#include <Molecule.h>

Inheritance diagram for bio::molecular::Molecule:

Collaboration diagram for bio::molecular::Molecule:

Public Member Functions
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 Attributes
	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

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

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 Attributes inherited from bio::chemical::Elementary< LinearMotif< Surface * > >
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)

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

Detailed Description

As a combination of relativistic Waves and chemical Bonds, Molecules are rather complicated. They're kinda like viewing particle physics from mathematical topology. I'm not sure I have the english words to describe this view of the world adequately, so looking at the code might be better. Still, I'll try to describe the idea as an imagination exercise:

Imagine a Quantum Wave (aka a built-in type, like bool or int) as a sphere. These quantum balls are the maximum resolution we can see any Molecule through (it doesn't get any more basic than built-in types). Next, imagine a collection of these spheres as some kind of glob. This represents a collection of basic types and would be akin to a class or struct. However, these globs can take whatever form we want and do not have to map into any hard-coded structure. We call these globular constructs a Surface. Most of the time, Surfaces will be singular globs, with a 1 to 1 Surface to primitive type correspondence. However, they can be arbitrarily knobby. Now imagine 10 or so of these Surfaces all stuck together as a Molecule. So, a Molecule is just a big globby mass. Surfaces do not (usually) overlap. They are, instead, distinct, identifiable (Identifiable<StandardDimension>) regions on a Molecule. Imagine identical 2 Molecules that have 1 globby collection (Surface) that differs between them. That kind of comparative difference helps us Identify the Surfaces from the otherwise indistinguishable mass of globs. Next, imagine 2 Molecules bumping into each other so that 1 or more of their Surfaces touch. When Surfaces interact in this manner, they can change each other. In computer science, we can just conjure change whenever, however, and wherever we want. However, in the real world, the idea that matter / energy is conserved requires that matter / energy be moved between the interacting surfaces in order to effect change. This same concept has been modeled here (see Transfer..., etc., below); though we can still do whatever the **** we want cause computers.

You can create Surfaces in 1 Molecule and then Transfer them to another. However, doing so may change (or break) the Molecules' interactions with other Molecules and systems. This would be like transferring variables between objects at runtime. This Transfer system is why Molecules are Perspectives. The Id of Surfaces in 1 Molecule may not hold within another Molecule and we don't want to enforce a global Surface labeling at this time. You can think of Surface::Ids as numbered variables. When an class (Molecule) is instantiated, we go through and number its member variables. Members can then be added or removed throughout the life of the object and each one will have a number that is unique to that Molecule. In other words, there is no absolutely right number for "MyVar"; instead, "MyVar" can be an int in one Molecule and a bool in another.

The ability to Transfer Surfaces between Molecules is just one advantage that comes from this member abstraction. Another advantage is Symmetry (i.e. reflection into other languages, like json). Beyond this point, Spin() and Reify(), which are native to physical::Waves, should no longer require definition, as we will be able to use the Biology structures we've created to determine those implementations dynamically.

Lastly, Surfaces also give us the ability to store methods via Proteins. See Protein.h for more on that.

In order realize the behavior described above, we have to employ a non-native, Biology-specific syntax. In short, Define<>() creates a member and RotateTo gets a member. For example: MyType myVar = SomeFunction(); => Define<MyType>("myVar", SomeFunction()); MyType another = myVar; => Define<MyType>("another", RotateTo("myVar")); Of course, in order to avoid slower string lookups, you can cache the Id of "myVar" within a Molecule by calling GetIdFromName("myVar"), which can then be used with RotateTo(...).

You can think of members as globs on the surface of our Molecule and we rotate this globby mass until the side we want is facing us. This allows us to interact with our desired Surface. In order to set a member, you would do something like: RotateTo("myVar")->operator=(*RotateTo("another")); or, more simply, (*RotateTo("myVar")) = (*RotateTo("another")) NOTE: if "myVar" or "another" don't exist in the Molecule, this will segfault. To avoid crashing, you may want to use BIO_SANITIZE() (from bio/common/Macros.h) This can be done because Surfaces can be treated as the values they are Bonded to.

Lastly, if you want to create a Molecule from a hard-coded data structure, you can call Use() instead of Define<>(), which will create a Surface from a (member) pointer. Surfaces created with Use will not be Transferable.

Definition at line 72 of file Molecule.h.

Constructor & Destructor Documentation

◆ ~Molecule()

bio::molecular::Molecule::~Molecule ( )

virtual

Definition at line 44 of file Molecule.cpp.

45{

46}

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::molecular::Molecule::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	molecular	,
		Molecule
	)

Ensure virtual methods point to Class implementations. Standard ctors.

