BALL::Bond Class Reference
[Miscellaneous]

#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 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.
bool	operator!= (const Bond &bond) const
	Inequality operator. Two bonds are not equal, if they are different instances.
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.
Atom *	getFirstAtom ()
	Return a pointer to the first atom.
const Atom *	getSecondAtom () const
	Return a pointer to the second atom.
Atom *	getSecondAtom ()
	Return a pointer to the second atom.
Atom *	getPartner (const Atom &atom) const
void	setName (const String &name)
	Assign the atom name.
const String &	getName () const
	Return the atom name.
void	setOrder (Order bond_order)
	Assign the bond order.
Order	getOrder () const
	Return the bond order.
bool	isAromatic () const
void	setType (Type bond_type)
	Set the bond type.
Type	getType () const
	Return the bond type.
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
Protected Attributes
Atributes

Atom *	first_
Atom *	second_
String	name_
Order	bond_order_
Type	bond_type_
Private Member Functions
void	arrangeBonds_ ()
void	clear_ ()
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)

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

void BALL::Bond::arrangeBonds_ ( ) [private]

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.

void BALL::Bond::clear_ ( ) [private]

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.

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::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::getFirstAtom ( )

Return a pointer to the first atom.

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

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

Atom* BALL::Bond::getSecondAtom ( )

Return a pointer to the second atom.

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

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.

BALL::Bond Class Reference [Miscellaneous]

Classes

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Constructors and Destructors

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

BALL::Bond Class Reference
[Miscellaneous]