| UnorderedMotif< TranscriptionFactor >::AbstractMotif() | bio::chemical::AbstractMotif | |
| UnorderedMotif< TranscriptionFactor >::AbstractMotif(const AbstractMotif &other) | bio::chemical::AbstractMotif | |
| bio::molecular::Vesicle::AbstractMotif() | bio::chemical::AbstractMotif | |
| bio::molecular::Vesicle::AbstractMotif(const AbstractMotif &other) | bio::chemical::AbstractMotif | |
| Activate(const Id &proteinId) | bio::genetic::Expressor | |
| Activate(const Name &proteinName) | bio::genetic::Expressor | |
| Activate() | bio::genetic::Expressor | inline |
| Add(const T t) | bio::chemical::UnorderedStructureInterface | inline |
| Add(Pointer< T > t) | bio::chemical::UnorderedStructureInterface | inline |
| bio::UnorderedMotif< TranscriptionFactor >::AddImplementation(const TranscriptionFactor content) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::AddImplementation(ContentPointer content) | bio::chemical::DependentMotif< Solute, Solution > | inlinevirtual |
| bio::chemical::LinearMotif::AddImplementation(ContentPointer content) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::AddImplementation(const Pointer< CONTENT_TYPE > content) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| AddSharedImplementation(ContentPointer content) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlineprotectedvirtual |
| bio::UnorderedMotif< TranscriptionFactor >::AddSharedWaveByContentType(Pointer< physical::Wave > wave) | bio::chemical::AbstractMotif | inlinevirtual |
| bio::molecular::Vesicle::AddSharedWaveByContentType(Pointer< physical::Wave > wave) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| AddToTranscriptome(Pointer< const RNA > toExpress) | bio::genetic::Expressor | virtual |
| bio::UnorderedMotif< TranscriptionFactor >::AddWaveByContentType(Pointer< physical::Wave > wave) | bio::chemical::AbstractMotif | inlinevirtual |
| bio::molecular::Vesicle::AddWaveByContentType(Pointer< physical::Wave > wave) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| bio::UnorderedMotif< TranscriptionFactor >::AllocateContents enum value | bio::chemical::UnorderedMotif< TranscriptionFactor > | protected |
| bio::molecular::Vesicle::AllocateContents enum value | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | protected |
| Apoptose() BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| As() const | bio::chemical::Atom | |
| AsAtom() const | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| AsAtom() | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| AsBonded() const | bio::chemical::Atom | |
| AsBondedQuantum() const | bio::chemical::Atom | inline |
| AsLogWriter() const BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| AsWave() | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| AsWave() const | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| Atom() | bio::chemical::Atom | explicit |
| Atom(const Atom &other) | bio::chemical::Atom | explicit |
| Attenuate(Pointer< const ::bio::physical::Wave > other) BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| Class< CellularForwarder< CALLER, CLOBBER > >::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< T > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Substance > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Solution > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Attenuate(Pointer< const physical::Wave > other) | bio::chemical::DependentMotif< Solute, Solution > | inlinevirtual |
| bio::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecular, Vesicle, filter::Molecular()) Vesicle(const Vesicle &toCopy) | bio::molecular::Vesicle | |
| bio::chemical::Solution::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical, Solution, filter::Chemical()) virtual Id Dissolve(Pointer< Substance > toDissolve | bio::chemical::Solution | protected |
| bio::molecular::Vesicle::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecular, Vesicle, filter::Molecular()) Vesicle(const Vesicle &toCopy) | bio::molecular::Vesicle | |
| bio::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR(chemical, Substance, filter::Chemical()) Substance(const UnorderedMotif< Property > &properties | bio::chemical::Substance | |
| bio::molecular::Molecule::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR(molecular, Molecule, filter::Molecular()) Molecule(const Molecule &toCopy) | bio::molecular::Molecule | |
| bio::genetic::Expressor::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR(genetic, Expressor, filter::Genetic()) virtual ~Expressor() | bio::genetic::Expressor | |
| 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 | |
| BreakDonatedBonds(Pointer< chemical::Atom > receiver) | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inlinestatic |
| BreakDonatedCollectVisitor(const chemical::Bond &bond, void *ctx) | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inlinestatic |
| CacheProteins() BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| CellularForwarder() | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| CellularForwarder(const Name &name) | bio::CellularForwarder< CALLER, CLOBBER > | inlineexplicit |
| CellularForwarder(const Id &id) | bio::CellularForwarder< CALLER, CLOBBER > | inlineexplicit |
| CheckIn() BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| Class(Pointer< CellularForwarder< CALLER, CLOBBER > > object, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval()) | bio::cellular::Class< CellularForwarder< CALLER, CLOBBER > > | inline |
| Class(Pointer< CellularForwarder< CALLER, CLOBBER > > object, const Name &name, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval()) | bio::cellular::Class< CellularForwarder< CALLER, CLOBBER > > | inline |
| Class(Pointer< CellularForwarder< CALLER, CLOBBER > > object, const Id &id, Filter filter=filter::Default(), Milliseconds interval=GetDefaultInterval()) | bio::cellular::Class< CellularForwarder< CALLER, CLOBBER > > | inline |
| bio::genetic::Class::Class(Pointer< T > object, Filter filter=filter::Default()) | bio::genetic::Class< T > | inline |
| bio::genetic::Class::Class(Pointer< T > object, const Name &name, Filter filter=filter::Default()) | bio::genetic::Class< T > | inline |
| bio::genetic::Class::Class(Pointer< T > object, const Id &id, Filter filter=filter::Default()) | bio::genetic::Class< T > | inline |
| bio::molecular::Class::Class(Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< T > | inline |
| bio::molecular::Class::Class(Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< T > | inline |
