bio::chemical::Atom Class Reference

#include <Atom.h>

Inheritance diagram for bio::chemical::Atom:

Collaboration diagram for bio::chemical::Atom:

Public Member Functions
	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::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

Protected Member Functions
virtual bool	BreakBondImplementation (Wave *toDisassociate, AtomicNumber id, BondType type)
virtual bool	FormBondImplementation (Wave *toBond, AtomicNumber id, BondType type)

Protected Attributes
Bonds	m_bonds
Protected Attributes inherited from bio::physical::Class< Atom >
Atom *	m_object
Protected Attributes inherited from bio::physical::Wave
Wave *	m_signal
Symmetry *	m_symmetry

Additional Inherited Members
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)

Detailed Description

Atom MUST be virtually inherited! Atom is an interface for other implementations. Atom objects form Bonds with Waves (such as Quantum Waves, like real-life electrons). Counter to how atoms are often described, here, you can Bond things that are not Atoms (iff they are a Wave). This is similar to forming ionic bonds or radicals where the "bonded" target is a sub-atomic particle (also a shared resource). Waves have a unique class name to Id mapping that is stored in the PeriodicTable. Atom objects take advantage of this to store and retrieve pointers to any type. Bonds are arbitrarily flexible, so this system can be (ab)used in many ways. Unlike real chemistry, the actual valence of a Atom changes to accommodate new Bonds. NOTE: m_bonds[0] is always empty. This may change in a future release.

NOTE: iff using a C++ version below 11, only Quantum<> Bonds are supported. This is due to an inability to evaluate IsPrimitive<>() expressions at compile time and the compiler following all "possible" execution paths, which are necessarily incompatible.

Definition at line 50 of file Atom.h.

Constructor & Destructor Documentation

Atom()

bio::chemical::Atom::Atom ( const Atom &  other )

explicit

We CANNOT copy Atoms contents at this time. m_bonds must contain uniquely bonded Waves.

Parameters

other

Definition at line 29 of file Atom.cpp.

 :
 physical::Class< Atom >(this),
 m_bonds(4)
{
}

~Atom()

bio::chemical::Atom::~Atom ( )

virtual

Definition at line 44 of file Atom.cpp.

{
 
}

Member Function Documentation

As() [1/2]

template<typename T >

T bio::chemical::Atom::As ( )

inline

This method is here so that we can add different As____ methods without changing the downstream interfaces.

Template Parameters

T

Returns

this as a T or NULL.

Definition at line 176 of file Atom.h.

 {
 #if BIO_CPP_VERSION < 11
 return AsBondedQuantum< T >();
 #else
 if (IsPrimitive< T >())
 {
 return AsBondedQuantum< T >();
 }
 else
 {
 return AsBonded< T >();
 }
 #endif
 }

Referenced by bio::chemical::LinearMotif< CONTENT_TYPE >::Attenuate(), bio::chemical::LinearMotif< CONTENT_TYPE >::Disattenuate(), and bio::chemical::LinearMotif< CONTENT_TYPE >::ForEachImplementation().

As() [2/2]

template<typename T >

const T bio::chemical::Atom::As ( ) const

inline

Const version of As(). This method is here so that we can add different As____ methods without changing the downstream interfaces.

Template Parameters

T

Returns

this as a const T or NULL.

Definition at line 199 of file Atom.h.

 {
 #if BIO_CPP_VERSION < 11
 return AsBondedQuantum< T >();
 #else
 if (IsPrimitive< T >())
 {
 return AsBondedQuantum< T >();
 }
 else
 {
 return AsBonded< T >();
 }
 #endif
 }

AsBonded() [1/2]

template<typename T >

T bio::chemical::Atom::AsBonded ( )

inline

Gets the bond to an bonded of type T from this, then casts the Bond()ed Wave to T.

Template Parameters

T

Returns

a T* that is Bond()ed with *this; else NULL.

Definition at line 125 of file Atom.h.

 {
 Valence position = GetBondPosition< T >();
 BIO_SANITIZE(position, ,
 return NULL);
 return ForceCast< T >(m_bonds.OptimizedAccess(position)->GetBonded());
 }

References BIO_SANITIZE, m_bonds, and bio::physical::Arrangement< TYPE >::OptimizedAccess().

