#include <Pore.h>

Inheritance diagram for bio::molecular::Pore:

[legend]

Collaboration diagram for bio::molecular::Pore:

[legend]

Public Member Functions
	Pore ()

	Pore (const Name &name, Pointer< Vesicle > environment=Pointer< Vesicle >())

virtual	~Pore ()

virtual void	SetEnvironment (Pointer< Vesicle > environment)

Public Member Functions inherited from bio::molecular::Class< Pore >
	Class (Pointer< Pore > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Pore > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Pore > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

virtual	~Class ()

void	SetEnvironment (Pointer< ENVIRONMENT > environment)

Pointer< ENVIRONMENT >	GetEnvironment ()

const Pointer< ENVIRONMENT >	GetEnvironment () const

Public Member Functions inherited from bio::chemical::Class< T >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< T > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< T > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

virtual Code	Attenuate (Pointer< const physical::Wave > other)

virtual Code	Disattenuate (Pointer< const physical::Wave > other)

Public Member Functions inherited from bio::physical::Class< T >
	Class (Pointer< T > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< T > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< T >	GetWaveObject ()

virtual Pointer< const T >	GetWaveObject () const

virtual	operator T& ()

virtual	operator const T & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Wave
	Wave (Pointer< Symmetry > symmetry=NULL)

	Wave (const Wave &other)

Wave &	operator= (const Wave &other)

virtual	~Wave ()

Pointer< const Symmetry >	GetSymmetry () const

virtual bool	Superpose (Pointer< const Wave > displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Superpose (const ConstWaves &displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Modulate (Pointer< Wave > signal)

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual void	operator\| (Pointer< Symmetry > symmetry)

virtual Pointer< Wave >	operator* (Pointer< Wave > signal)

virtual Pointer< Wave >	operator* ()

virtual Pointer< const Wave >	operator* () const

virtual void	operator+ (Pointer< const Wave > other)

virtual void	operator- (Pointer< const Wave > other)

uint16_t	GetTypeId () const

void	SetTypeId (uint16_t typeId)

Public Member Functions inherited from bio::physical::Identifiable< Id >
	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Public Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Public Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Public Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

Public Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::chemical::Atom
	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Public Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Public Member Functions inherited from bio::chemical::Substance
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_COMMON_CONSTRUCTOR (chemical, Substance, filter::Chemical()) Substance(const UnorderedMotif< Property > &properties

virtual	~Substance ()

virtual void	Enable ()

virtual void	Disable ()

virtual bool	IsEnabled () const

Public Member Functions inherited from bio::chemical::Class< Substance >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< Substance > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Substance > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Substance > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

virtual Code	Attenuate (Pointer< const physical::Wave > other)

virtual Code	Disattenuate (Pointer< const physical::Wave > other)

Public Member Functions inherited from bio::Covalent< UnorderedMotif< Property > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< UnorderedMotif< Property > >	Object ()

Pointer< const UnorderedMotif< Property > >	Object () const

Public Member Functions inherited from bio::Covalent< UnorderedMotif< State > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< UnorderedMotif< State > >	Object ()

Pointer< const UnorderedMotif< State > >	Object () const

Public Member Functions inherited from bio::chemical::Structure
	Structure ()

virtual	~Structure ()

Public Member Functions inherited from bio::chemical::UnorderedStructureInterface
	UnorderedStructureInterface ()

virtual	~UnorderedStructureInterface ()

template<typename T >
T	Add (const T t)

template<typename T >
Pointer< T >	Add (Pointer< T > t)

template<typename T >
Code	Remove (const T t)

template<typename T >
Code	Remove (Pointer< T > t)

template<typename T >
void	Import (Pointer< const UnorderedMotif< T > > other)

template<typename T >
void	Import (Pointer< const LinearMotif< T > > other)

template<typename T >
void	Import (const ::bio::Arrangement< T > &other)

Code	ImportAll (Pointer< const physical::Wave > other)

template<typename T >
Index	GetCount () const

template<typename T >
Pointer< Container >	GetAll ()

template<typename T >
Pointer< const Container >	GetAll () const

template<typename T >
bool	Has (T content) const

template<typename T >
bool	Has (Pointer< T > content) const

template<typename T >
unsigned int	GetNumMatching (Pointer< const Container > other) const

template<typename T >
bool	HasAll (Pointer< const Container > contents) const

template<typename T >
void	Clear ()

template<typename T >
std::string	GetStringFrom (std::string separator=", ")

template<typename T >
void	Log (const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId())