| bio::molecular::Class::Class(Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< T > | inline |
| bio::chemical::Class::Class(const Class &other) | bio::chemical::Class< T > | 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 |
| bio::Identifiable< Id >::Class(Pointer< T > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< T > | inline |
| bio::Identifiable< Id >::Class(Pointer< T > object, SymmetryFactory symmetryFactory) | bio::physical::Class< T > | inline |
| bio::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 |
| 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::molecular::Molecule::Class(Pointer< Molecule > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Molecule > | inline |
| bio::molecular::Molecule::Class(Pointer< Molecule > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Molecule > | inline |
| bio::molecular::Molecule::Class(Pointer< Molecule > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Molecule > | inline |
| bio::chemical::Class::Class(const Class &other) | bio::chemical::Class< T > | inline |
| bio::genetic::Expressor::Class(Pointer< Expressor > object, Filter filter=filter::Default()) | bio::genetic::Class< Expressor > | inline |
| bio::genetic::Expressor::Class(Pointer< Expressor > object, const Name &name, Filter filter=filter::Default()) | bio::genetic::Class< Expressor > | inline |
| bio::genetic::Expressor::Class(Pointer< Expressor > object, const Id &id, Filter filter=filter::Default()) | bio::genetic::Class< Expressor > | inline |
| bio::molecular::Class::Class(Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< T > | inline |
| bio::molecular::Class::Class(Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< T > | inline |
| bio::molecular::Class::Class(Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< T > | inline |
| bio::chemical::Class::Class(const Class &other) | bio::chemical::Class< T > | 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 |
| bio::UnorderedMotif< TranscriptionFactor >::Class(const Class &other) | bio::chemical::Class< T > | 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 |
| bio::genetic::Expressor::Class(Pointer< Vesicle > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Vesicle > | inline |
| bio::molecular::Vesicle::Class(Pointer< Vesicle > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Vesicle > | inline |
| bio::molecular::Vesicle::Class(Pointer< Vesicle > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Vesicle > | inline |
| bio::genetic::Expressor::Class(Pointer< Solution > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Solution > | inline |
| bio::chemical::Solution::Class(Pointer< Solution > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Solution > | inline |
| bio::chemical::Solution::Class(Pointer< Solution > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< Solution > | inline |
| bio::chemical::Solution::Class(const Class &other) | bio::chemical::Class< Solution > | inline |
| bio::genetic::Expressor::Class(Pointer< LinearMotif< CONTENT_TYPE > > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inline |
| 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 > > | inline |
| 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 > > | inline |
| bio::chemical::LinearMotif::Class(const Class &other) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inline |
| bio::physical::Periodic::Class(Pointer< Periodic > object, Pointer< Symmetry > symmetry=NULL) | bio::physical::Class< Periodic > | inline |
| bio::physical::Periodic::Class(Pointer< Periodic > object, SymmetryFactory symmetryFactory) | bio::physical::Class< Periodic > | inline |
| bio::physical::Periodic::Class(const Class &other) | bio::physical::Class< Periodic > | inline |
| bio::molecular::Vesicle::Class(Pointer< Vesicle > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Vesicle > | inline |
| bio::molecular::Vesicle::Class(Pointer< Vesicle > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Vesicle > | inline |
| bio::molecular::Vesicle::Class(Pointer< Vesicle > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object()) | bio::molecular::Class< Vesicle > | inline |
| bio::chemical::Class::Class(const Class &other) | bio::chemical::Class< T > | 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 |
| bio::UnorderedMotif< TranscriptionFactor >::ClearImplementation() | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::ClearImplementation() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| ClearTranscriptome() | bio::genetic::Expressor | protected |
| Clone() const | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| CloneBondsFrom(const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy) | bio::chemical::Atom | |
| CommonConstructor() | bio::genetic::Expressor | |
| bio::UnorderedMotif< TranscriptionFactor >::Contents typedef | bio::chemical::UnorderedMotif< TranscriptionFactor > | |
| bio::molecular::Vesicle::Contents typedef | bio::chemical::LinearMotif< CONTENT_TYPE > | |
| bio::UnorderedMotif< TranscriptionFactor >::ContentsAllocation enum name | bio::chemical::UnorderedMotif< TranscriptionFactor > | protected |
| bio::molecular::Vesicle::ContentsAllocation enum name | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | protected |
| bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| bio::Identifiable< Id >::bio::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 |
| bio::chemical::Substance::Class< Substance >::bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| bio::molecular::Molecule::Class< Molecule >::bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| bio::genetic::Expressor::Class< Expressor >::bio::Class< Expressor >::Class< Expressor >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| bio::physical::Periodic::Convert(Pointer< Wave > wave) | bio::physical::Class< Periodic > | inlinestatic |
| bio::molecular::Vesicle::Class< Vesicle >::bio::Class< Vesicle >::Class< Vesicle >::Convert(Pointer< Wave > wave) | bio::physical::Class< T > | inlinestatic |
| bio::Covalent< UnorderedMotif< Property > >::Covalent() | bio::Covalent< UnorderedMotif< Property > > | inline |
| bio::Covalent< UnorderedMotif< Property > >::Covalent(const Covalent &other) | bio::Covalent< UnorderedMotif< Property > > | inline |
| bio::Covalent< UnorderedMotif< State > >::Covalent() | bio::Covalent< UnorderedMotif< State > > | inline |