Referenced by AsBondedQuantum().

AsBonded() [2/2]

template<typename T >

const T bio::chemical::Atom::AsBonded ( ) const

inline

Gets the bond to an bonded of type T from this, then casts the Bond()ed Wave to T.

Template Parameters

T

Returns

a const T* that is Bond()ed with *this; else NULL.

Definition at line 139 of file Atom.h.

 {
 Valence position = GetBondPosition< T >();
 
 BIO_SANITIZE(position, ,
 return NULL);
 return ForceCast< const T >(m_bonds.OptimizedAccess(position)->GetBonded());
 }

References BIO_SANITIZE, m_bonds, and bio::physical::Arrangement< TYPE >::OptimizedAccess().

AsBondedQuantum() [1/2]

template<typename T >

T bio::chemical::Atom::AsBondedQuantum ( )

inline

If T IsPrimitive(), you can use *this to get the Bonded Quantum Wave for that primitive.

Template Parameters

T

Returns

this as a T, from a Bonded Quantum Wave, or NULL.

Definition at line 154 of file Atom.h.

 {
 return Cast< T >(AsBonded< physical::Quantum< T >* >());
 }

References AsBonded().

AsBondedQuantum() [2/2]

template<typename T >

const T bio::chemical::Atom::AsBondedQuantum ( ) const

inline

Const version of AsBondedQuantum().

Template Parameters

T

Returns

this as a const T, from a Bonded Quantum Wave.

Definition at line 165 of file Atom.h.

 {
 return *AsBonded< physical::Quantum< T >* >();
 }

Attenuate()

Code bio::chemical::Atom::Attenuate ( const Wave *  other )

virtual

If the given Wave Resonates with any Bonded Wave in *this, the given Wave will be Demodulated and Attenuated by the Bonded Wave. Attenuation here operates slightly differently from the real world concept. Because we have a continuous flow of electrons providing the power to run this code, doing work is essentially free (or at least abstracted and we don't HAVE to worry about it), Attenuation is more like amplification, where flux, in terms of work, is generated, rather than dispersed. However, if we treat some desired state as flux and any deviation from that state as offering resistance, "information flux" is lost as the desired state is approached, making Attenuation technically correct.

Parameters

other

Definition at line 49 of file Atom.cpp.

{
 BIO_SANITIZE(other, ,
 return code::BadArgument1())
 
 const physical::Wave* demodulated = other->Demodulate();
 Code ret = code::Success();
 
 Bond* bondBuffer;
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->IsEmpty())
 {
 continue;
 }
 if (physical::Wave::GetResonanceBetween(
 bondBuffer->GetBonded(),
 other
 ).size())
 {
 if (bondBuffer->GetBonded()->Attenuate(demodulated) != code::Success())
 {
 ret = code::UnknownError(); //user can debug from logs for now.
 }
 }
 }
 return ret;
}

References bio::physical::Wave::Attenuate(), bio::code::BadArgument1(), BIO_SANITIZE, bio::physical::Wave::Demodulate(), bio::Container::End(), bio::chemical::Bond::GetBonded(), bio::physical::Wave::GetResonanceBetween(), bio::SmartIterator::IsAtBeginning(), bio::chemical::Bond::IsEmpty(), m_bonds, bio::code::Success(), and bio::code::UnknownError().

BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::chemical::Atom::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	physical	,
		Atom
	)

Ensure virtual methods point to Class implementations.

BreakBond()

template<typename T >

bool bio::chemical::Atom::BreakBond ( T  toDisassociate, BondType  type = bond_type::Unknown()  )

inline

Breaking a Bond Break()s the associated position. Removal of the Bond object is done upon destruction. Updating a Bond requires both Breaking and Forming steps to be done manually.

Template Parameters

T

Parameters

toDisassociate
type

Returns

true if the Bond was Broken; false otherwise.

Definition at line 279 of file Atom.h.

