#include <Protein.h>

Inheritance diagram for bio::molecular::Protein:

Collaboration diagram for bio::molecular::Protein:

Public Member Functions
virtual Code	Activate ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, Protein) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON(molecular

	filter::Molecular ()) virtual ~Protein()

virtual Code	Fold ()

virtual const DNA *	GetSource () const

virtual Code	operator() ()

&	ProteinPerspective::Instance ()

virtual Code	RecruitChaperones (Vesicle *environment)

virtual Code	SetSource (const DNA *source)

Public Member Functions inherited from bio::molecular::Molecule
virtual	~Molecule ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, Molecule) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(molecular

StandardDimension	Define (Name varName)

template<typename T >
StandardDimension	Define (Name varName)

template<typename T >
StandardDimension	Define (Name varName, const T &assignment)

virtual bool	DuplicateFrom (Molecule *source, Name surface)

	filter::Molecular ()) Molecule(const Molecule &toCopy)

&	MoleculePerspective::Instance ()

virtual Molecule *	operator<< (Molecule *source)

virtual Molecule *	operator<< (Surface *source)

virtual Molecule *	operator>> (Molecule *target)

virtual Surface *	operator>> (Surface *target)

virtual Code	Reify (physical::Symmetry *symmetry)

virtual Surface *	RotateTo (Name surfaceName)

virtual const Surface *	RotateTo (Name surfaceName) const

template<typename T >
T	RotateTo (Name surfaceName) const

virtual Surface *	RotateTo (StandardDimension surfaceId)

virtual const Surface *	RotateTo (StandardDimension surfaceId) const

template<typename T >
T	RotateTo (StandardDimension surfaceId) const

virtual physical::Symmetry *	Spin () const

virtual bool	TransferFrom (Molecule *source, Name surface)

template<typename T >
StandardDimension	Use (Name varName, T *varPtr)

virtual Surface *	operator() (StandardDimension surfaceId)

virtual const Surface *	operator() (StandardDimension surfaceId) const

template<typename T >
Surface *	operator() (StandardDimension surfaceId)

virtual Surface *	operator() (Name name)

virtual const Surface *	operator() (Name name) const

template<typename T >
Surface *	operator() (Name surfaceName)

Public Member Functions inherited from bio::molecular::Class< Molecule >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, Molecule) Class(Molecule *object

Public Member Functions inherited from bio::chemical::Class< T >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, T) Class(T *object

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

T *	Convert (Wave *wave)

virtual	operator T* ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::physical::Wave
	Wave (Symmetry *symmetry=NULL)

virtual	~Wave ()

virtual chemical::Atom *	AsAtom ()

virtual const chemical::Atom *	AsAtom () const

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Code	Attenuate (const Wave *other)

virtual Wave *	Clone () const

virtual Wave *	Demodulate ()

virtual const Wave *	Demodulate () const

virtual Code	Disattenuate (const Wave *other)

virtual Properties	GetProperties () const

virtual Wave *	Modulate (Wave *signal)

virtual Wave *	operator* ()

virtual const Wave *	operator* () const

virtual Wave *	operator* (Wave *signal)

virtual void	operator+ (const Wave *other)

virtual void	operator- (const Wave *other)

virtual void	operator\| (Symmetry *symmetry)

virtual Code	Reify (Symmetry *symmetry)

virtual Symmetry *	Spin () const

Public Member Functions inherited from bio::physical::Identifiable< StandardDimension >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective

void	CloneIntoName (Name name)

Public Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
	Observer (const Observer &other)

	Observer (Perspective *perspective=NULL)

virtual	~Observer ()

virtual Perspective *	GetPerspective () const

virtual void	SetPerspective (Perspective *perspective)

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Identifiable< StandardDimension > *	Convert (Wave *wave)

virtual	operator Identifiable< StandardDimension > * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::log::Writer
	Writer (Engine *logEngine, Filter logFilter)

virtual	~Writer ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Writer) Writer()

void	ExternalLog (Filter logFilter, Level level, const char *format,...) const

Engine *	GetLogEngine ()

const Engine *	GetLogEngine () const

bool	HasLogEngine () const

virtual void	SetLogEngine (Engine *logEngine)

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

virtual	~Filterable ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Filterable) Filterable()