| bio::Covalent< UnorderedMotif< State > >::Covalent(const Covalent &other) | bio::Covalent< UnorderedMotif< State > > | inline |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< Plasmid > >::Covalent() | bio::Covalent< chemical::LinearMotif< Plasmid > > | inline |
| bio::Covalent< chemical::LinearMotif< Plasmid > >::Covalent(const Covalent &other) | bio::Covalent< chemical::LinearMotif< Plasmid > > | inline |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< molecular::Protein > >::Covalent() | bio::Covalent< chemical::LinearMotif< molecular::Protein > > | inline |
| Covalent< chemical::LinearMotif< molecular::Protein > >::Covalent(const Covalent &other) | bio::Covalent< chemical::LinearMotif< molecular::Protein > > | inline |
| CreateDefaultProteins() BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| 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 |
| Crest() BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| DefaultBondClonePolicy(const Bond &bond) | bio::chemical::Atom | static |
| bio::UnorderedMotif< TranscriptionFactor >::DeferContents enum value | bio::chemical::UnorderedMotif< TranscriptionFactor > | protected |
| bio::molecular::Vesicle::DeferContents enum value | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | protected |
| Define(const Name &varName) | bio::molecular::Molecule | inline |
| Define(const Id &id) | bio::molecular::Molecule | inline |
| Define(const Name &varName) | bio::molecular::Molecule | inline |
| Define(const Id &id) | bio::molecular::Molecule | inline |
| Define(const Name &varName, const T &assignment) | bio::molecular::Molecule | inline |
| Define(const Id &id, const T &assignment) | bio::molecular::Molecule | inline |
| Demodulate() BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| Demodulate() const BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| 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 | protected |
| diffusionTime | bio::chemical::Solution | protected |
| Disable() | bio::chemical::Substance | virtual |
| Disattenuate(Pointer< const ::bio::physical::Wave > other) BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| Class< CellularForwarder< CALLER, CLOBBER > >::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< T > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Substance > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::Class< Solution > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Disattenuate(Pointer< const physical::Wave > other) | bio::chemical::DependentMotif< Solute, Solution > | inlinevirtual |
| DonateBonds(Pointer< chemical::Atom > donor, Pointer< chemical::Atom > receiver) | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inlinestatic |
| DonateCollectVisitor(const chemical::Bond &bond, void *ctx) | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inlinestatic |
| DuplicateFrom(Pointer< Molecule > source, const Name &surface) | bio::molecular::Molecule | virtual |
| Efflux(const Id &soluteId) | bio::chemical::Solution | protectedvirtual |
| Efflux(const Id &soluteId) const | bio::chemical::Solution | protectedvirtual |
| Efflux(const Name &substanceName) | bio::chemical::Solution | protectedvirtual |
| Efflux(const Name &substanceName) const | bio::chemical::Solution | protectedvirtual |
| bio::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inlineprotected |
| bio::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 |
| bio::molecular::Molecule::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inline |
| bio::molecular::Molecule::Elementary() | bio::chemical::Elementary< T > | inline |
| bio::genetic::Expressor::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inline |
| bio::genetic::Expressor::Elementary() | bio::chemical::Elementary< T > | inline |
| UnorderedMotif< TranscriptionFactor >::bio::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inline |
| UnorderedMotif< TranscriptionFactor >::bio::Elementary() | bio::chemical::Elementary< T > | inline |
| bio::molecular::Vesicle::Elementary(const Properties properties) | bio::chemical::Elementary< T > | inline |
| bio::molecular::Vesicle::Elementary() | bio::chemical::Elementary< T > | inline |
| Enable() | bio::chemical::Substance | virtual |
| EnvironmentDependent(EnvironmentPointer environment=NULL) | bio::chemical::EnvironmentDependent< T > | inlineprotected |
| EnvironmentType typedef | bio::chemical::EnvironmentDependent< T > | protected |
| ExpressGenes() | bio::genetic::Expressor | virtual |
| 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 | |
| bio::UnorderedMotif< TranscriptionFactor >::GetAllImplementation() | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::UnorderedMotif< TranscriptionFactor >::GetAllImplementation() const | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::GetAllImplementation() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| bio::molecular::Vesicle::GetAllImplementation() const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| 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 | protectedvirtual |
| GetAllSolutes() const | bio::chemical::Solution | protectedvirtual |
| 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 | |
| bio::GetBondType(Valence position) const | bio::chemical::Atom | |
| bio::GetBondType() const | bio::chemical::Atom | inline |
| bio::molecular::Molecule::Metallic< chemical::DependentMotif< Surface, Molecule > >::GetBondType() | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inlinestatic |
| 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 |
| bio::UnorderedMotif< TranscriptionFactor >::GetClassProperties() | bio::chemical::AbstractMotif | static |
| bio::molecular::Vesicle::GetClassProperties() | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinestatic |
| bio::physical::Periodic::GetClassProperties() | bio::physical::Periodic | static |
| bio::UnorderedMotif< TranscriptionFactor >::GetContentTypeId() const | bio::chemical::AbstractMotif | inlinevirtual |
| bio::molecular::Vesicle::GetContentTypeId() const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| GetCount() const | bio::chemical::UnorderedStructureInterface | inline |
| bio::UnorderedMotif< TranscriptionFactor >::GetCountImplementation() const | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::GetCountImplementation() const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| GetDefaultInterval() | bio::physical::Periodic | static |
