#include <BALL/KERNEL/bond.h>

Inheritance diagram for BALL::Bond:

Classes
class	NotBound

Public Types
Enumerations
enum	BondOrder { ORDER__UNKNOWN = 0, ORDER__SINGLE = 1, ORDER__DOUBLE = 2, ORDER__TRIPLE = 3, ORDER__QUADRUPLE = 4, ORDER__AROMATIC = 5, ORDER__ANY = 6, NUMBER_OF_BOND_ORDERS }

enum	BondType { TYPE__UNKNOWN = 0, TYPE__COVALENT = 1, TYPE__HYDROGEN = 2, TYPE__DISULPHIDE_BRIDGE = 3, TYPE__SALT_BRIDGE = 4, TYPE__PEPTIDE = 5, NUMBER_OF_BOND_TYPES }

enum	Property { IS_AROMATIC = 0, NUMBER_OF_PROPERTIES }

Type definitions
typedef short	Order

typedef short	Type

Public Types inherited from BALL::Composite
typedef ForwardIterator < Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorIterator

typedef ConstForwardIterator < Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorConstIterator

typedef BidirectionalIterator < Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeIterator

typedef ConstBidirectionalIterator < Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeConstIterator

typedef std::reverse_iterator < ChildCompositeIterator >	ChildCompositeReverseIterator

typedef std::reverse_iterator < ChildCompositeConstIterator >	ChildCompositeConstReverseIterator

typedef BidirectionalIterator < Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeIterator

typedef ConstBidirectionalIterator < Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeConstIterator

typedef std::reverse_iterator < CompositeIterator >	CompositeReverseIterator

typedef std::reverse_iterator < CompositeConstIterator >	CompositeConstReverseIterator

enum	StampType { MODIFICATION = 1, SELECTION = 2, BOTH = 3 }

typedef UnaryPredicate< Composite >	KernelPredicateType

Public Member Functions
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const

void	persistentRead (PersistenceManager &pm)

void	finalize ()

Predicates
bool	operator== (const Bond &bond) const
	Equality operator. Two bonds are equal, if they are identical instances. More...

bool	operator!= (const Bond &bond) const
	Inequality operator. Two bonds are not equal, if they are different instances. More...

bool	isBondOf (const Atom &atom) const

bool	isBound () const

bool	isInterBond () const

bool	isInterBondOf (const AtomContainer &atom_container) const

bool	isIntraBond () const

bool	isIntraBondOf (const AtomContainer &atom_container) const

Assignment methods
Bond &	operator= (const Bond &bond)

void	swap (Bond &bond)

Accessors
void	setFirstAtom (Atom *atom)

void	setSecondAtom (Atom *atom)

const Atom *	getFirstAtom () const
	Return a pointer to the first atom. More...

Atom *	getFirstAtom ()
	Return a pointer to the first atom. More...

const Atom *	getSecondAtom () const
	Return a pointer to the second atom. More...

Atom *	getSecondAtom ()
	Return a pointer to the second atom. More...

Atom *	getPartner (const Atom &atom) const

void	setName (const String &name)
	Assign the atom name. More...

const String &	getName () const
	Return the atom name. More...

void	setOrder (Order bond_order)
	Assign the bond order. More...

Order	getOrder () const
	Return the bond order. More...

bool	isAromatic () const

void	setType (Type bond_type)
	Set the bond type. More...

Type	getType () const
	Return the bond type. More...

float	getLength () const

const Atom *	getBoundAtom (const Atom &atom) const

Atom *	getBoundAtom (const Atom &atom)

Debugging and diagnostics
virtual bool	isValid () const

virtual void	dump (std::ostream &s=std::cout, Size depth=0) const

Public Member Functions inherited from BALL::Composite
template<typename T >
bool	applyLevel (ConstUnaryProcessor< T > &processor, long level) const

AncestorIterator	beginAncestor ()

AncestorIterator	endAncestor ()

AncestorConstIterator	beginAncestor () const

AncestorConstIterator	endAncestor () const

ChildCompositeIterator	beginChildComposite ()

ChildCompositeIterator	endChildComposite ()

ChildCompositeConstIterator	beginChildComposite () const

ChildCompositeConstIterator	endChildComposite () const

ChildCompositeReverseIterator	rbeginChildComposite ()

ChildCompositeReverseIterator	rendChildComposite ()

