment(EnvironmentPointer environment) | bio::chemical::EnvironmentDependent< T > | inlineprotectedvirtual |
| 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< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::log::Writer::Class< Writer >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| DependentMotif< Solute, Solution >::bio::SetTypeId(uint16_t typeId) | bio::physical::Wave | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::bio::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::Class< LinearMotif< CONTENT_TYPE > >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inlineprotected |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::bio::SetTypeId(uint16_t typeId) | bio::physical::Wave | inlineprotected |
| ShouldLog(Pointer< const Writer > writer, LogLevel level) | bio::log::Writer | static |
| Class< Solution >::bio::Spin() const | bio::physical::Wave | virtual |
| Class< Solution >::bio::log::Writer::bio::physical::Filterable::Spin() const | bio::physical::Filterable | virtual |
| bio::chemical::Atom::Spin() const | bio::chemical::Atom | virtual |
| states | bio::chemical::Substance | |
| Structure() | bio::chemical::Structure | |
| Class< Solution >::Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Solution > | inlinevirtual |
| Class< Solution >::Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Solution > | inlinevirtual |
| Class< Solution >::bio::physical::Class::Superpose(Pointer< const Wave > displacement, Pointer< Interference > pattern) | bio::physical::Wave | virtual |
| Class< Solution >::bio::physical::Class::Superpose(const ConstWaves &displacement, Pointer< Interference > pattern) | bio::physical::Wave | virtual |
| bio::chemical::Substance::Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Substance > | inlinevirtual |
| bio::chemical::Substance::Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| bio::chemical::LinearMotif::Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| ThreadSafe() | bio::ThreadSafe | |
| ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| UnindexBond(AtomicNumber bondedId) | bio::chemical::Atom | protected |
| UnlockMutexShared() const | bio::ThreadSafe | |
| UnlockThread() const | bio::ThreadSafe | |
| UnorderedMotif() | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotected |
| UnorderedMotif(ContentsAllocation allocation) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineexplicitprotected |
| UnorderedMotif(Pointer< const Contents > contents) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotected |
| UnorderedMotif(Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > toCopy) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotected |
| UnorderedMotif(const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotected |
| UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inline |
| VirtualBase() | bio::VirtualBase | protected |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(const Wave &other) | bio::physical::Wave | |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| Identifiable< Id >::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(const Wave &other) | bio::physical::Wave | |
| bio::log::Writer::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::log::Writer::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Atom::Class< Solution >::Class< Solution >::Class< Solution >::Class< Solution >::Wave(const Wave &other) | bio::physical::Wave | |
| bio::chemical::Substance::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Substance::Wave(const Wave &other) | bio::physical::Wave | |
| DependentMotif< Solute, Solution >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | protected |
| DependentMotif< Solute, Solution >::Wave(const Wave &other) | bio::physical::Wave | protected |
| bio::chemical::LinearMotif::DependentMotif< Solute, Solution >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | protected |
| bio::chemical::LinearMotif::DependentMotif< Solute, Solution >::Wave(const Wave &other) | bio::physical::Wave | protected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | protected |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::Wave(const Wave &other) | bio::physical::Wave | protected |
| Writer() | bio::log::Writer | |
| Writer(Filter logFilter) | bio::log::Writer | |
| ~AbstractMotif() | bio::chemical::AbstractMotif | protectedvirtual |
| ~Atom() | bio::chemical::Atom | virtual |
| Class< Solution >::~Class() | bio::chemical::Class< Solution > | inlinevirtual |
| bio::chemical::Substance::~Class() | bio::chemical::Class< Substance > | inlinevirtual |
| DependentMotif< Solute, Solution >::bio::~Class() | bio::chemical::Class< T > | inlineprotectedvirtual |
| DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::Class< LinearMotif< CONTENT_TYPE > >::~Class() | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlineprotectedvirtual |
| Covalent< UnorderedMotif< Property > >::~Covalent() | bio::Covalent< UnorderedMotif< Property > > | inlinevirtual |
| Covalent< UnorderedMotif< State > >::~Covalent() | bio::Covalent< UnorderedMotif< State > > | inlinevirtual |
| ~DependentMotif() | bio::chemical::DependentMotif< Solute, Solution > | inlineprotectedvirtual |
| ~Elementary() | bio::chemical::Elementary< T > | inlineprotectedvirtual |
| ~EnvironmentDependent() | bio::chemical::EnvironmentDependent< T > | inlineprotectedvirtual |
| ~Filterable() | bio::physical::Filterable | virtual |
| ~Identifiable() | bio::physical::Identifiable< Id > | inlinevirtual |
| ~LinearMotif() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| ~LinearStructureInterface() | bio::chemical::LinearStructureInterface | inlinevirtual |
| ~Observer() | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| ~Structure() | bio::chemical::Structure | virtual |
| ~Substance() | bio::chemical::Substance | virtual |
| ~ThreadSafe() | bio::ThreadSafe | |
| ~UnorderedMotif() | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineprotectedvirtual |
| ~UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inlinevirtual |
| ~VirtualBase() | bio::VirtualBase | protectedvirtual |
| ~Wave() | bio::physical::Wave | virtual |
| ~Writer() | bio::log::Writer | virtual |
