bio::chemical::Bond Class Reference

#include <Bond.h>

Public Member Functions
	Bond ()
	Bond (AtomicNumber id, Pointer< physical::Wave > bonded, BondType type=bond_type::Unknown())
	Bond (AtomicNumber id, Pointer< physical::Wave > bonded, BondType type, bool ownsBonded)
	~Bond ()
bool	operator== (const AtomicNumber id) const
bool	operator== (const Bond &other) const
bool	Form (AtomicNumber id, Pointer< physical::Wave > bonded, BondType type=bond_type::Unknown())
bool	Form (AtomicNumber id, Pointer< physical::Wave > bonded, BondType type, bool ownsBonded)
AtomicNumber	GetId () const
Pointer< physical::Wave >	GetBonded ()
Pointer< const physical::Wave >	GetBonded () const
Pointer< physical::Wave >	DetachBondedForWrite ()
bool	IsBondedShared () const
bool	IsBondedOwned () const
BondType	GetType () const
bool	OwnsBonded () const
bool	IsEmpty () const
void	Break ()

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.

Constructor & Destructor Documentation

Bond() [1/3]

bio::chemical::Bond::Bond

(

)

Bond() [2/3]

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

Parameters

id
bonded
type

Bond() [3/3]

bio::chemical::Bond::Bond	(	AtomicNumber	id,
		Pointer< physical::Wave >	bonded,
		BondType	type,
		bool	ownsBonded
	)

~Bond()

bio::chemical::Bond::~Bond

(

)

Member Function Documentation

Break()

void bio::chemical::Bond::Break

(

)

Empties the contents of *this.

DetachBondedForWrite()

Pointer< physical::Wave > bio::chemical::Bond::DetachBondedForWrite

(

)

COPY-ON-WRITE detach: if mBonded is an owning reference shared with another bond (e.g. a COW-shared clone), deep-copy it (via physical::Wave::Clone()) into a private owned reference and re-point *this at the copy; then return the now uniquely-owned bonded for mutation. A unique owning bond is mutated in place (no copy). A borrowed bond is never detached (the real owner manages it) — its raw bonded is returned as-is. The CALLER MUST hold the host Atom's EXCLUSIVE lock (this re-points the bond's storage). RFC_BONDED_COW_HANDLE §12.

Returns

the uniquely-owned (post-detach) bonded Wave, or NULL if empty.

Form() [1/2]

bool bio::chemical::Bond::Form	(	AtomicNumber	id,
		Pointer< physical::Wave >	bonded,
		BondType	type,
		bool	ownsBonded
	)

Form() [2/2]

bool bio::chemical::Bond::Form	(	AtomicNumber	id,
		Pointer< 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)

GetBonded() [1/2]

Pointer< physical::Wave > bio::chemical::Bond::GetBonded

(

)

Returns

the mBonded of *this.

GetBonded() [2/2]

Pointer< const physical::Wave > bio::chemical::Bond::GetBonded

(

)

const

Returns

the mBonded of *this.

GetId()

AtomicNumber bio::chemical::Bond::GetId

(

)

const

Returns

the mId of *this.

GetType()

BondType bio::chemical::Bond::GetType

(

)

const

Returns

the mType of *this.

IsBondedOwned()

bool bio::chemical::Bond::IsBondedOwned

(

)

const

Returns

true iff mBonded is an OWNING reference (its CowPtr deletes the payload on last release and is copy-on-write shareable). False for borrowed references and empty bonds. Lets CloneBondsFrom COW-SHARE owning bonded payloads while still deep-cloning borrowed-but-DEEP ones (e.g. Surface-Managed bonds, whose lifetime a manager owns — sharing those would double-free).

IsBondedShared()

bool bio::chemical::Bond::IsBondedShared

(

)

const

Returns

true iff mBonded is an OWNING reference shared with another bond (refcount

‍1) — i.e. a mutable access must copy-on-write detach it. Borrowed and uniquely owned bonds return false: they are mutated in place, no detach (and so need no exclusive lock). RFC_BONDED_COW_HANDLE §12.

IsEmpty()

bool bio::chemical::Bond::IsEmpty

(

)

const

Returns

whether or not *this points to anything.

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.

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.

OwnsBonded()

bool bio::chemical::Bond::OwnsBonded

(

)

const

Returns

whether this Bond owns (and must delete) its bonded payload. Derived from the CowPtr's ownership (IsBondedOwned()) rather than a stored flag — an owning bond is one whose CowPtr deletes the payload on last release (i.e. formed with ownsBonded || type == AutoDelete()).

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

• Bond.h
• Bond.cpp