ChildCompositeConstReverseIterator	rbeginChildComposite () const

ChildCompositeConstReverseIterator	rendChildComposite () const

CompositeIterator	beginComposite ()

CompositeIterator	endComposite ()

CompositeConstIterator	beginComposite () const

CompositeConstIterator	endComposite () const

CompositeReverseIterator	rbeginComposite ()

CompositeReverseIterator	rendComposite ()

CompositeConstReverseIterator	rbeginComposite () const

CompositeConstReverseIterator	rendComposite () const

void	deleteChildrenList_ (std::list< Composite * > &composites)

template<typename T >
BALL_INLINE bool	apply (UnaryProcessor< T > &processor)

template<typename T >
BALL_INLINE bool	apply (ConstUnaryProcessor< T > &processor) const

template<typename T >
BALL_INLINE T *	getAncestor (const T &)

template<typename T >
BALL_INLINE const T *	getAncestor (const T &) const

template<typename T >
BALL_INLINE T *	getPrevious (const T &)

template<typename T >
BALL_INLINE const T *	getPrevious (const T &dummy) const

template<typename T >
BALL_INLINE T *	getNext (const T &)

template<typename T >
BALL_INLINE const T *	getNext (const T &dummy) const

template<typename T >
BALL_INLINE bool	hasAncestor (const T &dummy) const

	Composite ()

	Composite (const Composite &composite, bool deep=true)

virtual	~Composite ()

void	destroy (bool virtual_destroy)

void *	clone (Composite &root) const

bool	operator== (const Composite &composite) const

bool	operator!= (const Composite &composite) const

bool	isEmpty () const

bool	isRoot () const

bool	isRootOf (const Composite &composite) const

bool	isInterior () const

bool	hasChild () const

bool	isChildOf (const Composite &composite) const

bool	isFirstChild () const

bool	isFirstChildOf (const Composite &composite) const

bool	isLastChild () const

bool	isLastChildOf (const Composite &composite) const

bool	hasParent () const

bool	isParentOf (const Composite &composite) const

bool	hasSibling () const

bool	isSiblingOf (const Composite &composite) const

bool	hasPreviousSibling () const

bool	isPreviousSiblingOf (const Composite &composite) const

bool	hasNextSibling () const

bool	isNextSiblingOf (const Composite &composite) const

bool	isDescendantOf (const Composite &composite) const

template<typename T >
bool	hasAncestor (const T &dummy) const

bool	isAncestorOf (const Composite &composite) const

bool	isRelatedWith (const Composite &composite) const

bool	isHomomorph (const Composite &composite) const

bool	containsSelection () const

virtual bool	isAtom () const

virtual bool	isMolecule () const

virtual bool	isProtein () const

virtual bool	isFragment () const

virtual bool	isResidue () const

virtual bool	isChain () const

void	host (Visitor< Composite > &visitor)

template<typename T >
bool	applyAncestor (UnaryProcessor< T > &processor)

template<typename T >
bool	applyAncestor (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyChild (UnaryProcessor< T > &processor)

template<typename T >
bool	applyChild (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendant (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendant (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPreorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPostorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	apply (UnaryProcessor< T > &processor)

template<typename T >
bool	apply (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyLevel (UnaryProcessor< T > &processor, long level)

void	set (const Composite &composite, bool deep=true)

Composite &	operator= (const Composite &composite)

void	get (Composite &composite, bool deep=true) const

Size	getDegree () const

Size	count (const KernelPredicateType &predicate) const

Size	countDescendants () const

Size	getPathLength (const Composite &composite) const

Size	getDepth () const

Size	getHeight () const

Composite &	getRoot ()

const Composite &	getRoot () const

Composite *	getLowestCommonAncestor (const Composite &composite)

const Composite *	getLowestCommonAncestor (const Composite &composite) const

template<typename T >
T *	getAncestor (const T &)

template<typename T >
const T *	getAncestor (const T &) const

template<typename T >
T *	getPrevious (const T &)

template<typename T >
const T *	getPrevious (const T &dummy) const

template<typename T >
T *	getNext (const T &)

template<typename T >
const T *	getNext (const T &dummy) const

Composite *	getParent ()

const Composite *	getParent () const

Composite *	getChild (Index index)

const Composite *	getChild (Index index) const

Composite *	getSibling (Index index)

const Composite *	getSibling (Index index) const

Composite *	getFirstChild ()

const Composite *	getFirstChild () const

Composite *	getLastChild ()

const Composite *	getLastChild () const

const PreciseTime &	getModificationTime () const

const PreciseTime &	getSelectionTime () const

void	stamp (StampType stamp=BOTH)

void	prependChild (Composite &composite)

void	appendChild (Composite &composite)

void	insertBefore (Composite &composite)

void	insertAfter (Composite &composite)

void	spliceBefore (Composite &composite)

void	spliceAfter (Composite &composite)

void	splice (Composite &composite)

bool	removeChild (Composite &child)