Filter	GetFilter () const

virtual void	InitializeImplementation (ByteStreams args)

virtual Code	Reify (Symmetry *symmetry)

virtual void	SetFilter (Filter filter)

virtual Symmetry *	Spin () const

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Filterable *	Convert (Wave *wave)

virtual	operator Filterable * ()

virtual	operator Wave * ()

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Writer *	Convert (Wave *wave)

virtual	operator Wave * ()

virtual	operator Writer * ()

Public Member Functions inherited from bio::chemical::Atom
	Atom (const Atom &other)

virtual	~Atom ()

template<typename T >
T	As ()

template<typename T >
const T	As () const

template<typename T >
T	AsBonded ()

template<typename T >
const T	AsBonded () const

template<typename T >
T	AsBondedQuantum ()

template<typename T >
const T	AsBondedQuantum () const

virtual Code	Attenuate (const Wave *other)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Atom) explicit Atom()

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

virtual Code	Disattenuate (const Wave *other)

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

Bonds *	GetAllBonds ()

const Bonds *	GetAllBonds () const

Wave *	GetBonded (Valence position)

const Wave *	GetBonded (Valence position) const

template<typename T >
Valence	GetBondPosition () const

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (Name typeName) const

template<typename T >
BondType	GetBondType () const

BondType	GetBondType (Valence position) const

template<typename T >
	operator T ()

virtual Code	Reify (physical::Symmetry *symmetry)

virtual physical::Symmetry *	Spin () const

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Atom *	Convert (Wave *wave)

virtual	operator Atom * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::chemical::Substance
Substance	Substance (const typename UnorderedMotif< Property >::Contents properties, const typename UnorderedMotif< State >::Contents states)

virtual	~Substance ()

	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS_WITH_CTOR_COMMON (chemical, Substance, &SubstancePerspective::Instance(), filter::Chemical()) BIO_DISAMBIGUATE_ALL_CLASS_METHODS(chemical

virtual void	Disable ()

virtual void	Enable ()

virtual bool	IsEnabled () 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 >
void	Clear ()

template<typename T >
Container *	GetAll ()

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

template<typename T >
std::vector< T >	GetAllAsVector ()

template<typename T >
const std::vector< T >	GetAllAsVector () const

template<typename T >
unsigned long	GetCount () const

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

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

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

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

template<typename T >
void	Import (const std::vector< T > &other)

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

Code	ImportAll (const physical::Wave *other)

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

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

	ThreadSafe (const ThreadSafe &toCopy)

virtual	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

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

virtual	~LinearStructureInterface ()

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

template<typename T >
T	GetById (StandardDimension id)

template<typename T >
const T	GetById (StandardDimension id) const

template<typename T >
T	GetByName (Name name)

template<typename T >
const T	GetByName (Name name) const

template<typename T >
T	GetOrCreateById (StandardDimension id)

template<typename T >
T	GetOrCreateByName (Name name)

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

Public Member Functions inherited from bio::chemical::Class< Substance >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Substance) Class(Substance *object

Public Member Functions inherited from bio::chemical::UnorderedMotif< Property >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< Property > *toCopy)

virtual	~UnorderedMotif ()

virtual Property	AddImplementation (const Property content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Property >) UnorderedMotif()

virtual void	ClearImplementation ()

virtual unsigned long	GetCountImplementation () const

virtual unsigned int	GetNumMatchingImplementation (const Container *other) const

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

virtual bool	HasAllImplementation (const Container *contents) const

virtual bool	HasImplementation (const Property content) const

virtual void	ImportImplementation (const UnorderedMotif< Property > *other)

virtual Property	RemoveImplementation (const Property content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Property > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Property >) Class(UnorderedMotif< Property > *object

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

virtual	~AbstractMotif ()

virtual void	ClearImplementation ()

virtual Container *	GetAllImplementation ()

virtual const Container *	GetAllImplementation () const

virtual unsigned long	GetCountImplementation () const

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

virtual void	ImportImplementation (const void *other)

Public Member Functions inherited from bio::chemical::UnorderedMotif< State >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< State > *toCopy)

virtual	~UnorderedMotif ()

virtual State	AddImplementation (const State content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< State >) UnorderedMotif()

virtual void	ClearImplementation ()

virtual unsigned long	GetCountImplementation () const

virtual unsigned int	GetNumMatchingImplementation (const Container *other) const

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

virtual bool	HasAllImplementation (const Container *contents) const

virtual bool	HasImplementation (const State content) const

virtual void	ImportImplementation (const UnorderedMotif< State > *other)

virtual State	RemoveImplementation (const State content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< State > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< State >) Class(UnorderedMotif< State > *object