 {
 #if BIO_CPP_VERSION < 11
 return BreakBond< physical::Quantum< T >* >(
 NULL,
 type
 );
 #else
 if (IsPrimitive< T >())
 {
 return BreakBond< physical::Quantum< T >* >(NULL, type); //T matters, toDisassociate does not.
 }
 
 AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< T >();
 return BreakBondImplementation(
 toDisassociate,
 bondedId,
 type
 );
 #endif
 }

References BreakBondImplementation().

BreakBondImplementation()

bool bio::chemical::Atom::BreakBondImplementation ( Wave *  toDisassociate, AtomicNumber  id, BondType  type  )

protectedvirtual

Remove a Bond.

Parameters

toDisassociate
id
type

Returns

Definition at line 148 of file Atom.cpp.

{
 Valence position = GetBondPosition(id);
 
 BIO_SANITIZE(id && position, ,
 return false);
 BIO_SANITIZE(m_bonds.IsAllocated(position), ,
 return false);
 
 m_bonds.OptimizedAccess(position)->Break();
 //Let dtor cleanup.
 
 return true;
}

References BIO_SANITIZE, GetBondPosition(), bio::Container::IsAllocated(), m_bonds, and bio::physical::Arrangement< TYPE >::OptimizedAccess().

Referenced by BreakBond().

Disattenuate()

Code bio::chemical::Atom::Disattenuate ( const Wave *  other )

virtual

If the given Wave Resonates with any Bonded Wave in *this, the given Wave will be Demodulated and Disattenuated by the Bonded Wave. This is the opposite of Attenuation (above).

Parameters

other

Definition at line 83 of file Atom.cpp.

{
 BIO_SANITIZE(other, ,
 return code::BadArgument1())
 
 const physical::Wave* demodulated = other->Demodulate();
 Code ret = code::Success();
 
 Bond* bondBuffer;
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 bondBuffer = bnd;
 if (bondBuffer->IsEmpty())
 {
 continue;
 }
 if (physical::Wave::GetResonanceBetween(
 bondBuffer->GetBonded(),
 other
 ).size())
 {
 if (bondBuffer->GetBonded()->Disattenuate(demodulated) != code::Success())
 {
 ret = code::UnknownError(); //user can debug from logs for now.
 }
 }
 }
 return ret;
}

References bio::code::BadArgument1(), BIO_SANITIZE, bio::physical::Wave::Demodulate(), bio::physical::Wave::Disattenuate(), bio::Container::End(), bio::chemical::Bond::GetBonded(), bio::physical::Wave::GetResonanceBetween(), bio::SmartIterator::IsAtBeginning(), bio::chemical::Bond::IsEmpty(), m_bonds, bio::code::Success(), and bio::code::UnknownError().

FormBond()

template<typename T >

bool bio::chemical::Atom::FormBond ( T  toBond, BondType  type = bond_type::Unknown()  )

inline

Adds a new Bond to *this or updates an Empty Bond for T. Updating a Bond requires both Breaking and Forming steps to be done manually. You CANNOT bond the same T twice (without Breaking the initial Bond). See Molecule.h if you would like to Bond multiple Ts.

Template Parameters

T	A pointer to an instance of a class deriving from Wave and which is not already Bonded.

Parameters

toBond

what to Bond

Returns

true, if the Bond was created; false otherwise.

Definition at line 237 of file Atom.h.

 {
 #if BIO_CPP_VERSION < 11
 AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >();
 return FormBondImplementation((new physical::Quantum< T >(toBond))->AsWave(),
 bondedId,
 type
 );
 #else
 if (IsPrimitive< T >())
 {
 AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >();
 return FormBondImplementation(
 (new physical::Quantum< T >(toBond))->AsWave(),
 bondedId,
 type
 );
 }
 else
 {
 AtomicNumber bondedId = PeriodicTable::Instance().GetIdFromType< T >();
 return FormBondImplementation(
 toBond->AsWave(),
 bondedId,
 type
 );
 }
 #endif
 }

References bio::physical::Class< Atom >::AsWave(), and FormBondImplementation().

Referenced by bio::molecular::Surface::Bind(), bio::molecular::Surface::Manage(), and bio::molecular::Surface::Use().

