#include <Surface.h>

Inheritance diagram for bio::molecular::Surface:

Collaboration diagram for bio::molecular::Surface:

Public Member Functions
	Surface (const Surface &toCopy)

virtual	~Surface ()

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

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (molecular, Surface) Surface(Name name

template<typename T >
T	Manage (T varPtr)

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

virtual physical::Waves	operator-- ()

virtual chemical::Substance *	operator-= (Name toRelease)

virtual physical::Wave *	operator-= (physical::Wave *toRelease)

virtual chemical::Substance *	operator-= (StandardDimension toRelease)

virtual Code	Reify (physical::Symmetry *symmetry)

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

virtual physical::Wave *	Release (physical::Wave *toRelease, BondType bondType=bond_type::Temporary())

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

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

virtual void	SetEnvironment (Molecule *environment)

virtual void	SetPerspective (Molecule *perspective)

virtual physical::Symmetry *	Spin () const

template<typename T >
T	Use (T varPtr)

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

	LinearMotif (const LinearMotif< Molecule * > &toCopy)

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

virtual	~LinearMotif ()

virtual Molecule *	AddImplementation (Molecule * content)

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

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

virtual void	ClearImplementation ()

virtual Molecule *	CreateImplementation (StandardDimension id)

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

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual Molecule *	GetByIdImplementation (StandardDimension id)

virtual const Molecule *	GetByIdImplementation (StandardDimension id) const

virtual Molecule *	GetByNameImplementation (Name name)

virtual const Molecule *	GetByNameImplementation (Name name) const

virtual Molecule *	GetOrCreateByIdImplementation (StandardDimension id)

virtual Molecule *	GetOrCreateByNameImplementation (Name name)

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

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

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

virtual bool	HasImplementation (const Molecule * &content) const

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

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

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

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

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

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

	UnorderedMotif (const UnorderedMotif< Molecule * > *toCopy)

virtual	~UnorderedMotif ()

virtual Molecule *	AddImplementation (const Molecule * content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< Molecule * >) 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 Molecule * content) const

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

virtual Molecule *	RemoveImplementation (const Molecule * content)

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

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

virtual	~EnvironmentDependent ()

virtual Molecule *	GetEnvironment ()

virtual const Molecule *	GetEnvironment () const

virtual void	SetEnvironment (Molecule *environment)

Public Attributes
Molecule *	environment

Public Attributes inherited from bio::molecular::Class< Surface >
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< Molecule * >
physical::Perspective< StandardDimension > *	m_perspective

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

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< Molecule * > >
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::chemical::LinearMotif< Molecule * >
typedef physical::Line	Contents

Public Types inherited from bio::chemical::UnorderedMotif< Molecule * >
typedef physical::Arrangement< Molecule * >	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::chemical::LinearMotif< Molecule * >
static LinearMotif< Molecule * > Properties	GetClassProperties ()

Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< Molecule * > >
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::molecular::EnvironmentDependent< Molecule >
Molecule *	m_environment

Detailed Description

Surfaces can be thought of as variables for the Biology syntax. They either hold a single, Quantum value, or are composed of a complex array of Molecules. See Molecule.h for a more detailed explanation.

Definition at line 41 of file Surface.h.

Constructor & Destructor Documentation

◆ Surface()

bio::molecular::Surface::Surface ( const Surface & toCopy )

Copying a Surface generates a new set of Molecules and will Clone any Manage()d Waves from toCopy into *this. NOTE: all Use()d Waves will be lost. Since *this does not control what it Uses, it cannot (will not) duplicate it. Keep in mind that *this will delete all Managed Waves on destruction.

Parameters

toCopy

Definition at line 30 of file Surface.cpp.

    :
    molecular::Class< Surface >(
        this,
        name,
        environment,
        filter::Molecular(),
        symmetry_type::Variable()),
    EnvironmentDependent< Molecule >(environment)
{
 
}

◆ ~Surface()

bio::molecular::Surface::~Surface ( )

virtual

deletes all Manage()d Bonds.