Public Member Functions inherited from bio::chemical::LinearStructureInterface
	LinearStructureInterface ()

virtual	~LinearStructureInterface ()

template<typename T >
Code	Insert (typename LinearStructureRequest< T >::PointerType toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

template<typename T >
LinearStructureRequest< T >::PointerType	GetById (const Id &id)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetById (const Id &id) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetByName (const Name &name)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetByName (const Name &name) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateById (Id id)

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateByName (const Name &name)

template<typename T >
Code	RemoveById (const Id &id)

template<typename T >
Code	RemoveByName (const Name &name)

template<typename T >
LinearMotif< typenameLinearStructureRequest< T >::Pointee >::Contents	GetAllLike (Pointer< const Affinity > affinity) const

template<typename T >
Emission	ForEach (Pointer< ExcitationBase > excitation)

Public Member Functions inherited from bio::molecular::Surface
	Surface ()

	Surface (const Name &name, Pointer< Molecule > environment=Pointer< Molecule >())

	Surface (const Id &id, Pointer< Molecule > environment=Pointer< Molecule >())

	Surface (const Surface &toCopy)

virtual	~Surface ()

virtual Pointer< const physical::Symmetry >	Spin () const

virtual Code	Reify (Pointer< const physical::Symmetry > symmetry)

virtual bool	IsBound () const

template<typename T >
T &	Manage (Pointer< T > varPtr)

template<typename T >
T &	Use (Pointer< T > varPtr)

virtual Pointer< physical::Wave >	Probe ()

virtual Pointer< const physical::Wave >	Probe () const

template<typename T >
T &	Probe ()

template<typename T >
const T &	Probe () const

template<typename T >
T &	Bind (T toBind, const BondType bondType=bond_type::Temporary())

Pointer< physical::Wave >	Bind (Pointer< physical::Wave > toBind, const chemical::AtomicNumber type, const BondType bondType)

virtual Pointer< physical::Wave >	Release (Pointer< physical::Wave > toRelease, BondType bondType=bond_type::Temporary())

virtual Pointer< chemical::Substance >	Release (const Name &toRelease, Pointer< physical::Perspective< Id > > perspective=NULL, BondType bondType=bond_type::Temporary())

virtual Pointer< chemical::Substance >	Release (Id toRelease, Pointer< physical::Perspective< Id > > perspective=NULL, BondType bondType=bond_type::Temporary())

virtual physical::Waves	Release (BondType bondType=bond_type::Temporary())

virtual void	SetEnvironment (Pointer< Molecule > environment)

template<typename T >
T	operator+= (T toBind)

virtual Pointer< physical::Wave >	operator-= (Pointer< physical::Wave > toRelease)

virtual Pointer< chemical::Substance >	operator-= (const Name &toRelease)

virtual Pointer< chemical::Substance >	operator-= (const Id &toRelease)

virtual physical::Waves	operator-- ()

Public Member Functions inherited from bio::molecular::Class< Surface >
	Class (Pointer< Surface > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Surface > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Surface > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

virtual	~Class ()

void	SetEnvironment (Pointer< ENVIRONMENT > environment)

Pointer< ENVIRONMENT >	GetEnvironment ()

const Pointer< ENVIRONMENT >	GetEnvironment () const

Public Member Functions inherited from bio::chemical::EnvironmentDependent< Molecule >
	EnvironmentDependent (EnvironmentPointer environment=NULL)

virtual	~EnvironmentDependent ()

virtual EnvironmentPointer	GetEnvironment ()

virtual const EnvironmentPointer	GetEnvironment () const

virtual void	SetEnvironment (EnvironmentPointer environment)

Protected Attributes
TransMembraneDomain	mTransMembraneDomain

Protected Attributes inherited from bio::physical::Class< T >
Pointer< T >	mObject

Protected Attributes inherited from bio::physical::Wave
LazyPointer< Symmetry >	mSymmetry

bool	mHasSignal

uint16_t	mTypeId

Protected Attributes inherited from bio::VirtualBase
bool	mHasBeenInitialized

Protected Attributes inherited from bio::physical::Class< Writer >
Pointer< Writer >	mObject

Protected Attributes inherited from bio::physical::Filterable
Filter	mFilter

Protected Attributes inherited from bio::physical::Class< Filterable >
Pointer< Filterable >	mObject

Protected Attributes inherited from bio::chemical::Atom
Bonds	mBonds

::std::map< AtomicNumber, Valence >	mBondIndex

Arrangement< Pointer< const physical::Wave > >	mBackflowPreventer

Protected Attributes inherited from bio::physical::Class< Atom >
Pointer< Atom >	mObject