Size	removeSelected ()

Size	removeUnselected ()

void	replace (Composite &composite)

void	swap (Composite &composite)

virtual void	select ()

virtual void	deselect ()

Public Member Functions inherited from BALL::PersistentObject
	PersistentObject ()

virtual	~PersistentObject ()

PersistenceManager &	operator>> (PersistenceManager &pm) const

Public Member Functions inherited from BALL::Object
	Object ()
	Default constructor. More...

	Object (const Object &object)
	Copy constructor. More...

virtual	~Object ()
	Destructor. More...

const Object &	operator= (const Object &)

bool	operator== (const Object &object) const

bool	operator!= (const Object &object) const

bool	operator< (const Object &object) const

bool	operator<= (const Object &object) const

bool	operator>= (const Object &object) const

bool	operator> (const Object &object) const

int	compare (const Object &object) const

virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const

Handle	getHandle () const

Public Member Functions inherited from BALL::AutoDeletable
virtual	~AutoDeletable ()

void *	operator new (size_t size)

void	operator delete (void *ptr)

void *	operator new (size_t size, void *ptr)

void	operator delete (void ptr, void )

bool	isAutoDeletable () const

void	setAutoDeletable (bool enable)

Public Member Functions inherited from BALL::Selectable
	Selectable ()

	Selectable (const Selectable &selectable, bool deep=true)

virtual	~Selectable ()

void	set (const Selectable &selectable, bool deep=true)

const Selectable &	operator= (const Selectable &selectable)

void	get (Selectable &selectable, bool deep=true) const

void	swap (Selectable &selectable)

virtual void	setSelected (bool selected)

bool	isSelected () const

bool	operator== (const Selectable &selectable) const

bool	operator!= (const Selectable &selectable) const

void	write (PersistenceManager &pm) const

bool	read (PersistenceManager &pm)

virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const

Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE	PropertyManager ()
	Default constructor. More...

BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor. More...

virtual	~PropertyManager ()
	Destructor. More...

void	set (const PropertyManager &property_manager)

const PropertyManager &	operator= (const PropertyManager &property_manager)

void	get (PropertyManager &property_manager) const

void	swap (PropertyManager &property_manager)

BitVector &	getBitVector ()

const BitVector &	getBitVector () const

	operator BitVector & ()

void	setProperty (Property property)

void	clearProperty (Property property)

void	toggleProperty (Property property)

Size	countProperties () const

const NamedProperty &	getNamedProperty (Position index) const

NamedProperty &	getNamedProperty (Position index)

void	setProperty (const NamedProperty &property)

void	setProperty (const std::string &name)

void	setProperty (const std::string &name, bool value)

void	setProperty (const std::string &name, int value)

void	setProperty (const std::string &name, unsigned int value)

void	setProperty (const std::string &name, float value)

void	setProperty (const std::string &name, double value)

void	setProperty (const std::string &name, const std::string &value)

void	setProperty (const std::string &name, const PersistentObject &value)

const NamedProperty &	getProperty (const std::string &name) const

NamedPropertyIterator	beginNamedProperty ()

NamedPropertyIterator	endNamedProperty ()

void	clearProperty (const std::string &name)

Size	countNamedProperties () const

bool	hasProperty (Property property) const
	Query for an unnamed property. More...

bool	hasProperty (const std::string &name) const
	Query for a named property. More...

bool	operator== (const PropertyManager &pm) const

bool	operator!= (const PropertyManager &pm) const
	Inequality operator. More...

void	write (PersistenceManager &pm) const
	Persistent stream writing. More...

bool	read (PersistenceManager &pm)
	Persistent stream reading. More...