Definition at line 76 of file Surface.cpp.

{
    chemical::Bond* bondBuffer;
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        bondBuffer = bnd;
        if (bondBuffer->GetType() == bond_type::Manage())
        {
            //bypass BreakBondImplementation and just do it.
            delete bondBuffer->GetBonded();
            bondBuffer->Break();
        }
    }
}

References bio::chemical::Bond::Break(), bio::Container::End(), bio::chemical::Bond::GetBonded(), bio::chemical::Bond::GetType(), bio::SmartIterator::IsAtBeginning(), bio::chemical::Atom::m_bonds, and bio::bond_type::Manage().

Member Function Documentation

◆ Bind()

template<typename T >

T bio::molecular::Surface::Bind	(	T	toBind,
		BondType	bondType = `bond_type::Temporary()`
	)

inline

Binding, as opposed to permanent Bonding, forms a temporary association with the given Substance. Binding forms a Temporary Bond, allowing *this to be treated as the Bound Substance.

Template Parameters

T

Parameters

toBind
bondType

Returns: the Bound type.

Definition at line 129 of file Surface.h.

    {
        FormBond(
            toBind,
            bondType
        );
        return toBind;
    }

References bio::chemical::Atom::FormBond().

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

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::molecular::Surface::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	molecular	,
		Surface
	)

Ensure virtual methods point to Class implementations.

Parameters

name

◆ Manage()

template<typename T >

T bio::molecular::Surface::Manage ( T varPtr )

inline

Create a Manage()d Bond with the given var. varPtr will be deleted when *this is destroyed. See Bonds.h for more on what Manage() does.

Template Parameters

T

Parameters

varPtr

Returns

Definition at line 97 of file Surface.h.

    {
        FormBond(
            varPtr,
            bond_type::Manage());
    }

References bio::chemical::Atom::FormBond(), and bio::bond_type::Manage().

Referenced by bio::molecular::Molecule::Define().

◆ operator+=()

template<typename T >

T bio::molecular::Surface::operator+= ( T toBind )

inline

Wrapper around Bind

Parameters

toBind

Returns: result of Bind(...)

Definition at line 200 of file Surface.h.

    {
        return Bind< T >(toBind);
    }

◆ operator--()

physical::Waves bio::molecular::Surface::operator-- ( )

virtual

Wrapper around ReleaseAll

Returns: all Temporarily Bound Substances.

Definition at line 242 of file Surface.cpp.

{
    return ReleaseAll();
}

References ReleaseAll().

◆ operator-=() [1/3]

chemical::Substance * bio::molecular::Surface::operator-= ( Name toRelease )

virtual

Wrapper around Release

Parameters

toRelease

Returns: result of Release

Definition at line 232 of file Surface.cpp.

{
    return Release(toRelease);
}

References Release().

◆ operator-=() [2/3]

physical::Wave * bio::molecular::Surface::operator-= ( physical::Wave * toRelease )

virtual

Wrapper around Release

Parameters

toRelease

Returns: result of Release

Definition at line 227 of file Surface.cpp.

{
    return Release(toRelease);
}

References Release().

◆ operator-=() [3/3]

chemical::Substance * bio::molecular::Surface::operator-= ( StandardDimension toRelease )

virtual

Wrapper around Release

Parameters

toRelease

Returns: result of Release

Definition at line 237 of file Surface.cpp.

{
    return Release(toRelease);
}

References Release().

◆ Reify()

Code bio::molecular::Surface::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 107 of file Surface.cpp.

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

References bio::code::NotImplemented().

◆ Release() [1/3]

chemical::Substance * bio::molecular::Surface::Release	(	Name	toRelease,
		physical::Perspective< StandardDimension > *	perspective = `NULL`,
		BondType	bondType = `bond_type::Temporary()`
	)

virtual

Breaks the Temporary Bond formed by Bind. NOTE: the given Substance could be Identifiable through some unknown Perspective, so this does actual string comparison. Unless a Perspective is given, in which case numeric comparison is done on the given Name.