Public Member Functions inherited from bio::physical::Perspective< StandardDimension >
	Perspective ()

virtual	~Perspective ()

virtual bool	AssociateType (Id id, Wave *type)

virtual bool	DisassociateType (Id id)

Hadits::iterator	Find (Id id)

Hadits::const_iterator	Find (Id id) const

virtual Id	GetIdFromName (Name name)

virtual Id	GetIdWithoutCreation (Name name) const

virtual Name	GetNameFromId (Id id) const

virtual Wave *	GetNewObjectFromId (Id id) const

T	GetNewObjectFromIdAs (Id id)

virtual Wave *	GetNewObjectFromName (Name name)

T	GetNewObjectFromNameAs (Name name)

virtual Id	GetNumUsedIds () const

virtual const Wave *	GetTypeFromId (Id id) const

const T	GetTypeFromIdAs (Id id) const

virtual const Wave *	GetTypeFromName (Name name) const

const T	GetTypeFromNameAs (Name name) const

virtual Id	GetUniqueIdFor (Name name)

Public Member Functions inherited from bio::chemical::LinearMotif< Surface * >
	LinearMotif (const Contents contents, physical::Perspective< StandardDimension > perspective=NULL)

	LinearMotif (const LinearMotif< Surface * > &toCopy)

	LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)

virtual	~LinearMotif ()

virtual Surface *	AddImplementation (Surface * content)

virtual Code	Attenuate (const physical::Wave *other)

	BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Surface * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical

virtual void	ClearImplementation ()

virtual Surface *	CreateImplementation (StandardDimension id)

virtual Code	Disattenuate (const physical::Wave *other)

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual Surface *	GetByIdImplementation (StandardDimension id)

virtual const Surface *	GetByIdImplementation (StandardDimension id) const

virtual Surface *	GetByNameImplementation (Name name)

virtual const Surface *	GetByNameImplementation (Name name) const

virtual Surface *	GetOrCreateByIdImplementation (StandardDimension id)

virtual Surface *	GetOrCreateByNameImplementation (Name name)

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

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

const physical::Perspective< StandardDimension > *	GetStructuralPerspective () const

virtual bool	HasImplementation (const Surface * &content) const

virtual void	ImportImplementation (const LinearMotif< Surface * > *other)

virtual Code	InsertImplementation (Surface * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
	Elementary ()

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

Public Member Functions inherited from bio::chemical::Class< LinearMotif< Surface * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Surface * >) Class(LinearMotif< Surface * > *object

Public Member Functions inherited from bio::chemical::UnorderedMotif< Surface * >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< Surface * > *toCopy)

virtual	~UnorderedMotif ()

virtual Surface *	AddImplementation (const Surface * content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Surface * >) UnorderedMotif()

virtual void	ClearImplementation ()

virtual unsigned long	GetCountImplementation () const

virtual unsigned int	GetNumMatchingImplementation (const Container *other) const

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

virtual bool	HasAllImplementation (const Container *contents) const

virtual bool	HasImplementation (const Surface * content) const

virtual void	ImportImplementation (const UnorderedMotif< Surface * > *other)

virtual Surface *	RemoveImplementation (const Surface * content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Surface * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Surface * >) Class(UnorderedMotif< Surface * > *object

Public Member Functions inherited from bio::molecular::Class< Protein >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, Protein) Class(Protein *object

Public Member Functions inherited from bio::chemical::LinearMotif< Protein * >
	LinearMotif (const Contents contents, physical::Perspective< StandardDimension > perspective=NULL)

	LinearMotif (const LinearMotif< Protein * > &toCopy)

	LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)

virtual	~LinearMotif ()

virtual Protein *	AddImplementation (Protein * content)

virtual Code	Attenuate (const physical::Wave *other)

	BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< Protein * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical

virtual void	ClearImplementation ()

virtual Protein *	CreateImplementation (StandardDimension id)

virtual Code	Disattenuate (const physical::Wave *other)