bool	isValid () const

void	dump (std::ostream &s=std::cout, Size depth=0) const

Protected Attributes
Atributes
Atom *	first_

Atom *	second_

String	name_

Order	bond_order_

Type	bond_type_

Protected Attributes inherited from BALL::Selectable
bool	selected_

Friends
class	Atom

Constructors and Destructors
	Bond ()

	Bond (const Bond &bond, bool deep=true)

	Bond (const String &name, Atom &first, Atom &second, Order order=BALL_BOND_DEFAULT_ORDER, Type type=BALL_BOND_DEFAULT_TYPE)

virtual	~Bond ()

virtual void	clear ()

virtual void	destroy ()

static Bond *	createBond (Bond &bond, Atom &first, Atom &second)

Additional Inherited Members
Static Public Member Functions inherited from BALL::Composite
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)

Static Public Member Functions inherited from BALL::Object
static Handle	getNextHandle ()

static Handle	getNewHandle ()

Static Public Member Functions inherited from BALL::AutoDeletable
static void	clearLastPtr ()

Static Public Attributes inherited from BALL::Composite
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR

static KernelPredicateType	DEFAULT_UNARY_PREDICATE

Protected Member Functions inherited from BALL::AutoDeletable
	AutoDeletable ()

	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

Detailed Description

Bond class. An instance of Bond represents a bond between two atoms. There can be only one bond between two atoms (double, triple, etc. bonds are represented using just one bond and an appropriate value for the bond order attribute, see setBondOrder ).

: The "first" and "second" atom are assigned in a unique way: the first atom is always the atom with the lower Handle than the second atom.

: The "state" of a bond is defined by its attributes:

"first atom" ( Bond::first_ )
"second atom" ( Bond::second_ )
"bond name" ( Bond::name_ ): an arbitrary name
"bond order" ( Bond::bond_order_ ): the order, i.e. single, double, triple,...
"bond type" ( Bond::bond_type_ ): covalent, hydrogen bond, etc. to identify non-standard bond types

Bond equality is defined as bond identity. A linear ordering of bonds is defined as the linear order of the Object::Handle s.

Definition at line 54 of file bond.h.

Member Typedef Documentation

typedef short BALL::Bond::Order

Bond type.

Definition at line 86 of file bond.h.

typedef short BALL::Bond::Type

Definition at line 87 of file bond.h.

Member Enumeration Documentation

enum BALL::Bond::BondOrder

Predefined constants for the bond order

Enumerator
ORDER__UNKNOWN	Default value.
ORDER__SINGLE	Single bond.
ORDER__DOUBLE	Double bond.
ORDER__TRIPLE	Triple Bond.
ORDER__QUADRUPLE	Quadruple bond.
ORDER__AROMATIC	Aromatic bonds.
ORDER__ANY	Any bond orders (useful for predicates).
NUMBER_OF_BOND_ORDERS	The number of bond orders.

Definition at line 96 of file bond.h.

enum BALL::Bond::BondType

Predefined constants for the bond type. Those are just defined for convenience but they are not used right now.

Enumerator
TYPE__UNKNOWN
TYPE__COVALENT
TYPE__HYDROGEN
TYPE__DISULPHIDE_BRIDGE
TYPE__SALT_BRIDGE
TYPE__PEPTIDE
NUMBER_OF_BOND_TYPES

Definition at line 120 of file bond.h.

enum BALL::Bond::Property

Predefined properties. Enumeration of all properties that are used by Bond.

Enumerator
IS_AROMATIC	This property can be used to store aromaticity information without overwriting bond orders.
NUMBER_OF_PROPERTIES

Definition at line 141 of file bond.h.

Constructor & Destructor Documentation

BALL::Bond::Bond ( )

Default constructor. The state of this bond is:

bond has no first atom (=0)
bond has no second atom (=0)
bond name is the empty string (="")
bond order is unknown (= Bond::ORDER__UNKNOWN )
bond type is unknown (= Bond::TYPE__UNKNOWN )

BALL::Bond::Bond	(	const Bond &	bond,
		bool	deep = `true`
	)

Copy constructor. Calls Bond::createBond . The state of this bond is initialized to the state of bond.

: Note: Deep copying of bonds makes no sense, the parameter deep is therefore ignored. The use of this method is not recommended because it may result in inconcistencies of the whole the kernel data structure. This if for internal use only!