| GetEnvironment() | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| GetEnvironment() const | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| GetExpressedProteinByName(const Name &proteinName) | bio::genetic::Expressor | inline |
| GetFilter() const | bio::physical::Filterable | |
| GetId() const | bio::physical::Identifiable< Id > | inlinevirtual |
| GetInterval() const | bio::physical::Periodic | |
| GetIntervalInSeconds() const | bio::physical::Periodic | |
| GetName() const | bio::physical::Identifiable< Id > | inlinevirtual |
| GetNumMatching(Pointer< const Container > other) const | bio::chemical::UnorderedStructureInterface | inline |
| bio::UnorderedMotif< TranscriptionFactor >::GetNumMatchingImplementation(Pointer< const Container > other) const | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::GetNumMatchingImplementation(Pointer< const Container > other) const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| 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 |
| GetProperties() const BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | 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 >::bio::bio::bio::bio::bio::bio::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::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::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 |
| bio::molecular::Molecule::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::molecular::Molecule::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::molecular::Molecule::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::genetic::Expressor::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::genetic::Expressor::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::genetic::Expressor::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| UnorderedMotif< TranscriptionFactor >::bio::bio::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| UnorderedMotif< TranscriptionFactor >::bio::bio::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| UnorderedMotif< TranscriptionFactor >::bio::bio::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::physical::Periodic::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::physical::Periodic::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::physical::Periodic::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| bio::molecular::Vesicle::GetResonanceBetween(ConstWaves waves) | bio::physical::Wave | static |
| bio::molecular::Vesicle::GetResonanceBetween(Pointer< const Wave > wave1, Pointer< const Wave > wave2) | bio::physical::Wave | static |
| bio::molecular::Vesicle::GetResonanceBetween(Pointer< const Wave > wave, const Properties &properties) | bio::physical::Wave | static |
| GetStringFrom(std::string separator=", ") | bio::chemical::UnorderedStructureInterface | inline |
| bio::UnorderedMotif< TranscriptionFactor >::GetStringFromImplementation(String separator=", ") | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::UnorderedMotif< TranscriptionFactor >::bio::chemical::AbstractMotif::GetStringFromImplementation(std::string separator=", ") | bio::chemical::AbstractMotif | inline |
| bio::molecular::Vesicle::GetStringFromImplementation(std::string separator=", ") | bio::chemical::LinearMotif< CONTENT_TYPE > | inline |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::GetStringFromImplementation(String separator=", ") | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| bio::GetSymmetry() const | bio::physical::Wave | |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::GetSymmetry() const | bio::physical::Wave | |
| bio::log::Writer::Class< Writer >::GetSymmetry() const | bio::physical::Wave | |
| bio::chemical::Atom::GetSymmetry() const | bio::physical::Wave | |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::GetSymmetry() const | bio::physical::Wave | |
| bio::molecular::Molecule::bio::Class< Molecule >::GetSymmetry() const | bio::physical::Wave | |
| bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::GetSymmetry() const | bio::physical::Wave | |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::GetSymmetry() const | bio::physical::Wave | |
| bio::physical::Periodic::GetSymmetry() const | bio::physical::Wave | |
| bio::molecular::Vesicle::bio::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::GetSymmetry() const | bio::physical::Wave | |
| GetTimeLastCrested() const | bio::physical::Periodic | |
| bio::GetTypeId() const | bio::physical::Wave | inline |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::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::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::GetTypeId() const | bio::physical::Wave | inline |
| bio::molecular::Molecule::bio::Class< Molecule >::GetTypeId() const | bio::physical::Wave | inline |
| bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::GetTypeId() const | bio::physical::Wave | inline |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::GetTypeId() const | bio::physical::Wave | inline |
| bio::physical::Periodic::GetTypeId() const | bio::physical::Wave | inline |
| bio::molecular::Vesicle::bio::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::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 |
| bio::physical::Periodic::GetWaveObject() | bio::physical::Class< Periodic > | inlinevirtual |
| bio::physical::Periodic::GetWaveObject() const | bio::physical::Class< Periodic > | 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 |
| bio::UnorderedMotif< TranscriptionFactor >::HasAllImplementation(Pointer< const Container > contents) const | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::HasAllImplementation(Pointer< const Container > contents) const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| bio::UnorderedMotif< TranscriptionFactor >::HasImplementation(const TranscriptionFactor content) const | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::HasImplementation(const ContentPointer &content) const | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::HasImplementation(const Pointer< CONTENT_TYPE > content) const | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | 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 > | |
| 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 |
