bio::chemical::Bond Class Reference

#include <Bond.h>

Public Member Functions
	Bond ()
	Bond (AtomicNumber id, physical::Wave *bonded, BondType type=bond_type::Unknown())
	~Bond ()
void	Break ()
bool	Form (AtomicNumber id, physical::Wave *bonded, BondType type=bond_type::Unknown())
physical::Wave *	GetBonded ()
const physical::Wave *	GetBonded () const
AtomicNumber	GetId () const
BondType	GetType () const
bool	IsEmpty () const
bool	operator== (const AtomicNumber id) const
bool	operator== (const Bond &other) const

Detailed Description

Bonds are used by Atom to form relationships to Waves. These can be thought of as edges in a directed graph. See Atom.h for more info.

NOTE: Bonds may currently only be of a single BondType. This may change in a future release.

Definition at line 43 of file Bond.h.

Constructor & Destructor Documentation

Bond() [1/2]

bio::chemical::Bond::Bond

(

)

Definition at line 30 of file Bond.cpp.

    :
    m_id(PeriodicTable::InvalidId()),
    m_bonded(NULL),
    m_type(bond_type::Empty())
{
}

Bond() [2/2]

bio::chemical::Bond::Bond	(	AtomicNumber	id,
		physical::Wave *	bonded,
		BondType	type = bond_type::Unknown()
	)

Parameters

id
bonded
type

Definition at line 38 of file Bond.cpp.

    :
    m_id(id),
    m_bonded(bonded),
    m_type(type)
{
}

~Bond()

bio::chemical::Bond::~Bond

(

)

Definition at line 50 of file Bond.cpp.

{
 
}

Member Function Documentation

Break()

void bio::chemical::Bond::Break

(

)

Empties the contents of *this.

Definition at line 94 of file Bond.cpp.

{
    //leave m_id intact.
    m_bonded = NULL;
    m_type = bond_type::Empty();
}

References bio::bond_type::Empty().

Referenced by bio::molecular::Surface::~Surface(), bio::molecular::Surface::Release(), and bio::molecular::Surface::ReleaseAll().

Form()

bool bio::chemical::Bond::Form	(	AtomicNumber	id,
		physical::Wave *	bonded,
		BondType	type = bond_type::Unknown()
	)

Update the contents of *this. Only works if *this IsEmpty().

Parameters

id
bonded
type

Returns

true if *this was updated; false otherwise (e.g. if *this is already pointing to something)

Definition at line 55 of file Bond.cpp.

{
    BIO_SANITIZE(bonded, ,
        return false);
    m_id = id;
    m_bonded = bonded;
    m_type = type;
    return true;
}

References BIO_SANITIZE.

Referenced by bio::chemical::Atom::FormBondImplementation().

GetBonded() [1/2]

physical::Wave * bio::chemical::Bond::GetBonded

(

)

Returns

the m_bonded of *this.

Definition at line 74 of file Bond.cpp.

{
    return m_bonded;
}

Referenced by bio::molecular::Surface::~Surface(), bio::chemical::Atom::Attenuate(), bio::chemical::Atom::Disattenuate(), bio::chemical::UnorderedStructureInterface::ImportAll(), bio::chemical::LinearMotif< CONTENT_TYPE >::InsertImplementation(), bio::molecular::Surface::Release(), and bio::molecular::Surface::ReleaseAll().

GetBonded() [2/2]

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

(

)

const

Returns

the m_bonded of *this.

Definition at line 79 of file Bond.cpp.

{
    return m_bonded;
}

GetId()

AtomicNumber bio::chemical::Bond::GetId

(

)

const

Returns

the m_id of *this.

Definition at line 69 of file Bond.cpp.

{
    return m_id;
}

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

GetType()

BondType bio::chemical::Bond::GetType

(

)

const

Returns

the m_type of *this.

Definition at line 84 of file Bond.cpp.

{
    return m_type;
}

Referenced by bio::molecular::Surface::~Surface(), bio::molecular::Surface::Release(), and bio::molecular::Surface::ReleaseAll().

IsEmpty()

bool bio::chemical::Bond::IsEmpty

(

)

const

Returns

whether or not *this points to anything.

Definition at line 89 of file Bond.cpp.

{
    return m_bonded == NULL && m_type == bond_type::Empty();
}

References bio::bond_type::Empty().

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

operator==() [1/2]

bool bio::chemical::Bond::operator==

(

const AtomicNumber

id

)

const

Parameters

id

Returns

whether or not the given id matches that of *this.

Definition at line 101 of file Bond.cpp.

{
    return m_id == id;
}

operator==() [2/2]

bool bio::chemical::Bond::operator==

(

const Bond &

other

)

const

Parameters

other

Returns

whether or not id of other matches that of *this.

Definition at line 106 of file Bond.cpp.

{
    return m_id == other.m_id;
}

---

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

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