Parameters

bond	the bond to be copied
deep	ignored

See also: createBond

BALL::Bond::Bond	(	const String &	name,
		Atom &	first,
		Atom &	second,
		Order	order = `BALL_BOND_DEFAULT_ORDER`,
		Type	type = `BALL_BOND_DEFAULT_TYPE`
	)

Detailed constructor. Calls createBond to create a new bond between the two atoms

Parameters

name	name of the constructed bond
first	first atom of the constructed bond
second	second atom of the constructed bond
order	order of the constructed bond
type	type of the constructed bond

Exceptions

TooManyBonds if one of the atom already possesses Atom::MAX_NUMBER_OF_BONDS bonds.

virtual BALL::Bond::~Bond ( )

virtual

Destructor. If the bond is connecting two atoms, they are disconnected.

Member Function Documentation

virtual void BALL::Bond::clear ( )

virtual

Disconnect and reset to default state. Reset the bond attributes to their default values. The state of this bond is:

bond has no connectivity with first atom (=0)
bond has no connectivity with second atom (=0)
bond name is the empty string (="")
bond order is unknown (= Bond::ORDER__UNKNOWN )
bond type is unknown (= Bond::TYPE__UNKNOWN )

Reimplemented from BALL::Composite.

static Bond* BALL::Bond::createBond	(	Bond &	bond,
		Atom &	first,
		Atom &	second
	)

static

Create a bond. Connect the two atoms first and second via a bond.

Parameters

bond	the instantiated bond that connects the first atom `first` to the second atom `second`
first	the first atom of the bond
second	the second atom of the bond

Returns: Bond* this

Exceptions

TooManyBonds if one of the atom already possesses Atom::MAX_NUMBER_OF_BONDS bonds.

virtual void BALL::Bond::destroy ( )

virtual

Explicit destructor. Destroy this bond explicitly without releasing its heap memory thus this bond may exist further. Calls Bond::clear . Set the state of this bond to the default values. Note: Destroy is equivalent to Bond::clear .

See also: Bond::clear

Reimplemented from BALL::Composite.

virtual void BALL::Bond::dump	(	std::ostream &	s = `std::cout`,
		Size	depth = `0`
	)		const

virtual

Internal state dump. Dump the current internal state of this bond to the output ostream s with dumping depth depth .

Parameters

s	output stream where to output the internal state of this bond
depth	the dumping depth

Reimplemented from BALL::Composite.

void BALL::Bond::finalize ( )

virtual

Finalize the deserialization. Bond might have to swap first_ and second_ to ensure the correct order (see Bond ).

Reimplemented from BALL::PersistentObject.

const Atom* BALL::Bond::getBoundAtom ( const Atom & atom ) const

Return the partner of the atom in this bond.

Parameters

atom an atom

Returns: Atom a constant pointer to the atom, 0 if the atom is not part of the bond

Atom* BALL::Bond::getBoundAtom ( const Atom & atom )

Return the partner of the atom in this bond.

Parameters

atom an atom

Returns: Atom a pointer to the atom, 0 if the atom is not part of the bond

const Atom* BALL::Bond::getFirstAtom ( ) const

Return a pointer to the first atom.

Atom* BALL::Bond::getFirstAtom ( )

Return a pointer to the first atom.

float BALL::Bond::getLength ( ) const

Return the bond length

Returns: float - the distance between the two atoms

Exceptions

NotBound if the bond is not bound to two atoms

const String& BALL::Bond::getName ( ) const

Return the atom name.

Order BALL::Bond::getOrder ( ) const

Return the bond order.

Atom* BALL::Bond::getPartner ( const Atom & atom ) const

Return the partner atom of an atom. If the given atom is part of this bond, the other atom of the bond is returned. 0 is returned if atom is not one of the bond's atoms.

Parameters

atom	one of the bond's atoms

Returns: the atom's bond partner

const Atom* BALL::Bond::getSecondAtom ( ) const

Return a pointer to the second atom.

Atom* BALL::Bond::getSecondAtom ( )

Return a pointer to the second atom.

Type BALL::Bond::getType ( ) const

Return the bond type.

bool BALL::Bond::isAromatic ( ) const

Returns true if this bond is aromatic.

A bond is defined as aromatic, if it has the property Bond::IS_AROMATIC or if it has the order Bond::ORDER__AROMATIC

bool BALL::Bond::isBondOf ( const Atom & atom ) const

Determine whether the bond belongs to an atom. Calls Atom::hasBond .