Protected Attributes inherited from bio::Covalent< UnorderedMotif< Property > >
Pointer< UnorderedMotif< Property > >	mT

Protected Attributes inherited from bio::Covalent< UnorderedMotif< State > >
Pointer< UnorderedMotif< State > >	mT

Protected Attributes inherited from bio::molecular::Surface
chemical::Valence	mBondPosition

Protected Attributes inherited from bio::chemical::EnvironmentDependent< Molecule >
EnvironmentPointer	mEnvironment

Additional Inherited Members
Public Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Public Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Public Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Public Types inherited from bio::chemical::EnvironmentDependent< Molecule >
typedef type::RemovePointer< Molecule >::Type	EnvironmentType

typedef Pointer< EnvironmentType >	EnvironmentPointer

Static Public Member Functions inherited from bio::physical::Class< T >
static Pointer< T >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (ConstWaves waves)

static Properties	GetResonanceBetween (Pointer< const Wave > wave1, Pointer< const Wave > wave2)

static Properties	GetResonanceBetween (Pointer< const Wave > wave, const Properties &properties)

Static Public Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Public Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Public Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::UnorderedStructureInterface
static void	ImportAllCollectVisitor (const chemical::Bond &bond, void *ctx)

Public Attributes inherited from bio::chemical::Substance
const UnorderedMotif< State > &	states

Protected Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Protected Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Protected Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Protected Member Functions inherited from bio::chemical::Elementary< T >
void	RegisterType ()

	Elementary (const Properties properties)

	Elementary ()

virtual	~Elementary ()

Protected Member Functions inherited from bio::physical::Identifiable< Id >
virtual void	InitializeImplementation (ByteStreams &args)

friend::std::ostream &	operator<< (std::ostream &out, const Identifiable< Id > &t)

	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Protected Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Protected Member Functions inherited from bio::VirtualBase
	VirtualBase ()

virtual	~VirtualBase ()

void	Initialize (ByteStreams &args)

void	Initialize (ByteStream arg1)

void	Initialize (ByteStream arg1, ByteStream arg2)

void	Initialize (ByteStream arg1, ByteStream arg2, ByteStream arg3)

Protected Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Protected Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

Protected Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::chemical::Atom
void	IndexBond (AtomicNumber bondedId, Valence position)

void	UnindexBond (AtomicNumber bondedId)

	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Protected Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Protected Member Functions inherited from bio::chemical::LinearStructureInterface
template<typename T >
Pointer< LinearMotif< T > >	ResolveLinearMotif ()

template<typename T >
Pointer< const LinearMotif< T > >	ResolveLinearMotif () const

Protected Member Functions inherited from bio::molecular::Surface
chemical::Valence	FormSurfaceBond (Pointer< physical::Wave > toBond, chemical::AtomicNumber bondedId, BondType bondType)

Static Protected Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Protected Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Protected Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Detailed Description

Pores are simply Surfaces with TransMembraneDomains.
The role of a Pore is to facilitate, restrict, and / or monitor the transfer of Molecules in and out of Vesicles.
In programming terms, Pores define APIs, where the program is the protected Vesicle contents and the application is the environment or another Vesicle interacting with the contents through a Pore: micro-APIs, if you will.
It is up to you to define how you'd like to wrap the methods provided by TransMembraneDomain.
See OpenChannel for a simple implementation.
NOTE: we use "channel" to designate a Pore implementation and "pore" to designate an abstract, "disarmed" class.
Channels "run on" Pores the way sockets "run on" ports; though here Pores scale precisely with Channels.

Constructor & Destructor Documentation

◆ Pore() [1/2]

bio::molecular::Pore::Pore ( )

Ensure virtual methods point to Class implementations.
Don't use this.

◆ Pore() [2/2]

bio::molecular::Pore::Pore	(	const Name &	name,
		Pointer< Vesicle >	environment = `Pointer< Vesicle >()`
	)

Parameters

name

◆ ~Pore()

bio::molecular::Pore::~Pore ( )

virtual

Member Function Documentation

◆ SetEnvironment()

void bio::molecular::Pore::SetEnvironment ( Pointer< Vesicle > environment )

virtual

Sets mEnvironment & mTransMembaneDomain.mInterior.
Don't let the environment go out of scope or be deleted before *this!

Parameters

environment

Member Data Documentation

◆ mTransMembraneDomain

TransMembraneDomain bio::molecular::Pore::mTransMembraneDomain

protected

The documentation for this class was generated from the following files:

Public Member Functions

Protected Attributes

Additional Inherited Members