Parameters

toRelease
perspective
bondType

Returns: the previously bound Substance or NULL.

Definition at line 145 of file Surface.cpp.

{
    chemical::Substance* ret = NULL;
    chemical::Bond* bondBuffer;
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        bondBuffer = bnd;
        if (bondBuffer->GetType() == bondType)
        {
            ret = ChemicalCast< chemical::Substance* >(bondBuffer->GetBonded());
            BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
                continue);
            BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret->IsName(toRelease), ,
                continue);
            BIO_SANITIZE_AT_SAFETY_LEVEL_2(perspective && ret->GetPerspective() != perspective,
                continue,);
            bondBuffer->Break();
            break;
        }
    }
    return ret;
}

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, bio::chemical::Bond::Break(), bio::Container::End(), bio::chemical::Bond::GetBonded(), bio::physical::Observer< PERSPECTIVE >::GetPerspective(), bio::chemical::Bond::GetType(), bio::SmartIterator::IsAtBeginning(), bio::chemical::Atom::m_bonds, and bio::molecular::Class< Surface >::perspective.

◆ Release() [2/3]

physical::Wave * bio::molecular::Surface::Release	(	physical::Wave *	toRelease,
		BondType	bondType = `bond_type::Temporary()`
	)

virtual

Breaks the Temporary Bond formed by Bind.

Parameters

toRelease
bondType

Returns: the previously bound Substance or NULL.

Definition at line 119 of file Surface.cpp.

{
    physical::Wave* ret = NULL;
    chemical::Bond* bondBuffer;
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        bondBuffer = bnd;
        if (bondBuffer->GetType() == bondType)
        {
            ret = ChemicalCast< physical::Wave* >(bondBuffer->GetBonded());
            BIO_SANITIZE_AT_SAFETY_LEVEL_2(!ret || ret != toRelease,
                continue,);
            bondBuffer->Break();
            break;
        }
    }
    return ret;
}

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, bio::chemical::Bond::Break(), bio::Container::End(), bio::chemical::Bond::GetBonded(), bio::chemical::Bond::GetType(), bio::SmartIterator::IsAtBeginning(), and bio::chemical::Atom::m_bonds.

Referenced by operator-=().

◆ Release() [3/3]

chemical::Substance * bio::molecular::Surface::Release	(	StandardDimension	toRelease,
		physical::Perspective< StandardDimension > *	perspective = `NULL`,
		BondType	bondType = `bond_type::Temporary()`
	)

virtual

Breaks the Temporary Bond formed by Bind. NOTE: the given Substance could be Identifiable through some unknown Perspective, so this does an unreliable numeric comparison. However, if a Perspective is given, we can be certain if the id we find is correct or not.

Parameters

toRelease
perspective
bondType

Returns: the previously bound Substance or NULL.

Definition at line 176 of file Surface.cpp.

{
    chemical::Substance* ret = NULL;
    chemical::Bond* bondBuffer;
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        bondBuffer = bnd;
        if (bondBuffer->GetType() == bondType)
        {
            ret = ChemicalCast< chemical::Substance* >(bondBuffer->GetBonded());
            BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret, ,
                continue);
            BIO_SANITIZE_AT_SAFETY_LEVEL_2(ret->IsId(toRelease), ,
                continue);
            BIO_SANITIZE_AT_SAFETY_LEVEL_2(perspective && ret->GetPerspective() != perspective,
                continue,);
            bondBuffer->Break();
            break;
        }
    }
    return ret;
}

References BIO_SANITIZE_AT_SAFETY_LEVEL_2, bio::chemical::Bond::Break(), bio::Container::End(), bio::chemical::Bond::GetBonded(), bio::physical::Observer< PERSPECTIVE >::GetPerspective(), bio::chemical::Bond::GetType(), bio::SmartIterator::IsAtBeginning(), bio::chemical::Atom::m_bonds, and bio::molecular::Class< Surface >::perspective.