Parameters

atom	the atom that is queried to connect this bond to another atom

Returns: bool - true if bond connects the atom atom with another atom, false otherwise

See also: Atom::hasBond

bool BALL::Bond::isBound ( ) const

Determine whether this bond contains any atom.

Returns: bool - true if bond connects the atom atom with another atom, false otherwise

See also: Atom::hasBond

bool BALL::Bond::isInterBond ( ) const

Determine whether the bond connects two fragments. If both atoms have no roots, the result is false. Calls Composite::getRoot .

Returns: bool - true if this bond is intermolecular, false otherwise

See also: Composite::getRoot

bool BALL::Bond::isInterBondOf ( const AtomContainer & atom_container ) const

Request for the intermolecular bonding of this bond within {atom_container}. Query, if this bond connects a atom within {atom_container} instance with an atom outside. Calls Composite::isDescendantOf .

Parameters

atom_container the queried parent fragment.

Returns: bool - true if this bond is intermolecular, false otherwise

See also: Composite::isDescendantOf

bool BALL::Bond::isIntraBond ( ) const

Request for the intramolecular bonding of this bond. Query, if this bond connects its two atoms within a common parent Composite instance. If both atoms have no roots, the result is true. Calls Composite::getRoot .

Returns: bool - true if this bond is intramolecular, false otherwise

See also: Composite::getRoot

bool BALL::Bond::isIntraBondOf ( const AtomContainer & atom_container ) const

Request for the intramolecular bonding of this bond within {atom_container}. Query, if this bond connects its two atoms within the common parent {atom_container} instance. Calls Composite::isDescendantOf .

Parameters

atom_container the queried parent fragment.

Returns: bool - true if this bond is intramolecular, false otherwise

See also: Composite::isDescendantOf

virtual bool BALL::Bond::isValid ( ) const

virtual

Internal state and consistency self-validation.

Returns: bool - true if the internal state of this bond is correct (self-validated) and consistent, false otherwise

Reimplemented from BALL::Composite.

bool BALL::Bond::operator!= ( const Bond & bond ) const

Inequality operator. Two bonds are not equal, if they are different instances.

Bond& BALL::Bond::operator= ( const Bond & bond )

Assignment operator. Assign a deep copy (on the level of Composite ).

Note: The use of this method is not recommended because it may result in inconcistencies of the whole system. This is for internal use only.

Parameters

bond	the bond to be copied

Returns: Bond - this bond

See also: Bond::set

bool BALL::Bond::operator== ( const Bond & bond ) const

Equality operator. Two bonds are equal, if they are identical instances.

void BALL::Bond::persistentRead ( PersistenceManager & pm )

virtual

Read a bond from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Composite.

void BALL::Bond::persistentWrite	(	PersistenceManager &	pm,
		const char *	name = `0`
	)		const

virtual

Write a bond to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Composite.

void BALL::Bond::setFirstAtom ( Atom * atom )

Set the first atom. This method does not ensure the correct order of atoms (see Bond ), so its use is recommended for internal purposes only.

void BALL::Bond::setName ( const String & name )

Assign the atom name.

void BALL::Bond::setOrder ( Order bond_order )

Assign the bond order.

void BALL::Bond::setSecondAtom ( Atom * atom )

Set the second atom. This method does not ensure the correct order of atoms (see Bond ), so its use is recommended for internal purposes only.

void BALL::Bond::setType ( Type bond_type )

Set the bond type.

void BALL::Bond::swap ( Bond & bond )

Swap the contents of two bonds

Parameters

bond	the bond `this` is being swapped with

See also: Bond::Bond

Friends And Related Function Documentation

friend class Atom

friend

Definition at line 61 of file bond.h.

Member Data Documentation

Order BALL::Bond::bond_order_

protected

Definition at line 455 of file bond.h.

Type BALL::Bond::bond_type_

protected

Definition at line 458 of file bond.h.

Atom* BALL::Bond::first_

protected

Definition at line 446 of file bond.h.

String BALL::Bond::name_

protected

Definition at line 452 of file bond.h.

Atom* BALL::Bond::second_

protected

Definition at line 449 of file bond.h.

Classes

Public Types

Public Member Functions

Protected Attributes

Friends

Constructors and Destructors

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Detailed Description

Member Typedef Documentation

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Constructor & Destructor Documentation

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