| bio::UnorderedMotif< TranscriptionFactor >::ImportImplementation(Pointer< const UnorderedMotif< TranscriptionFactor > > other) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::UnorderedMotif< TranscriptionFactor >::ImportImplementation(const void *other) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::ImportImplementation(Pointer< const LinearMotif< CONTENT_TYPE > > other) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| bio::molecular::Vesicle::ImportImplementation(const void *other) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::ImportImplementation(Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > other) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| IndexBond(AtomicNumber bondedId, Valence position) | bio::chemical::Atom | protected |
| Influx(const Solute &toInflux) | bio::chemical::Solution | protectedvirtual |
| bio::Initialize(ByteStreams &args) | bio::VirtualBase | protected |
| bio::Initialize(ByteStream arg1) | bio::VirtualBase | protected |
| bio::Initialize(ByteStream arg1, ByteStream arg2) | bio::VirtualBase | protected |
| bio::Initialize(ByteStream arg1, ByteStream arg2, ByteStream arg3) | bio::VirtualBase | protected |
| bio::physical::Periodic::Initialize(ByteStreams &args) | bio::VirtualBase | protected |
| bio::physical::Periodic::Initialize(ByteStream arg1) | bio::VirtualBase | protected |
| bio::physical::Periodic::Initialize(ByteStream arg1, ByteStream arg2) | bio::VirtualBase | protected |
| bio::physical::Periodic::Initialize(ByteStream arg1, ByteStream arg2, ByteStream arg3) | bio::VirtualBase | protected |
| bio::Identifiable< Id >::InitializeImplementation(ByteStreams &args) | bio::physical::Identifiable< Id > | inlineprotectedvirtual |
| bio::log::Writer::InitializeImplementation(ByteStreams &args) | bio::physical::Filterable | virtual |
| bio::physical::Periodic::InitializeImplementation(ByteStreams &args) | bio::physical::Periodic | 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 |
| bio::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 |
| bio::LockMutexShared() const | bio::ThreadSafe | |
| bio::ThreadSafe::LockMutexShared() const | bio::ThreadSafe | |
| bio::LockThread() const | bio::ThreadSafe | |
| bio::ThreadSafe::LockThread() const | bio::ThreadSafe | |
| Log(::bio::LogLevel level, const char *format, va_list args) const BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Log(LogLevel level, const char *format, va_list args) const | bio::log::Writer | virtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::Log(Pointer< const Writer > writer, LogLevel level, const char *format,...) | bio::log::Writer | static |
| Class< CellularForwarder< CALLER, CLOBBER > >::Log(const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId()) | bio::chemical::UnorderedStructureInterface | inline |
| bio::UnorderedMotif< TranscriptionFactor >::LogImplementation(const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId()) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::LogImplementation(const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId()) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| MakePeriodicSymmetry() | bio::physical::Periodic | static |
| mBackflowPreventer | bio::chemical::Atom | protected |
| mBondIndex | bio::chemical::Atom | protected |
| mBonds | bio::chemical::Atom | protected |
| mcApoptosis | bio::cellular::Class< CellularForwarder< CALLER, CLOBBER > > | protected |
| mcCrest | bio::cellular::Class< CellularForwarder< CALLER, CLOBBER > > | protected |
| mContentId | bio::chemical::LinearMotif< CONTENT_TYPE > | mutableprotected |
| UnorderedMotif< TranscriptionFactor >::mContents | bio::chemical::AbstractMotif | mutableprotected |
| bio::molecular::Vesicle::mContents | bio::chemical::AbstractMotif | mutableprotected |
| mEnvironment | bio::chemical::EnvironmentDependent< T > | protected |
| Metallic() | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inline |
| Metallic(const Metallic &other) | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inline |
| mFilter | bio::physical::Filterable | protected |
| bio::mHasBeenInitialized | bio::VirtualBase | protected |
| bio::physical::Periodic::mHasBeenInitialized | bio::VirtualBase | protected |
| bio::mHasSignal | bio::physical::Wave | protected |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::mHasSignal | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::mHasSignal | bio::physical::Wave | protected |
| bio::chemical::Atom::mHasSignal | bio::physical::Wave | protected |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::mHasSignal | bio::physical::Wave | protected |
| bio::molecular::Molecule::bio::Class< Molecule >::mHasSignal | bio::physical::Wave | protected |
| bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::mHasSignal | bio::physical::Wave | protected |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::mHasSignal | bio::physical::Wave | protected |
| bio::physical::Periodic::mHasSignal | bio::physical::Wave | protected |
| bio::molecular::Vesicle::bio::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::mHasSignal | bio::physical::Wave | protected |
| mInterval | bio::physical::Periodic | protected |
| mLastCrestTimestamp | bio::physical::Periodic | protected |
| bio::mObject | bio::physical::Class< T > | mutableprotected |
| bio::Identifiable< Id >::bio::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 |
| bio::chemical::Substance::Class< Substance >::bio::mObject | bio::physical::Class< T > | mutableprotected |
| bio::molecular::Molecule::Class< Molecule >::bio::mObject | bio::physical::Class< T > | mutableprotected |
| bio::genetic::Expressor::Class< Expressor >::bio::Class< Expressor >::Class< Expressor >::mObject | bio::physical::Class< T > | mutableprotected |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::mObject | bio::physical::Class< T > | mutableprotected |
| bio::physical::Periodic::mObject | bio::physical::Class< Periodic > | mutableprotected |
| bio::molecular::Vesicle::Class< Vesicle >::bio::Class< Vesicle >::Class< Vesicle >::mObject | bio::physical::Class< T > | mutableprotected |
| Modulate(Pointer< ::bio::physical::Wave > signal) BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| bio::physical::Class::Modulate(Pointer< Wave > signal) | bio::physical::Wave | virtual |
| bio::mSymmetry | bio::physical::Wave | mutableprotected |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::log::Writer::Class< Writer >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::chemical::Atom::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::molecular::Molecule::bio::Class< Molecule >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::physical::Periodic::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::molecular::Vesicle::bio::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::mSymmetry | bio::physical::Wave | mutableprotected |