FormBondImplementation()

bool bio::chemical::Atom::FormBondImplementation ( Wave *  toBond, AtomicNumber  id, BondType  type  )

protectedvirtual

Create a Bond.

Parameters

toBond
id
type

Definition at line 117 of file Atom.cpp.

{
 BIO_SANITIZE(!toBond || !id, ,
 return false);
 
 Valence position = GetBondPosition(id);
 Bond* bondBuffer;
 if (m_bonds.IsAllocated(position))
 {
 bondBuffer = m_bonds.OptimizedAccess(position);
 BIO_SANITIZE(!bondBuffer->IsEmpty(), ,
 return false)
 return bondBuffer->Form(
 id,
 toBond,
 type
 );
 }
 //implicitly cast the addition index to a bool.
 return m_bonds.Add(
 Bond(
 id,
 toBond,
 type
 ));
}

References bio::physical::Arrangement< TYPE >::Add(), BIO_SANITIZE, bio::chemical::Bond::Form(), GetBondPosition(), bio::Container::IsAllocated(), bio::chemical::Bond::IsEmpty(), m_bonds, and bio::physical::Arrangement< TYPE >::OptimizedAccess().

Referenced by FormBond().

GetAllBonds() [1/2]

Bonds * bio::chemical::Atom::GetAllBonds

(

)

DANGEROUS!

Returns

a pointer to the Bonds in *this.

Definition at line 224 of file Atom.cpp.

{
 return &m_bonds;
}

References m_bonds.

Referenced by bio::chemical::UnorderedStructureInterface::ImportAll().

GetAllBonds() [2/2]

const Bonds * bio::chemical::Atom::GetAllBonds

(

)

const

DANGEROUS! (but slightly less so).

Returns

a pointer to the Bonds in *this.

Definition at line 229 of file Atom.cpp.

{
 return &m_bonds;
}

References m_bonds.

GetBonded() [1/2]

physical::Wave * bio::chemical::Atom::GetBonded

(

Valence

position

)

Simply get a bond.

Parameters

position

Returns

the Bonded Wave*

Definition at line 210 of file Atom.cpp.

{
 BIO_SANITIZE(m_bonds.IsAllocated(position), ,
 return NULL)
 return m_bonds.OptimizedAccess(position)->GetBonded();
}

References BIO_SANITIZE, bio::Container::IsAllocated(), m_bonds, and bio::physical::Arrangement< TYPE >::OptimizedAccess().

Referenced by bio::chemical::UnorderedStructureInterface::ImportAll(), and bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation().

GetBonded() [2/2]

const physical::Wave * bio::chemical::Atom::GetBonded

(

Valence

position

)

const

Simply get a bond.

Parameters

position

Returns

the Bonded Wave*

Definition at line 217 of file Atom.cpp.

{
 BIO_SANITIZE(m_bonds.IsAllocated(position), ,
 return NULL)
 return m_bonds.OptimizedAccess(position)->GetBonded();
}

References BIO_SANITIZE, bio::Container::IsAllocated(), m_bonds, and bio::physical::Arrangement< TYPE >::OptimizedAccess().

GetBondPosition() [1/3]

template<typename T >

Valence bio::chemical::Atom::GetBondPosition ( ) const

inline

GetBondPosition via a type, rather than an Wave Id.

Template Parameters

T

Returns

GetBondPosition() for the given type; else 0.

Definition at line 326 of file Atom.h.

 {
 #if BIO_CPP_VERSION < 11
 return GetBondPosition(PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >());
 #else
 if (IsPrimitive< T >())
 {
 return GetBondPosition(PeriodicTable::Instance().GetIdFromType< physical::Quantum< T >* >());
 }
 return GetBondPosition(PeriodicTable::Instance().GetIdFromType< T >());
 #endif
 }

References GetBondPosition().

Referenced by BreakBondImplementation(), FormBondImplementation(), GetBondPosition(), and GetBondType().

GetBondPosition() [2/3]

Valence bio::chemical::Atom::GetBondPosition

(

AtomicNumber

bondedId

)

const

Gives the array index of a Bond()ed Wave.