◆ ReleaseAll()

physical::Waves bio::molecular::Surface::ReleaseAll ( BondType bondType = bond_type::Temporary() )

virtual

Releases all Temporarily Bound Substances

Returns: all Temporarily Bound Substances

Definition at line 207 of file Surface.cpp.

{
    physical::Waves ret;
    chemical::Bond* bondBuffer;
    for (
        SmartIterator bnd = m_bonds.End();
        !bnd.IsAtBeginning();
        --bnd
        )
    {
        bondBuffer = bnd;
        if (bondBuffer->GetType() == bondType)
        {
            ret.push_back(ChemicalCast< physical::Wave* >(bondBuffer->GetBonded()));
            bondBuffer->Break();
        }
    }
    return ret;
}

References bio::chemical::Bond::Break(), bio::Container::End(), bio::chemical::Bond::GetBonded(), bio::chemical::Bond::GetType(), bio::SmartIterator::IsAtBeginning(), and bio::chemical::Atom::m_bonds.

Referenced by bio::genetic::FetchPlasmid::Activate(), bio::genetic::RegisterPlasmid::Activate(), operator--(), and bio::genetic::Plasmid::TranscribeFor().

◆ SetEnvironment()

void bio::molecular::Surface::SetEnvironment ( Molecule * environment )

virtual

Sets both the m_environment and m_perspective and updates m_id.

Parameters

environment

Reimplemented from bio::molecular::EnvironmentDependent< Molecule >.

Definition at line 95 of file Surface.cpp.

{
    m_environment = environment;
    SetId(0); //0 should always be invalid.
    Identifiable< StandardDimension >::SetPerspective(environment);
}

References environment, bio::molecular::EnvironmentDependent< Molecule >::m_environment, and bio::physical::Observer< Perspective< StandardDimension > >::SetPerspective().

Referenced by SetPerspective().

◆ SetPerspective()

void bio::molecular::Surface::SetPerspective ( Molecule * perspective )

virtual

Sets both the m_environment and m_perspective and updates m_id.

Parameters

perspective a Molecule.

Definition at line 102 of file Surface.cpp.

{
    SetEnvironment(perspective);
}

References bio::molecular::Class< Surface >::perspective, and SetEnvironment().

◆ Spin()

physical::Symmetry * bio::molecular::Surface::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 113 of file Surface.cpp.

{
    //TODO...
    return NULL;
}

◆ Use()

template<typename T >

T bio::molecular::Surface::Use ( T varPtr )

inline

Create a Use()d Bond with the given var. These will not be deleted by *this. See Bonds.h for more on what Use() does.

Template Parameters

T

Parameters

varPtr

Returns

Definition at line 113 of file Surface.h.

    {
        FormBond(
            varPtr,
            bond_type::Use());
    }

References bio::chemical::Atom::FormBond(), and bio::bond_type::Use().

Referenced by bio::molecular::Molecule::Use().

Member Data Documentation

◆ environment

Molecule* bio::molecular::Surface::environment

Initial value:

= NULL

)

Definition at line 59 of file Surface.h.

Referenced by SetEnvironment().

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

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Surface()

◆ ~Surface()

Member Function Documentation

◆ Bind()

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

◆ Manage()

◆ operator+=()

◆ operator--()

◆ operator-=() [1/3]

◆ operator-=() [2/3]

◆ operator-=() [3/3]

◆ Reify()

◆ Release() [1/3]

◆ Release() [2/3]

◆ Release() [3/3]

◆ ReleaseAll()

◆ SetEnvironment()

◆ SetPerspective()

◆ Spin()

◆ Use()

Member Data Documentation

◆ environment