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual Protein *	GetByIdImplementation (StandardDimension id)

virtual const Protein *	GetByIdImplementation (StandardDimension id) const

virtual Protein *	GetByNameImplementation (Name name)

virtual const Protein *	GetByNameImplementation (Name name) const

virtual Protein *	GetOrCreateByIdImplementation (StandardDimension id)

virtual Protein *	GetOrCreateByNameImplementation (Name name)

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

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

const physical::Perspective< StandardDimension > *	GetStructuralPerspective () const

virtual bool	HasImplementation (const Protein * &content) const

virtual void	ImportImplementation (const LinearMotif< Protein * > *other)

virtual Code	InsertImplementation (Protein * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

Public Member Functions inherited from bio::chemical::Elementary< LinearMotif< Protein * > >
	Elementary ()

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

Public Member Functions inherited from bio::chemical::Class< LinearMotif< Protein * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< Protein * >) Class(LinearMotif< Protein * > *object

Public Member Functions inherited from bio::chemical::UnorderedMotif< Protein * >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< Protein * > *toCopy)

virtual	~UnorderedMotif ()

virtual Protein *	AddImplementation (const Protein * content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Protein * >) UnorderedMotif()

virtual void	ClearImplementation ()

virtual unsigned long	GetCountImplementation () const

virtual unsigned int	GetNumMatchingImplementation (const Container *other) const

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

virtual bool	HasAllImplementation (const Container *contents) const

virtual bool	HasImplementation (const Protein * content) const

virtual void	ImportImplementation (const UnorderedMotif< Protein * > *other)

virtual Protein *	RemoveImplementation (const Protein * content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< Protein * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< Protein * >) Class(UnorderedMotif< Protein * > *object

Public Member Functions inherited from bio::molecular::EnvironmentDependent< Vesicle >
	EnvironmentDependent (Vesicle *environment=NULL)

virtual	~EnvironmentDependent ()

virtual Vesicle *	GetEnvironment ()

virtual const Vesicle *	GetEnvironment () const

virtual void	SetEnvironment (Vesicle *environment)

Public Attributes
	Protein

Public Attributes inherited from bio::molecular::Molecule
	Molecule

Public Attributes inherited from bio::molecular::Class< Molecule >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< T >
physical::Perspective< StandardDimension > Filter	filter = filter::Default()

physical::Perspective< StandardDimension > *	perspective = NULL

Public Attributes inherited from bio::physical::Identifiable< StandardDimension >
Id	m_id

Public Attributes inherited from bio::chemical::Class< Substance >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Property > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< State > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::LinearMotif< Surface * >
physical::Perspective< StandardDimension > *	m_perspective

Public Attributes inherited from bio::chemical::Class< LinearMotif< Surface * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Surface * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::molecular::Class< Protein >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::LinearMotif< Protein * >
physical::Perspective< StandardDimension > *	m_perspective

Public Attributes inherited from bio::chemical::Class< LinearMotif< Protein * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Protein * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Protected Attributes
const DNA *	m_source

Protected Attributes inherited from bio::physical::Class< T >
T *	m_object

Protected Attributes inherited from bio::physical::Wave
Wave *	m_signal

Symmetry *	m_symmetry

Protected Attributes inherited from bio::VirtualBase
bool	m_hasBeenInitialized

Protected Attributes inherited from bio::physical::Class< Identifiable< StandardDimension > >
Identifiable< StandardDimension > *	m_object

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

Protected Attributes inherited from bio::physical::Class< Filterable >
Filterable *	m_object

Protected Attributes inherited from bio::physical::Class< Writer >
Writer *	m_object

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

Protected Attributes inherited from bio::physical::Class< Atom >
Atom *	m_object

Protected Attributes inherited from bio::chemical::AbstractMotif
Container *	m_contents

Protected Attributes inherited from bio::physical::Perspective< StandardDimension >
Hadits	m_hadits

Id	m_nextId

Protected Attributes inherited from bio::molecular::EnvironmentDependent< Vesicle >
Vesicle *	m_environment

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

typedef std::vector< Id >	Ids

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

Public Types inherited from bio::chemical::UnorderedMotif< Property >
typedef physical::Arrangement< Property >	Contents

Public Types inherited from bio::chemical::UnorderedMotif< State >
typedef physical::Arrangement< State >	Contents