Parameters

bondedId

Returns

The position of the given Wave (Id) within *this; else 0.

Definition at line 168 of file Atom.cpp.

{
 BIO_SANITIZE(bondedId, ,
 return 0);
 for (
 SmartIterator bnd = m_bonds.End();
 !bnd.IsAtBeginning();
 --bnd
 )
 {
 if ((*bnd).template As< Bond >() == bondedId)
 {
 return bnd.GetIndex();
 }
 }
 return 0;
}

References BIO_SANITIZE, bio::Container::End(), bio::SmartIterator::IsAtBeginning(), and m_bonds.

Referenced by bio::chemical::UnorderedStructureInterface::ImportAll(), and bio::chemical::Reactant::operator==().

GetBondPosition() [3/3]

Valence bio::chemical::Atom::GetBondPosition

(

Name

typeName

)

const

Converts the given typeName to and Id Gives the array index of a Bond()ed Wave.

Parameters

typeName

Returns

The position of the given Wave (Id) within *this; else 0.

Definition at line 186 of file Atom.cpp.

{
 return GetBondPosition(PeriodicTable::Instance().GetIdWithoutCreation(typeName));
}

References GetBondPosition().

GetBondType() [1/2]

template<typename T >

BondType bio::chemical::Atom::GetBondType ( ) const

inline

Get the type of a Bond.

Template Parameters

T

Returns

the BondType of the Bond for T or BondTypePerspective::InvalidId().

Definition at line 352 of file Atom.h.

 {
 #if BIO_CPP_VERSION < 11
 return GetBondType(GetBondPosition< physical::Quantum< T > >());
 #else
 if (IsPrimitive< T >())
 {
 return GetBondType(GetBondPosition< physical::Quantum< T > >());
 }
 return GetBondType(GetBondPosition< T >());
 #endif
 }

References GetBondPosition(), and GetBondType().

Referenced by GetBondType().

GetBondType() [2/2]

BondType bio::chemical::Atom::GetBondType

(

Valence

position

)

const

Get the type of a Bond.

Parameters

position

Returns

the BondType of the Bond at the given position or BondTypePerspective::InvalidId().

Definition at line 191 of file Atom.cpp.

{
 BIO_SANITIZE(m_bonds.IsAllocated(position), ,
 return BondTypePerspective::InvalidId());
 return m_bonds.OptimizedAccess(position)->GetId();
}

References BIO_SANITIZE, bio::Container::IsAllocated(), m_bonds, and bio::physical::Arrangement< TYPE >::OptimizedAccess().

operator T()

template<typename T >

bio::chemical::Atom::operator T ( )

inline

Atoms can be converted to anything they are bonded to.

Template Parameters

T

Returns

this as a T or NULL.

Definition at line 222 of file Atom.h.

 {
 return As< T >();
 }

Reify()

Code bio::chemical::Atom::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::physical::Wave.

Reimplemented in bio::molecular::Molecule, and bio::molecular::Surface.

Definition at line 204 of file Atom.cpp.

{
 //TODO...
 return Wave::Reify(symmetry);
}

Spin()

physical::Symmetry * bio::chemical::Atom::Spin ( ) const

virtual

Required method from Wave. See that class for details.

Returns

a Symmetrical image of *this

Reimplemented from bio::physical::Wave.

Reimplemented in bio::molecular::Molecule, and bio::molecular::Surface.

Definition at line 198 of file Atom.cpp.

{
 //TODO...
 return Wave::Spin();
}

Member Data Documentation

m_bonds

Bonds bio::chemical::Atom::m_bonds

protected

Definition at line 378 of file Atom.h.

Referenced by bio::molecular::Surface::~Surface(), AsBonded(), Attenuate(), BreakBondImplementation(), Disattenuate(), FormBondImplementation(), GetAllBonds(), GetBonded(), GetBondPosition(), GetBondType(), bio::molecular::Surface::Release(), and bio::molecular::Surface::ReleaseAll().

---

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

• /home/eons/git/biology/lib_bio/inc/bio/chemical/Atom.h
• /home/eons/git/biology/lib_bio/src/chemical/Atom.cpp