| bio::Covalent< UnorderedMotif< Property > >::mT | bio::Covalent< UnorderedMotif< Property > > | protected |
| bio::Covalent< UnorderedMotif< State > >::mT | bio::Covalent< UnorderedMotif< State > > | protected |
| bio::molecular::Molecule::Metallic< chemical::DependentMotif< Surface, Molecule > >::mT | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | protected |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< Plasmid > >::mT | bio::Covalent< chemical::LinearMotif< Plasmid > > | protected |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< molecular::Protein > >::mT | bio::Covalent< chemical::LinearMotif< molecular::Protein > > | protected |
| mTranscriptome | bio::genetic::Expressor | protected |
| bio::mTypeId | bio::physical::Wave | protected |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::mTypeId | bio::physical::Wave | protected |
| bio::log::Writer::Class< Writer >::mTypeId | bio::physical::Wave | protected |
| bio::chemical::Atom::mTypeId | bio::physical::Wave | protected |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::mTypeId | bio::physical::Wave | protected |
| bio::molecular::Molecule::bio::Class< Molecule >::mTypeId | bio::physical::Wave | protected |
| bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::mTypeId | bio::physical::Wave | protected |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::mTypeId | bio::physical::Wave | protected |
| bio::physical::Periodic::mTypeId | bio::physical::Wave | protected |
| bio::molecular::Vesicle::bio::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::mTypeId | bio::physical::Wave | protected |
| bio::UnorderedMotif< TranscriptionFactor >::NewContents(Index expectedSize) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinestatic |
| bio::UnorderedMotif< TranscriptionFactor >::NewContents(const Contents &contents) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinestatic |
| bio::UnorderedMotif< TranscriptionFactor >::NewContents(Pointer< const Container > contents) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinestatic |
| bio::molecular::Vesicle::NewContents(Index expectedSize) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinestatic |
| bio::molecular::Vesicle::NewContents(const Contents &contents) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinestatic |
| bio::molecular::Vesicle::NewContents(Pointer< const Container > contents) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinestatic |
| bio::Covalent< UnorderedMotif< Property > >::Object() | bio::Covalent< UnorderedMotif< Property > > | inline |
| bio::Covalent< UnorderedMotif< Property > >::Object() const | bio::Covalent< UnorderedMotif< Property > > | inline |
| bio::Covalent< UnorderedMotif< State > >::Object() | bio::Covalent< UnorderedMotif< State > > | inline |
| bio::Covalent< UnorderedMotif< State > >::Object() const | bio::Covalent< UnorderedMotif< State > > | inline |
| bio::molecular::Molecule::Metallic< chemical::DependentMotif< Surface, Molecule > >::Object() | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inline |
| bio::Metallic< chemical::DependentMotif< Surface, Molecule > >::Object() const | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inline |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< Plasmid > >::Object() | bio::Covalent< chemical::LinearMotif< Plasmid > > | inline |
| bio::Covalent< chemical::LinearMotif< Plasmid > >::Object() const | bio::Covalent< chemical::LinearMotif< Plasmid > > | inline |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< molecular::Protein > >::Object() | bio::Covalent< chemical::LinearMotif< molecular::Protein > > | inline |
| Covalent< chemical::LinearMotif< molecular::Protein > >::Object() const | bio::Covalent< chemical::LinearMotif< molecular::Protein > > | inline |
| Observer(Pointer< Perspective > perspective=NULL) | bio::physical::Observer< PERSPECTIVE > | inlineexplicit |
| Observer(const Observer &other) | bio::physical::Observer< PERSPECTIVE > | inline |
| operator AS() | bio::CellularForwarder< CALLER, CLOBBER > | 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 Periodic &() const | bio::physical::Class< Periodic > | 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 Periodic &() | bio::physical::Class< Periodic > | inlinevirtual |
| operator Pointer< ::bio::physical::Wave >() | bio::CellularForwarder< CALLER, CLOBBER > | 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 |
| bio::physical::Periodic::operator Pointer< Wave >() | bio::physical::Class< Periodic > | inlinevirtual |
| operator T() const | bio::chemical::Atom | |
| operator T&() | bio::physical::Class< T > | inlinevirtual |
| operator Writer &() | bio::physical::Class< Writer > | inlinevirtual |
| operator()(const Id &surfaceId) | bio::molecular::Molecule | virtual |
| operator()(const Id &surfaceId) const | bio::molecular::Molecule | virtual |
| operator()(const Id &surfaceId) | bio::molecular::Molecule | inline |
| operator()(const Name &name) | bio::molecular::Molecule | virtual |
| operator()(const Name &name) const | bio::molecular::Molecule | virtual |
| operator()(const Name &surfaceName) | bio::molecular::Molecule | inline |
| 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 |
| bio::operator<<(std::ostream &out, const Identifiable< Id > &t) | bio::physical::Identifiable< Id > | inlineprotected |
| bio::molecular::Molecule::operator<<(Pointer< Surface > source) | bio::molecular::Molecule | virtual |
| bio::molecular::Molecule::operator<<(Pointer< Molecule > source) | bio::molecular::Molecule | virtual |
| bio::operator=(const Wave &other) | bio::physical::Wave | |
| bio::Identifiable< Id >::bio::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 | |
| 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 |
| bio::ThreadSafe::operator=(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| bio::molecular::Molecule::operator=(const Wave &other) | bio::physical::Wave | |
| bio::molecular::Molecule::Metallic< chemical::DependentMotif< Surface, Molecule > >::operator=(const Metallic &other) | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inline |
| bio::genetic::Expressor::operator=(const Wave &other) | bio::physical::Wave | |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::operator=(const UnorderedMotif< TranscriptionFactor > &toCopy) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inline |
| bio::chemical::Class::operator=(const Wave &other) | bio::physical::Wave | |