Public Types inherited from bio::physical::Perspective< StandardDimension >
typedef std::vector< Hadit >	Hadits

typedef StandardDimension	Id

typedef std::vector< Id >	Ids

Public Types inherited from bio::chemical::LinearMotif< Surface * >
typedef physical::Line	Contents

Public Types inherited from bio::chemical::UnorderedMotif< Surface * >
typedef physical::Arrangement< Surface * >	Contents

Public Types inherited from bio::chemical::LinearMotif< Protein * >
typedef physical::Line	Contents

Public Types inherited from bio::chemical::UnorderedMotif< Protein * >
typedef physical::Arrangement< Protein * >	Contents

Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (const Wave *wave, const Properties &properties)

static Properties	GetResonanceBetween (const Wave wave1, const Wave wave2)

static Properties	GetResonanceBetween (ConstWaves waves)

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

Static Public Member Functions inherited from bio::physical::Perspective< StandardDimension >
static Id	InvalidId ()

static Name	InvalidName ()

Static Public Member Functions inherited from bio::chemical::LinearMotif< Surface * >
static LinearMotif< Surface * > Properties	GetClassProperties ()

Static Public Member Functions inherited from bio::chemical::LinearMotif< Protein * >
static LinearMotif< Protein * > Properties	GetClassProperties ()

Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
static bool	hasRegistered

Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Protein * > >
static bool	hasRegistered

Protected Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
virtual void	InitializeImplementation (ByteStreams args)

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

virtual	~VirtualBase ()

void	Initialize (ByteStream arg1)

void	Initialize (ByteStream arg1, ByteStream arg2)

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

void	Initialize (ByteStreams args)

virtual void	InitializeImplementation (ByteStreams args)=0

Protected Member Functions inherited from bio::log::Writer
virtual void	InitializeImplementation (ByteStreams args)

void	Log (Level level, const char *format,...) const

Protected Member Functions inherited from bio::chemical::Atom
virtual bool	BreakBondImplementation (Wave *toDisassociate, AtomicNumber id, BondType type)

virtual bool	FormBondImplementation (Wave *toBond, AtomicNumber id, BondType type)

Detailed Description

Please read the documentation for Molecule.h to understand how Proteins can best be used. In short, Proteins provide functions for the Biology programming syntax. Proteins are Molecules and can be stored inside Surfaces. This means they will work with Define<Protein>("MyFunction", *myProtein). Proteins can thus be Transferred, reflected, and treated as any other Molecule, chemical::Substance, physical::Wave, etc. NOTE: Because Proteins are Molecules, they are more than just simple functors; they can store variables, facilitate in Transferring variables, and act as any other data structure.

Definition at line 44 of file Protein.h.

Member Function Documentation

◆ Activate()

Code bio::molecular::Protein::Activate ( )

virtual

This should be overwritten to add whatever functionality is desired. It is likely desirable, though not enforced to call Protein::Activate() at the end of any overwritten functions. This will cause all sub-Proteins to be Activated.

Returns: result of Activation.

Reimplemented in bio::genetic::FetchPlasmid, bio::genetic::RegisterPlasmid, and bio::genetic::RNAPolymerase.

Definition at line 58 of file Protein.cpp.

{
 Code ret = code::Success();
 BIO_EXCITATION_CLASS(Protein, Code) activate(&Protein::Activate);
 chemical::Emission result = ForEach<Protein*>(activate);
 //We don't care about result right now.
 return ret;
}

References Activate(), BIO_EXCITATION_CLASS, and bio::code::Success().

Referenced by Activate(), bio::genetic::Expressor::Activate(), operator()(), and bio::genetic::Plasmid::TranscribeFor().

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::molecular::Protein::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	molecular	,
		Protein
	)

Ensure virtual methods point to Class implementations. These are easy to use but require setting the Source after instantiation. For example: Protein myProtein = Protein("MyProtein"); myProtein.SetSource(myDNA); //myDNA created sometime earlier.

◆ filter::Molecular()

bio::molecular::Protein::filter::Molecular ( )

◆ Fold()

Code bio::molecular::Protein::Fold ( )

virtual

Fold will ensure *this is functional in the Molecular environment (Vesicle) This means it will make sure all Molecules, Reactions, and other Proteins needed are present. It is your responsibility to make this true for your Proteins.

