#include <Solution.h>

Inheritance diagram for bio::chemical::Solution:

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Collaboration diagram for bio::chemical::Solution:

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Public Member Functions
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (chemical, Solution, filter::Chemical()) virtual Id Dissolve(Pointer< Substance > toDissolve

virtual Pointer< Substance >	Separate (const Id &id)

virtual Id	Influx (const Solute &toInflux)

virtual Solute	Efflux (const Id &soluteId)

virtual const Solute	Efflux (const Id &soluteId) const

virtual Solute	Efflux (const Name &substanceName)

virtual const Solute	Efflux (const Name &substanceName) const

virtual Pointer< physical::Line >	GetAllSolutes ()

virtual Pointer< const physical::Line >	GetAllSolutes () const

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

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

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

	Class (const Class &other)

virtual	~Class ()

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

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

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)

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

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

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	~Class ()

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 Attributes
const DiffusionTime &	diffusionTime = diffusion::time::Destruction()

const DiffusionTime const DiffusionEffort &	diffusionEffort

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

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)

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)

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 Types inherited from bio::chemical::LinearMotif< CONTENT_TYPE >
typedef physical::Line	Contents

Protected Types inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
enum	ContentsAllocation

typedef Arrangement< Pointer< CONTENT_TYPE > >	Contents

Protected Types inherited from bio::chemical::EnvironmentDependent< T >
typedef type::RemovePointer< T >::Type	EnvironmentType

typedef Pointer< EnvironmentType >	EnvironmentPointer

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

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

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)

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

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

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::chemical::DependentMotif< Solute, Solution >
virtual Code	Attenuate (Pointer< const physical::Wave > other)

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

	DependentMotif (EnvironmentPointer environment=NULL)

	DependentMotif (const typename LinearMotif< Solute >::Contents *contents, EnvironmentPointer environment=NULL)

	DependentMotif (const DependentMotif< Solute, Solution > &toCopy)

virtual	~DependentMotif ()

virtual void	SetEnvironment (EnvironmentPointer environment)

virtual ContentPointer	AddImplementation (ContentPointer content)

virtual Code	InsertImplementation (ContentPointer toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

Protected 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	~Class ()

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

Protected Member Functions inherited from bio::chemical::LinearMotif< CONTENT_TYPE >
	LinearMotif ()

	LinearMotif (const Contents *contents)

	LinearMotif (const LinearMotif< CONTENT_TYPE > &toCopy)

virtual	~LinearMotif ()

virtual AtomicNumber	GetContentTypeId () const

virtual bool	AddWaveByContentType (Pointer< physical::Wave > wave)

virtual bool	AddSharedWaveByContentType (Pointer< physical::Wave > wave)

virtual ContentPointer	AddImplementation (ContentPointer content)

virtual ContentPointer	AddSharedImplementation (ContentPointer content)

void	ReleaseContentOwnership ()

ReleaseResult	ReleaseImplementation (const ContentPointer content)

virtual Code	RemoveImplementation (const ContentPointer content)

virtual Code	InsertImplementation (ContentPointer toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

virtual ContentPointer	GetByIdImplementation (const Id &id)

virtual const ContentPointer	GetByIdImplementation (const Id &id) const

virtual ContentPointer	GetByNameImplementation (const Name &name)

virtual const ContentPointer	GetByNameImplementation (const Name &name) const

virtual ContentPointer	CreateImplementation ()

virtual ContentPointer	CreateWithIdImplementation (const Id &id)

virtual ContentPointer	CreateWithNameImplementation (const Name &name)

virtual ContentPointer	GetOrCreateByIdImplementation (const Id &id)

virtual ContentPointer	GetOrCreateByNameImplementation (const Name &name)

virtual Code	RemoveByIdImplementation (const Id &id)

virtual Code	RemoveByNameImplementation (const Name &name)

virtual bool	HasImplementation (const ContentPointer &content) const

virtual void	ImportImplementation (Pointer< const LinearMotif< CONTENT_TYPE > > other)

virtual void	ImportImplementation (const void *other)

virtual Contents	GetAllLikeImplementation (Pointer< const Affinity > affinity) const

virtual Emission	ForEachImplementation (Pointer< const ExcitationBase > excitation)

virtual ::std::string	GetStringFromImplementation (std::string separator=", ")

virtual void	ClearImplementation ()

virtual Pointer< Container >	GetAllImplementation ()

virtual Pointer< const Container >	GetAllImplementation () const

Protected Member Functions inherited from bio::chemical::Class< LinearMotif< CONTENT_TYPE > >
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< LinearMotif< CONTENT_TYPE > > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

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

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

	Class (const Class &other)

virtual	~Class ()

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

Protected Member Functions inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
	UnorderedMotif (ContentsAllocation allocation)

