Bond Class Reference
[Miscellaneous]

#include <bond.h>

Inheritance diagram for Bond:


Constructors and Destructors
	Bond () throw ()
	Default constructor.
	Bond (const Bond &bond, bool deep=true) throw ()
	Copy constructor.
	Bond (const String &name, Atom &first, Atom &second, Order order=BALL_BOND_DEFAULT_ORDER, Type type=BALL_BOND_DEFAULT_TYPE) throw (Exception::TooManyBonds)
	Detailed constructor.
virtual	~Bond () throw ()
	Destructor.
virtual void	clear () throw ()
	Disconnect and reset to default state.
virtual void	destroy () throw ()
	Explicit destructor.
Bond *	createBond (Bond &bond, Atom &first, Atom &second) throw (Exception::TooManyBonds)
	Create a bond.
Public Types
Type definitions
typedef short	Order
	Bond type.
typedef short	Type
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 }
	Predefined constants for the bond order. More...
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 }
	Predefined constants for the bond type. More...
enum	Property { NUMBER_OF_PROPERTIES = 0 }
	Predefined properties. More...
Public Member Functions
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Write a bond to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Read a bond from a persistent stream.
void	finalize () throw (Exception::GeneralException)
	Finalize the deserialization.
Predicates
bool	operator== (const Bond &bond) const throw ()
	Equality operator. Two bonds are equal, if they are identical instances.
bool	operator!= (const Bond &bond) const throw ()
	Inequality operator. Two bonds are not equal, if they are different instances.
Assignment methods
Bond &	operator= (const Bond &bond) throw ()
	Assignment operator.
void	swap (Bond &bond) throw ()
	Swap the contents of two bonds.
Accessors
void	setFirstAtom (Atom *atom) throw ()
	Set the first atom.
void	setSecondAtom (Atom *atom) throw ()
	Set the second atom.
const Atom *	getFirstAtom () const throw ()
	Return a pointer to the first atom.
const Atom *	getSecondAtom () const throw ()
	Return a pointer to the second atom.
Atom *	getPartner (const Atom &atom) const throw ()
	Return the partner atom of an atom.
void	setName (const String &name) throw ()
	Assign the atom name.
const String &	getName () const throw ()
	Return the atom name.
void	setOrder (Order bond_order) throw ()
	Assign the bond order.
Order	getOrder () const throw ()
	Return the bond order.
void	setType (Type bond_type) throw ()
	Set the bond type.
Type	getType () const throw ()
	Return the bond type.
float	getLength () const throw (NotBound)
	Return the bond length.
const Atom *	getBoundAtom (const Atom &atom) const throw ()
	Return the partner of the atom in this bond.
Predicates
bool	isBondOf (const Atom &atom) const throw ()
	Determine whether the bond belongs to an atom.
bool	isBound () const throw ()
	Determine whether this bond contains any atom.
bool	isInterBond () const throw ()
	Determine whether the bond connects two fragments.
bool	isInterBondOf (const AtomContainer &atom_container) const throw ()
	Request for the intermolecular bonding of this bond within {atom_container}.
bool	isIntraBond () const throw ()
	Request for the intramolecular bonding of this bond.
bool	isIntraBondOf (const AtomContainer &atom_container) const throw ()
	Request for the intramolecular bonding of this bond within {atom_container}.
Debugging and diagnostics
virtual bool	isValid () const throw ()
	Internal state and consistency self-validation.
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const throw ()
	Internal state dump.
Protected Attributes
Atributes
Atom *	first_
Atom *	second_
String	name_
Order	bond_order_
Type	bond_type_
Friends
class	Atom

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 thant 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.

Member Typedef Documentation

typedef short Bond::Order

Bond type.

Member Enumeration Documentation

enum Bond::BondOrder

Predefined constants for the bond order.

Enumeration values:

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.

enum Bond::BondType

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

enum Bond::Property

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

Constructor & Destructor Documentation

Bond::Bond ( ) throw ()

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 )

Bond::Bond ( const Bond & bond,

bool deep = true

) throw ()

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

Bond::Bond ( const String & name,

Atom & first,

Atom & second,

Order order = BALL_BOND_DEFAULT_ORDER,

Type type = BALL_BOND_DEFAULT_TYPE

) throw (Exception::TooManyBonds)

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 Bond::~Bond ( ) throw () [virtual]

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

Member Function Documentation

virtual void Bond::clear ( ) throw () [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 Composite.

Bond* Bond::createBond ( Bond & bond,

Atom & first,

Atom & second

) throw (Exception::TooManyBonds) [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 Bond::destroy ( ) throw () [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 Composite.

virtual void Bond::dump ( std::ostream & s = std::cout,

Size depth = 0

) const throw () [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 Composite.

void Bond::finalize ( ) throw (Exception::GeneralException) [virtual]

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

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

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

float Bond::getLength ( ) const throw (NotBound)

Return the bond length.

Exceptions:

NotBound if the bond has not two atoms

Returns:
float - the distance between the two atoms

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

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

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

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 Bond::isBound ( ) const throw ()

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 Bond::isInterBond ( ) const throw ()

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 Bond::isInterBondOf ( const AtomContainer & atom_container ) const throw ()

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 Bond::isIntraBond ( ) const throw ()

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 Bond::isIntraBondOf ( const AtomContainer & atom_container ) const throw ()

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 Bond::isValid ( ) const throw () [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 Composite.

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

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

void Bond::persistentRead ( PersistenceManager & pm ) throw (Exception::GeneralException) [virtual]

Read a bond from a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from Composite.

void Bond::persistentWrite ( PersistenceManager & pm,

const char * name = 0

) const throw (Exception::GeneralException) [virtual]

Write a bond to a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from Composite.

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

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 Bond::setSecondAtom ( Atom * atom ) throw ()

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 Bond::swap ( Bond & bond ) throw ()

Swap the contents of two bonds.

Parameters:

bond the bond this is being swapped with

See also:
Bond::Bond

Bond Class Reference [Miscellaneous]

Constructors and Destructors

Public Types

Public Member Functions