◆ Define() [1/3]

StandardDimension bio::molecular::Molecule::Define ( Name varName )

inline

Create a new variable within *this, the Biology way. The created variable will have no type set upon creation. Will fail if varName already exists within *this.

Parameters

varName

Returns: the Id of the Surface created or InvalidId().

Definition at line 135 of file Molecule.h.

    {
        BIO_SANITIZE(!RotateTo(varName), ,
            return InvalidId());
        Surface* toAdd = new Surface(
            varName,
            this
        );
        Add< Surface* >(toAdd);
        return toAdd->GetId();
    }

References BIO_SANITIZE, bio::physical::Perspective< StandardDimension >::InvalidId(), and RotateTo().

Referenced by bio::genetic::FetchPlasmid::FetchPlasmid(), bio::genetic::RegisterPlasmid::RegisterPlasmid(), and bio::genetic::RNAPolymerase::RNAPolymerase().

◆ Define() [2/3]

template<typename T >

StandardDimension bio::molecular::Molecule::Define ( Name varName )

inline

Create a new variable within *this, the Biology way. Will fail if varName already exists within *this.

Template Parameters

T

Parameters

varName

Returns: the Id of the Surface created or InvalidId().

Definition at line 155 of file Molecule.h.

    {
        BIO_SANITIZE(!RotateTo(varName), ,
            return InvalidId());
        Surface* toAdd = new Surface(
            varName,
            this
        );
        toAdd->Manage(new T());
        Add< Surface* >(toAdd);
        return toAdd->GetId();
    }

References BIO_SANITIZE, bio::physical::Perspective< StandardDimension >::InvalidId(), bio::molecular::Surface::Manage(), and RotateTo().

◆ Define() [3/3]

template<typename T >

StandardDimension bio::molecular::Molecule::Define	(	Name	varName,
		const T &	assignment
	)

inline

Create a new variable within *this, the Biology way. Assigns the new variable to the value provided. Will fail if varName already exists within *this.

Template Parameters

T

Parameters

varName
assignment

Returns: the Id of the Surface created or InvalidId().

Definition at line 178 of file Molecule.h.

    {
        BIO_SANITIZE(!RotateTo(varName), ,
            return InvalidId());
        Surface* toAdd = new Surface(
            varName,
            this
        );
        toAdd->Manage(new T(assignment));
        Add< Surface* >(toAdd);
        return toAdd->GetId();
    }

References BIO_SANITIZE, bio::physical::Perspective< StandardDimension >::InvalidId(), bio::molecular::Surface::Manage(), and RotateTo().

◆ DuplicateFrom()

bool bio::molecular::Molecule::DuplicateFrom	(	Molecule *	source,
		Name	surface
	)

virtual

Copy a Surface from another Molecule into *this.

Parameters

source
surface

Returns: whether or not the operation succeeded.

Definition at line 84 of file Molecule.cpp.

{
    BIO_SANITIZE(source, ,
        return false);
 
    BIO_SANITIZE(!RotateTo(surface), ,
        return false);
 
    Surface* toTransfer = NULL;
 
    BIO_SANITIZE_WITH_CACHE(source->RotateTo(surface),
        toTransfer = RESULT,
        return false);
 
    Add< Surface* >(CloneAndCast< Surface* >(toTransfer))->SetEnvironment(this);
    return true;
}

References BIO_SANITIZE, BIO_SANITIZE_WITH_CACHE, and RotateTo().

◆ filter::Molecular()

bio::molecular::Molecule::filter::Molecular ( ) const &

Copying a Molecule will duplicate all Surfaces of toCopy.

Parameters

toCopy

◆ MoleculePerspective::Instance()

& bio::molecular::Molecule::MoleculePerspective::Instance ( )

◆ operator()() [1/6]

Surface * bio::molecular::Molecule::operator() ( Name name )

virtual

Definition at line 137 of file Molecule.cpp.

{
    return RotateTo(name);
}

◆ operator()() [2/6]

const Surface * bio::molecular::Molecule::operator() ( Name name ) const

virtual

Definition at line 142 of file Molecule.cpp.

{
    return RotateTo(name);
}

◆ operator()() [3/6]

template<typename T >

Surface * bio::molecular::Molecule::operator() ( Name surfaceName )

inline

Definition at line 303 of file Molecule.h.

    {
        return ChemicalCast< T >(RotateTo(surfaceName));
    }

References RotateTo().

◆ operator()() [4/6]

Surface * bio::molecular::Molecule::operator() ( StandardDimension surfaceId )

virtual

operator wrappers around RotateTo

Parameters

surfaceId

Returns: RotateTo(...)

Definition at line 127 of file Molecule.cpp.