	UnorderedMotif ()

	UnorderedMotif (Pointer< const Contents > contents)

	UnorderedMotif (Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > toCopy)

	UnorderedMotif (const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy)

UnorderedMotif< Pointer< CONTENT_TYPE > > &	operator= (const UnorderedMotif< Pointer< CONTENT_TYPE > > &toCopy)

virtual	~UnorderedMotif ()

virtual Index	GetCountImplementation () const

virtual Pointer< CONTENT_TYPE >	AddImplementation (const Pointer< CONTENT_TYPE > content)

virtual Code	RemoveImplementation (const Pointer< CONTENT_TYPE > content)

virtual bool	HasImplementation (const Pointer< CONTENT_TYPE > content) const

virtual void	ImportImplementation (Pointer< const UnorderedMotif< Pointer< CONTENT_TYPE > > > other)

virtual unsigned int	GetNumMatchingImplementation (Pointer< const Container > other) const

virtual bool	HasAllImplementation (Pointer< const Container > contents) const

virtual String	GetStringFromImplementation (String separator=", ")

virtual void	LogImplementation (const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId())

Protected Member Functions inherited from bio::chemical::AbstractMotif
	AbstractMotif ()

	AbstractMotif (const AbstractMotif &other)

AbstractMotif &	operator= (const AbstractMotif &other)

virtual	~AbstractMotif ()

virtual ::std::string	GetStringFromImplementation (std::string separator=", ")

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

virtual	~EnvironmentDependent ()

virtual EnvironmentPointer	GetEnvironment ()

virtual const EnvironmentPointer	GetEnvironment () const

virtual void	SetEnvironment (EnvironmentPointer environment)

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)

Static Protected Member Functions inherited from bio::chemical::LinearMotif< CONTENT_TYPE >
static Properties	GetClassProperties ()

Static Protected Member Functions inherited from bio::chemical::UnorderedMotif< Pointer< CONTENT_TYPE > >
static Contents *	NewContents (Index expectedSize)

static Contents *	NewContents (const Contents &contents)

static Contents *	NewContents (Pointer< const Container > contents)

Static Protected Member Functions inherited from bio::chemical::AbstractMotif
static Properties	GetClassProperties ()

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::chemical::LinearMotif< CONTENT_TYPE >
AtomicNumber	mContentId

Protected Attributes inherited from bio::chemical::AbstractMotif
CowPtr< Container >	mContents

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

Detailed Description

Solutions contain Solutes and embody the idea of context.
This system provides traditional member access while simultaneously ensuring multiple conflicting writes from external sources never produce a conflict.

Solutions closely model physical::Lines & structural Motifs, but are intended to be more user facing and have a slightly different features. The main difference between Solutions and structural Motifs is that multiple Solutions cannot exist in the same context. Because Solutions represent context, combining 2 Solutions simply yields a novel context, i.e. a singular Solution. On the other hand, multiple Structures can be easily separated after being combined. With that said, Solutions can be nested (e.g. through Vesicles).
Another notable difference between Solutions and structural Motifs is that Structures can be formed of many different components, while Solutions are only comprised of Solutes; if you would like to add something to a Solution, it must be a Solute (i.e. a Dissolved Substance).
Solutions and structural Motifs define 2 points in a continuum of organization: Structural Motifs are highly ordered and predictable (i.e. they have a preset type) while Solutions are dynamic and more "chaotic" (i.e. any Substance can be Dissolved in them). The remainder of this continuum is populated by the usages of these 2 classes.

Solutes themselves are essentially shared pointers which track their reference count via their Concentration.
Effluxing a Solute to other Solutions increases the Concentration of the Solute and allows its Substance to be accessed from other "contexts".
Solutes can be Effluxed as const for read-only access or as non-const for read-write access.

This style of "Concentration goes up on access" is the inverse of real life. In the real world, "access", as quantified by binding affinity and reaction rate, is limited by a solute's concentration. We find this inversion to be more in line with state machine linear access semantics but may enforce a ConcentrationLimit or similar mechanism in a future release.

In real-world chemistry, the notation "[chemical]" is used to indicate the concentration of "chemical" in some Solution. However, Concentration is mostly irrelevant for access purposes and is thus ignored. You may access the ByteStream representation of a Solute with [Index || SmartIterator] or the Solute itself with [Id || Name].

Solutions rely on the IdPerspective to map their contents (all Solutes are Identifiable<Id>).

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS()

bio::chemical::Solution::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS	(	chemical	,
		Solution	,
		filter::Chemical()
	)

Ensure virtual methods point to Class implementations.
Dissolving a Substance in a Solution creates a Solute that represents the Substance.
The Solute will take ownership of the Substance and delete it when the Solute's Concentration drops to 0.
Dissolving a Substance which has already been Dissolved will result in the 2 Substances Mixing together.