| bio::chemical::AbstractMotif::operator=(const AbstractMotif &other) | bio::chemical::AbstractMotif | |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< Plasmid > >::operator=(const Covalent &other) | bio::Covalent< chemical::LinearMotif< Plasmid > > | inline |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< molecular::Protein > >::operator=(const Covalent &other) | bio::Covalent< chemical::LinearMotif< molecular::Protein > > | inline |
| bio::genetic::Expressor::bio::molecular::Vesicle::bio::chemical::Solution::DependentMotif< Solute, Solution >::bio::chemical::LinearMotif::UnorderedMotif< Pointer< CONTENT_TYPE > >::operator=(const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inline |
| bio::physical::Periodic::operator=(const Wave &other) | bio::physical::Wave | |
| bio::molecular::Vesicle::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< Surface > target) | bio::molecular::Molecule | virtual |
| operator>>(Pointer< Molecule > target) | bio::molecular::Molecule | virtual |
| operator|(Pointer< Symmetry > symmetry) | bio::physical::Wave | virtual |
| Periodic(Milliseconds interval=GetDefaultInterval()) | bio::physical::Periodic | |
| Perspective typedef | bio::physical::Observer< PERSPECTIVE > | |
| RegisterProperties(const ::bio::Properties &properties) BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::RegisterProperties(const Properties &properties) | bio::chemical::Class< T > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::RegisterProperties(const Properties &properties) | bio::chemical::Class< Substance > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::RegisterProperties(const Properties &properties) | bio::chemical::Class< Solution > | inlinevirtual |
| Class< CellularForwarder< CALLER, CLOBBER > >::RegisterProperties(const Properties &properties) | bio::chemical::Class< LinearMotif< CONTENT_TYPE > > | inlinevirtual |
| bio::RegisterType() | bio::chemical::Elementary< T > | inlineprotected |
| bio::chemical::Substance::RegisterType() | bio::chemical::Elementary< T > | inline |
| bio::molecular::Molecule::bio::RegisterType() | bio::chemical::Elementary< T > | inline |
| bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::RegisterType() | bio::chemical::Elementary< T > | inline |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::RegisterType() | bio::chemical::Elementary< T > | inline |
| bio::molecular::Vesicle::bio::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::RegisterType() | bio::chemical::Elementary< T > | inline |
| 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 |
| bio::molecular::Molecule::Reify(Pointer< const physical::Symmetry > symmetry) | bio::molecular::Molecule | virtual |
| bio::genetic::Expressor::Reify(Pointer< const physical::Symmetry > symmetry) | bio::genetic::Expressor | virtual |
| bio::physical::Periodic::Reify(Pointer< const Symmetry > symmetry) | bio::physical::Periodic | 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 |
| bio::UnorderedMotif< TranscriptionFactor >::RemoveImplementation(const TranscriptionFactor content) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::RemoveImplementation(const ContentPointer content) | bio::chemical::LinearMotif< CONTENT_TYPE > | inlinevirtual |
| UnorderedMotif< Pointer< CONTENT_TYPE > >::RemoveImplementation(const Pointer< CONTENT_TYPE > content) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| ResolveBondedForReadById(AtomicNumber bondId) const | bio::chemical::Atom | |
| ResolveBondedForWriteById(AtomicNumber bondId) | bio::chemical::Atom | |
| ResolveLinearMotif() | bio::chemical::LinearStructureInterface | inlineprotected |
| ResolveLinearMotif() const | bio::chemical::LinearStructureInterface | inlineprotected |
| RotateTo(const Id &surfaceId) | bio::molecular::Molecule | virtual |
| RotateTo(const Id &surfaceId) const | bio::molecular::Molecule | virtual |
| RotateTo(const Name &surfaceName) | bio::molecular::Molecule | virtual |
| RotateTo(const Name &surfaceName) const | bio::molecular::Molecule | virtual |
| RotateToOrDefine(const Id &surfaceId) | bio::molecular::Molecule | virtual |
| RotateToOrDefine(const Name &surfaceName) | bio::molecular::Molecule | |
| RotateToOrDefine(const Id &surfaceId, T &assignment) | bio::molecular::Molecule | inline |
| RotateToOrDefine(const Name &surfaceName, T &assignment) | bio::molecular::Molecule | inline |
| Separate(const Id &id) | bio::chemical::Solution | protectedvirtual |
| SetCrestFunction(bio::Code(CALLER::*forwardTo)(), Pointer< CALLER > caller) | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| SetEnvironment(Pointer< ENVIRONMENT > environment) | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| Class< CellularForwarder< CALLER, CLOBBER > >::SetEnvironment(EnvironmentPointer environment) | bio::chemical::DependentMotif< Solute, Solution > | inlinevirtual |
| bio::chemical::EnvironmentDependent::SetEnvironment(EnvironmentPointer environment) | bio::chemical::EnvironmentDependent< T > | inlinevirtual |
| SetFilter(Filter filter) | bio::physical::Filterable | virtual |
| SetId(Identifier id) | bio::physical::Identifiable< Id > | inlinevirtual |
| SetInterval(::bio::Milliseconds interval) BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inline |
| Class< CellularForwarder< CALLER, CLOBBER > >::SetInterval(Milliseconds period) | bio::cellular::Class< CellularForwarder< CALLER, CLOBBER > > | inlinevirtual |
| SetLastCrestTimestamp(Timestamp lastCrest) | bio::physical::Periodic | virtual |
| 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 >::bio::bio::bio::bio::bio::bio::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 |
| bio::chemical::Substance::bio::Class< Substance >::Class< Substance >::Class< Substance >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::molecular::Molecule::bio::Class< Molecule >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::genetic::Expressor::bio::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::Class< Expressor >::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::genetic::Expressor::UnorderedMotif< TranscriptionFactor >::bio::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::physical::Periodic::SetTypeId(uint16_t typeId) | bio::physical::Wave | inline |
| bio::molecular::Vesicle::bio::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::Class< Vesicle >::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 |
| bio::molecular::Molecule::Spin() const | bio::molecular::Molecule | virtual |