{
    return RotateTo(surfaceId);
}

◆ operator()() [5/6]

template<typename T >

Surface * bio::molecular::Molecule::operator() ( StandardDimension surfaceId )

inline

Definition at line 293 of file Molecule.h.

    {
        return ChemicalCast< T >(RotateTo(surfaceId));
    }

References RotateTo().

◆ operator()() [6/6]

const Surface * bio::molecular::Molecule::operator() ( StandardDimension surfaceId ) const

virtual

Definition at line 132 of file Molecule.cpp.

{
    return RotateTo(surfaceId);
}

◆ operator<<() [1/2]

Molecule * bio::molecular::Molecule::operator<< ( Molecule * source )

virtual

Molecule copy operation. Copies all Surfaces on the source Molecule onto *this.

Parameters

source

Returns: this

Definition at line 163 of file Molecule.cpp.

{
    BIO_SANITIZE(source, ,
        return this);
    Import< Surface* >(source);
    return this;
}

References BIO_SANITIZE.

◆ operator<<() [2/2]

Molecule * bio::molecular::Molecule::operator<< ( Surface * source )

virtual

Surface move operation. Moves a Surface onto *this.

Parameters

source

Returns: this

Definition at line 147 of file Molecule.cpp.

{
    BIO_SANITIZE(source, ,
        return this);
    Add< Surface* >(source)->SetEnvironment(this);
    return this;
}

References BIO_SANITIZE.

◆ operator>>() [1/2]

Molecule * bio::molecular::Molecule::operator>> ( Molecule * target )

virtual

Molecule move operation. Moves all Surfaces on *this onto the target Molecule. This REMOVES all Surfaces from *this.

Parameters

target

Returns: target

Definition at line 171 of file Molecule.cpp.

{
    BIO_SANITIZE(target, ,
        return target);
    target->Import< Surface* >(this);
    Clear< Surface* >();
    return target;
}

References BIO_SANITIZE, and bio::chemical::UnorderedStructureInterface::Import().

◆ operator>>() [2/2]

Surface * bio::molecular::Molecule::operator>> ( Surface * target )

virtual

Surface move operation. Places *this in a Surface. NOTE: There is no check that *this is not in multiple Surfaces.

Parameters

target

Returns: target

Definition at line 155 of file Molecule.cpp.

{
    BIO_SANITIZE(target, ,
        return target);
    target->Add< Molecule* >(this);
    return target;
}

References bio::chemical::UnorderedStructureInterface::Add(), and BIO_SANITIZE.

◆ Reify()

Code bio::molecular::Molecule::Reify ( physical::Symmetry * symmetry )

virtual

Required method from Wave. See that class for details. Reconstruct *this from the given Symmetry.

Parameters

symmetry

Reimplemented from bio::chemical::Atom.

Definition at line 186 of file Molecule.cpp.

{
    //TODO...
    return code::NotImplemented();
}

References bio::code::NotImplemented().

◆ RotateTo() [1/6]

Surface * bio::molecular::Molecule::RotateTo ( Name surfaceName )

virtual

Get a variable from within *this. Use for getting and/or setting.

Parameters

surfaceName

Returns: a Surface with the given Name from *this.

Definition at line 66 of file Molecule.cpp.

{
    BIO_SANITIZE_WITH_CACHE(GetByName< Surface* >(
        surfaceName
    ),
        return *Cast< Surface** >(RESULT),
        return NULL);
}

References BIO_SANITIZE_WITH_CACHE.

◆ RotateTo() [2/6]

const Surface * bio::molecular::Molecule::RotateTo ( Name surfaceName ) const

virtual

const version of RotateTo

Parameters

surfaceName

Returns: a const Surface with the given Name from *this.

Definition at line 75 of file Molecule.cpp.

{
    BIO_SANITIZE_WITH_CACHE(GetByName< Surface* >(
        surfaceName
    ),
        return *Cast< const Surface** >(RESULT),
        return NULL);
}

References BIO_SANITIZE_WITH_CACHE.

◆ RotateTo() [3/6]

template<typename T >

T bio::molecular::Molecule::RotateTo ( Name surfaceName ) const

inline

Ease of use methods for getting variables as the desired type.

Template Parameters

T

Returns: a Surface from *this casted to T.

Definition at line 242 of file Molecule.h.

    {
        return ChemicalCast< T >(RotateTo(surfaceName));
    }

References RotateTo().

◆ RotateTo() [4/6]

Surface * bio::molecular::Molecule::RotateTo ( StandardDimension surfaceId )

virtual

Get a variable from within *this. Use for getting and/or setting. REMINDER: use this->GetIdFromName("someName") to get the Id of a Surface with the given Name.

Parameters

surfaceId

Returns: a Surface with the given Id, as defined by *this, or NULL.