Parameters

toDissolve

Returns: the Id of the created Solute in *this or INVALID_ID.

◆ Efflux() [1/4]

Solute bio::chemical::Solution::Efflux ( const Id & soluteId )

virtual

Efflux a Solute to access it.
Effluxing a Solute will create a new Solute that has the relevant parent Solute information set. Thus, Effluxing that (already Effluxed) Solute will maintain the appropriate parent relationship and automatically handle Concentration changes.

This should be done for all non-native Solution access, e.g. sub-Solutions or external Solutions.
You don't have to use Efflux to access Solutes within *this iff "you" own it.

Parameters

soluteId the Id of the desired Solute.

Returns: a Solute from within *this.

◆ Efflux() [2/4]

const Solute bio::chemical::Solution::Efflux ( const Id & soluteId ) const

virtual

Efflux a Solute to access it.
Effluxing a Solute will create a new Solute that has the relevant parent Solute information set. Thus, Effluxing that (already Effluxed) Solute will maintain the appropriate parent relationship and automatically handle Concentration changes.

This should be done for all non-native Solution access, e.g. sub-Solutions or external Solutions.
You don't have to use Efflux to access Solutes within *this iff "you" own it.

Parameters

soluteId the Id of the desired Solute.

Returns: a Solute from within *this.

◆ Efflux() [3/4]

Solute bio::chemical::Solution::Efflux ( const Name & substanceName )

virtual

Efflux a Solute to access it.
Effluxing a Solute will create a new Solute that has the relevant parent Solute information set. Thus, Effluxing that (already Effluxed) Solute will maintain the appropriate parent relationship and automatically handle Concentration changes.

This should be done for all non-native Solution access, e.g. sub-Solutions or external Solutions.
You don't have to use Efflux to access Solutes within *this iff "you" own it.

Parameters

substanceName the Name of the Substance associated with the desired Solute.

Returns: a Solute from within *this.

◆ Efflux() [4/4]

const Solute bio::chemical::Solution::Efflux ( const Name & substanceName ) const

virtual

Efflux a Solute to access it.
Effluxing a Solute will create a new Solute that has the relevant parent Solute information set. Thus, Effluxing that (already Effluxed) Solute will maintain the appropriate parent relationship and automatically handle Concentration changes.

This should be done for all non-native Solution access, e.g. sub-Solutions or external Solutions.
You don't have to use Efflux to access Solutes within *this iff "you" own it.

Parameters

substanceName the Name of the Substance associated with the desired Solute.

Returns: a Solute from within *this.

◆ GetAllSolutes() [1/2]

Pointer< physical::Line > bio::chemical::Solution::GetAllSolutes ( )

virtual

USE WITH CARE!

Returns: a pointer to the Solutes in *this.

◆ GetAllSolutes() [2/2]

Pointer< const physical::Line > bio::chemical::Solution::GetAllSolutes ( ) const

virtual

USE WITH CARE!

Returns: a const pointer to the Solutes in *this.

◆ Influx()

Id bio::chemical::Solution::Influx ( const Solute & toInflux )

virtual

Influxing a Solute into a Solution does either one of 2 things:

If the Solute does not already exist in *this, Clones toInflux (including the associated Substance) and adds the clone to *this. After being Influxed, the original Solute can be safely deleted.
If the Solute already exists in *this, the existing Solute "mixes" with toInflux according to the Miscibility of the existing Solute.

Parameters

toInflux the Solute you want to add or combine within *this.

existing ignore this.

Returns
the Id of the Solute created or mixed in *this.

◆ Separate()

Pointer< Substance > bio::chemical::Solution::Separate ( const Id & id )

virtual

Separating a Substance from a Solution removes the associated Solute from the Solution (*this).
Use this method if you would like to take control of a previously Dissolved Substance.

Parameters

id

Returns: a previously Dissolved Substance of the given Id or NULL.

Member Data Documentation

◆ diffusionEffort

const DiffusionTime const DiffusionEffort& bio::chemical::Solution::diffusionEffort

Initial value:

= diffusion::effort::Active()

)

bio::diffusion::effort::Active

DiffusionEffort Active()

◆ diffusionTime

const DiffusionTime& bio::chemical::Solution::diffusionTime = diffusion::time::Destruction()

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

toInflux	the Solute you want to add or combine within *this.
existing	ignore this.

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS()

◆ Efflux() [1/4]

◆ Efflux() [2/4]

◆ Efflux() [3/4]

◆ Efflux() [4/4]

◆ GetAllSolutes() [1/2]

◆ GetAllSolutes() [2/2]

◆ Influx()

◆ Separate()

Member Data Documentation

◆ diffusionEffort

◆ diffusionTime