| bio::genetic::Expressor::Spin() const | bio::genetic::Expressor | virtual |
| bio::physical::Periodic::Spin() const | bio::physical::Periodic | virtual |
| states | bio::chemical::Substance | |
| Structure() | bio::chemical::Structure | |
| Superpose(const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern) BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| Superpose(Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern) BIO_FINAL | bio::CellularForwarder< CALLER, CLOBBER > | 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 |
| bio::ThreadSafe() | bio::ThreadSafe | |
| bio::ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| bio::ThreadSafe::ThreadSafe() | bio::ThreadSafe | |
| bio::ThreadSafe::ThreadSafe(const ThreadSafe &toCopy) | bio::ThreadSafe | |
| TransferFrom(Pointer< Molecule > source, const Name &surface) | bio::molecular::Molecule | virtual |
| Translate(Pointer< const RNA > mRNA) | bio::genetic::Expressor | virtual |
| UnindexBond(AtomicNumber bondedId) | bio::chemical::Atom | protected |
| bio::UnlockMutexShared() const | bio::ThreadSafe | |
| bio::ThreadSafe::UnlockMutexShared() const | bio::ThreadSafe | |
| bio::UnlockThread() const | bio::ThreadSafe | |
| bio::ThreadSafe::UnlockThread() const | bio::ThreadSafe | |
| bio::UnorderedMotif< TranscriptionFactor >::UnorderedMotif() | bio::chemical::UnorderedMotif< TranscriptionFactor > | inline |
| bio::UnorderedMotif< TranscriptionFactor >::UnorderedMotif(ContentsAllocation allocation) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlineexplicitprotected |
| bio::UnorderedMotif< TranscriptionFactor >::UnorderedMotif(Pointer< const Contents > contents) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inline |
| bio::UnorderedMotif< TranscriptionFactor >::UnorderedMotif(Pointer< const UnorderedMotif< TranscriptionFactor > > toCopy) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inline |
| bio::UnorderedMotif< TranscriptionFactor >::UnorderedMotif(const UnorderedMotif< TranscriptionFactor > &toCopy) | bio::chemical::UnorderedMotif< TranscriptionFactor > | inline |
| bio::molecular::Vesicle::UnorderedMotif() | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inline |
| bio::molecular::Vesicle::UnorderedMotif(ContentsAllocation allocation) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlineexplicitprotected |
| bio::molecular::Vesicle::UnorderedMotif(Pointer< const Contents > contents) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inline |
| bio::molecular::Vesicle::UnorderedMotif(Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > toCopy) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inline |
| bio::molecular::Vesicle::UnorderedMotif(const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy) | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inline |
| UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inline |
| Use(const Name &varName, Pointer< T > varPtr) | bio::molecular::Molecule | inline |
| Use(const Id &id, Pointer< T > varPtr) | bio::molecular::Molecule | inline |
| bio::VirtualBase() | bio::VirtualBase | protected |
| bio::physical::Periodic::VirtualBase() | bio::VirtualBase | protected |
| bio::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::Wave(const Wave &other) | bio::physical::Wave | |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| Identifiable< Id >::bio::bio::bio::bio::bio::bio::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 | |
| bio::chemical::Substance::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::chemical::Substance::Wave(const Wave &other) | bio::physical::Wave | |
| bio::molecular::Molecule::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::molecular::Molecule::Wave(const Wave &other) | bio::physical::Wave | |
| bio::genetic::Expressor::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::genetic::Expressor::Wave(const Wave &other) | bio::physical::Wave | |
| UnorderedMotif< TranscriptionFactor >::bio::bio::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| UnorderedMotif< TranscriptionFactor >::bio::bio::Wave(const Wave &other) | bio::physical::Wave | |
| bio::physical::Periodic::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::physical::Periodic::Wave(const Wave &other) | bio::physical::Wave | |
| bio::molecular::Vesicle::Wave(Pointer< Symmetry > symmetry=NULL) | bio::physical::Wave | |
| bio::molecular::Vesicle::Wave(const Wave &other) | bio::physical::Wave | |
| Writer() | bio::log::Writer | |
| Writer(Filter logFilter) | bio::log::Writer | |
| ~AbstractMotif() | bio::chemical::AbstractMotif | virtual |
| ~Atom() | bio::chemical::Atom | virtual |
| ~CellularForwarder() | bio::CellularForwarder< CALLER, CLOBBER > | inlinevirtual |
| ~Class() | bio::cellular::Class< CellularForwarder< CALLER, CLOBBER > > | inlinevirtual |
| bio::Covalent< UnorderedMotif< Property > >::~Covalent() | bio::Covalent< UnorderedMotif< Property > > | inlinevirtual |
| bio::Covalent< UnorderedMotif< State > >::~Covalent() | bio::Covalent< UnorderedMotif< State > > | inlinevirtual |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< Plasmid > >::~Covalent() | bio::Covalent< chemical::LinearMotif< Plasmid > > | inlinevirtual |
| bio::genetic::Expressor::Covalent< chemical::LinearMotif< molecular::Protein > >::~Covalent() | bio::Covalent< chemical::LinearMotif< molecular::Protein > > | 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 |
| ~Metallic() | bio::Metallic< chemical::DependentMotif< Surface, Molecule > > | inlinevirtual |
| ~Molecule() | bio::molecular::Molecule | virtual |
| ~Observer() | bio::physical::Observer< PERSPECTIVE > | inlinevirtual |
| ~Periodic() | bio::physical::Periodic | virtual |
| ~Structure() | bio::chemical::Structure | virtual |
| ~Substance() | bio::chemical::Substance | virtual |
| bio::~ThreadSafe() | bio::ThreadSafe | |
| bio::ThreadSafe::~ThreadSafe() | bio::ThreadSafe | |
| bio::UnorderedMotif< TranscriptionFactor >::~UnorderedMotif() | bio::chemical::UnorderedMotif< TranscriptionFactor > | inlinevirtual |
| bio::molecular::Vesicle::~UnorderedMotif() | bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > > | inlinevirtual |
| ~UnorderedStructureInterface() | bio::chemical::UnorderedStructureInterface | inlinevirtual |
| ~Vesicle() | bio::molecular::Vesicle | virtual |
| ~VirtualBase() | bio::VirtualBase | protectedvirtual |
| ~Wave() | bio::physical::Wave | virtual |
| ~Writer() | bio::log::Writer | virtual |