Definition at line 48 of file Molecule.cpp.

{
    BIO_SANITIZE_WITH_CACHE(GetById< Surface* >(
        surfaceId
    ),
        return *Cast< Surface** >(RESULT),
        return NULL);
}

References BIO_SANITIZE_WITH_CACHE.

Referenced by bio::genetic::FetchPlasmid::Activate(), bio::genetic::RegisterPlasmid::Activate(), Define(), DuplicateFrom(), bio::genetic::GenomeImplementation::FetchPlasmid(), operator()(), RotateTo(), bio::genetic::Plasmid::TranscribeFor(), TransferFrom(), and Use().

◆ RotateTo() [5/6]

const Surface * bio::molecular::Molecule::RotateTo ( StandardDimension surfaceId ) const

virtual

const version of RotateTo

Parameters

surfaceId

Returns: a const Surface with the given Id, as defined by *this, or NULL.

Definition at line 57 of file Molecule.cpp.

{
    BIO_SANITIZE_WITH_CACHE(GetById< Surface* >(
        surfaceId
    ),
        return *Cast< const Surface** >(RESULT),
        return NULL);
}

References BIO_SANITIZE_WITH_CACHE.

◆ RotateTo() [6/6]

template<typename T >

T bio::molecular::Molecule::RotateTo ( StandardDimension surfaceId ) const

inline

Ease of use methods for getting variables as the desired type.

Template Parameters

T

Returns: a Surface from *this casted to T.

Definition at line 216 of file Molecule.h.

    {
        return ChemicalCast< T >(RotateTo(surfaceId));
    }

References RotateTo().

◆ Spin()

physical::Symmetry * bio::molecular::Molecule::Spin ( ) const

virtual

Required method from Wave. See that class for details.

Returns: a Symmetrical image of *this

Reimplemented from bio::chemical::Atom.

Definition at line 180 of file Molecule.cpp.

{
    //TODO...
    return NULL;
}

◆ TransferFrom()

bool bio::molecular::Molecule::TransferFrom	(	Molecule *	source,
		Name	surface
	)

virtual

Move a Surface from another Molecule into *this.

Parameters

source
surface

Returns: whether or not the operation succeeded.

Definition at line 105 of file Molecule.cpp.

{
    BIO_SANITIZE(source, ,
        return false);
 
    BIO_SANITIZE(!RotateTo(surface), ,
        return false);
 
    Surface* toTransfer = NULL;
 
    BIO_SANITIZE_WITH_CACHE(source->RotateTo(surface),
        toTransfer = RESULT,
        return false);
 
    Add< Surface* >(toTransfer)->SetEnvironment(this);
    source->Remove< Surface* >(toTransfer);
    return true;
}

References BIO_SANITIZE, BIO_SANITIZE_WITH_CACHE, bio::chemical::UnorderedStructureInterface::Remove(), and RotateTo().

◆ Use()

template<typename T >

StandardDimension bio::molecular::Molecule::Use	(	Name	varName,
		T *	varPtr
	)

inline

Create a Surface from an existing (member) variable. Will fail if varName already exists within *this.

Template Parameters

T

Parameters

varName
varPtr

Returns: the Id of the Surface created or InvalidId().

Definition at line 112 of file Molecule.h.

    {
        BIO_SANITIZE(!RotateTo(varName), ,
            return InvalidId());
        Surface* toAdd = new Surface(
            varName,
            this
        );
        toAdd->Use(varPtr);
        Add< Surface* >(toAdd);
        return toAdd->GetId();
    }

References BIO_SANITIZE, bio::physical::Perspective< StandardDimension >::InvalidId(), RotateTo(), and bio::molecular::Surface::Use().

Member Data Documentation

◆ Molecule

bio::molecular::Molecule::Molecule

Definition at line 88 of file Molecule.h.

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

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~Molecule()

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

◆ Define() [1/3]

◆ Define() [2/3]

◆ Define() [3/3]

◆ DuplicateFrom()

◆ filter::Molecular()

◆ MoleculePerspective::Instance()

◆ operator()() [1/6]

◆ operator()() [2/6]

◆ operator()() [3/6]

◆ operator()() [4/6]

◆ operator()() [5/6]

◆ operator()() [6/6]

◆ operator<<() [1/2]

◆ operator<<() [2/2]

◆ operator>>() [1/2]

◆ operator>>() [2/2]

◆ Reify()

◆ RotateTo() [1/6]

◆ RotateTo() [2/6]

◆ RotateTo() [3/6]

◆ RotateTo() [4/6]

◆ RotateTo() [5/6]

◆ RotateTo() [6/6]

◆ Spin()

◆ TransferFrom()

◆ Use()

Member Data Documentation

◆ Molecule