This is to be called ONCE on startup. It is highly recommended, though not enforced, to call Protein::Fold at the end of any overwritten function. This will call initialize for any sub proteins. If that is not done, some proteins may not be initialized and the behavior will be undefined. (follow the RecruitChaperones example).

NOTE: If RecruitChaperones does not return code::Success(), Fold will not be called at all.

Returns: result of Folding.

Definition at line 39 of file Protein.cpp.

{
 Code ret = code::Success();
 BIO_EXCITATION_CLASS(Protein, Code) fold(&Protein::Fold);
 chemical::Emission result = ForEach<Protein*>(fold);
 //We don't care about result right now.
 return ret;
}

References BIO_EXCITATION_CLASS, Fold(), and bio::code::Success().

Referenced by Fold(), and bio::genetic::Plasmid::TranscribeFor().

◆ GetSource()

const DNA * bio::molecular::Protein::GetSource ( ) const

virtual

Proteins originate from DNA. This allows us to tell 2 otherwise identical Proteins apart. For example, Protein with name "DoMyAction" gets replaced with a "DoMyAction" from an updated Gene. Both Proteins will return true on == comparison but may have different functionality which would only be known by getting the m_source.

Returns: the m_source of *this.

Definition at line 78 of file Protein.cpp.

{
 return m_source;
}

References m_source.

◆ operator()()

Code bio::molecular::Protein::operator() ( )

virtual

The () operator is the primary function that will be called when accessing *this. Calling Protein::operator() just forwards to Activate.

Returns: Activate()

Definition at line 67 of file Protein.cpp.

{
 return Activate();
}

References Activate().

◆ ProteinPerspective::Instance()

& bio::molecular::Protein::ProteinPerspective::Instance ( )

◆ RecruitChaperones()

Code bio::molecular::Protein::RecruitChaperones ( Vesicle * environment )

virtual

RecruitChaperones can be used to make sure that the environment has all the necessary components for *this to function before it Fold()s. If this method returns Success, *this and its sub-Proteins will be Folded.

Override this method to add whatever start-up checks you need. It is recommended to call the parent method AFTER your own checks, which will call RecruitChaperones for all sub-Proteins.

For example: virtual Code RecruitChaperones(Vesicle* environment) { BIO_SANITIZE(MyChecks(),,return code::GeneralFailure()) return Protein::RecruitChaperones(environment); }

This also sets m_environment to the environment provided.

Parameters

environment

Returns: result of chaperone recruitment & whether or not Fold should be called.

Definition at line 48 of file Protein.cpp.

{
 SetEnvironment(environment);
 BIO_EXCITATION_CLASS(Protein, Code, Vesicle*) recruitChaperones(&Protein::RecruitChaperones, environment);
 chemical::Emission result = ForEach<Protein*>(&recruitChaperones);
 //We don't care about result right now.
 return code::Success();
}

References BIO_EXCITATION_CLASS, RecruitChaperones(), bio::molecular::EnvironmentDependent< Vesicle >::SetEnvironment(), and bio::code::Success().

Referenced by RecruitChaperones(), and bio::genetic::Plasmid::TranscribeFor().

◆ SetSource()

Code bio::molecular::Protein::SetSource ( const DNA * source )

virtual

Set the m_source of *this

Parameters

source

Returns: the result of setting (e.g. code::Success()).

Definition at line 72 of file Protein.cpp.

{
 m_source = source;
 return code::Success();
}

References m_source, and bio::code::Success().

Referenced by bio::genetic::RNAPolymerase::RNAPolymerase().

Member Data Documentation

◆ Protein

bio::molecular::Protein::Protein

Definition at line 64 of file Protein.h.

◆ m_source

const DNA* bio::molecular::Protein::m_source

protected

Definition at line 140 of file Protein.h.

Referenced by bio::genetic::RNAPolymerase::Activate(), GetSource(), and SetSource().

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

/home/eons/git/biology/lib_bio/inc/bio/molecular/Protein.h
/home/eons/git/biology/lib_bio/src/molecular/Protein.cpp

Public Member Functions

Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ Activate()

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

◆ filter::Molecular()

◆ Fold()

◆ GetSource()

◆ operator()()

◆ ProteinPerspective::Instance()

◆ RecruitChaperones()

◆ SetSource()

Member Data Documentation

◆ Protein

◆ m_source