#include <Bond.hpp>

Inheritance diagram for CDPL::Chem::Bond:

Public Types
typedef AtomContainer::AtomIterator	AtomIterator
	A mutable random access iterator used to iterate over the connected atoms. More...

typedef AtomContainer::ConstAtomIterator	ConstAtomIterator
	A constant random access iterator used to iterate over the connected atoms. More...

Public Types inherited from CDPL::Chem::AtomContainer
typedef Util::IndexedElementIterator< const Atom, ConstAtomAccessor >	ConstAtomIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Atom objects. More...

typedef Util::IndexedElementIterator< Atom, AtomAccessor >	AtomIterator
	A mutable random access iterator used to iterate over the stored Chem::Atom objects. More...

Public Types inherited from CDPL::Chem::Entity3DContainer
typedef Util::IndexedElementIterator< const Entity3D, ConstEntityAccessor >	ConstEntityIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Entity3D objects. More...

typedef Util::IndexedElementIterator< Entity3D, EntityAccessor >	EntityIterator
	A mutable random access iterator used to iterate over the stored Chem::Entity3D objects. More...

Public Types inherited from CDPL::Base::PropertyContainer
typedef PropertyMap::value_type	PropertyEntry
	A Base::LookupKey / Base::Any pair that stores the property value for a given property key. More...

typedef PropertyMap::const_iterator	ConstPropertyIterator
	A constant iterator used to iterate over the property entries. More...

Public Member Functions
virtual const Molecule &	getMolecule () const =0
	Returns a `const` reference to the parent molecule. More...

virtual Molecule &	getMolecule ()=0
	Returns a non-`const` reference to the parent molecule. More...

virtual const Atom &	getBegin () const =0
	Returns a `const` reference to the start atom of the bond. More...

virtual Atom &	getBegin ()=0
	Returns a non-`const` reference to the start atom of the bond. More...

virtual const Atom &	getEnd () const =0
	Returns a `const` reference to the end atom of the bond. More...

virtual Atom &	getEnd ()=0
	Returns a non-`const` reference to the end atom of the bond. More...

virtual const Atom &	getNeighbor (const Atom &atom) const =0
	Returns a `const` reference to the connected neighbor of the argument atom. More...

virtual Atom &	getNeighbor (const Atom &atom)=0
	Returns a non-`const` reference to the connected neighbor of the argument atom. More...

virtual std::size_t	getIndex () const =0
	Returns the index of the bond in its parent molecule. More...

virtual std::size_t	getNumAtoms () const =0
	Returns the number of atoms connected by the bond. More...

virtual const Atom &	getAtom (std::size_t idx) const =0
	Returns a `const` reference to the atom at index idx. More...

virtual Atom &	getAtom (std::size_t idx)=0
	Returns a non-`const` reference to the atom at index idx. More...

virtual bool	containsAtom (const Atom &atom) const =0
	Tells whether the bond is incident to the specified atom. More...

virtual std::size_t	getAtomIndex (const Atom &atom) const =0
	Returns the index of the specified atom. More...

Bond &	operator= (const Bond &bond)
	Assignment operator that replaces the current set of properties with the properties of bond;. More...

ConstAtomIterator	getAtomsBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Atom objects. More...

AtomIterator	getAtomsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects. More...

ConstAtomIterator	getAtomsEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Atom objects. More...

AtomIterator	getAtomsEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More...

Public Member Functions inherited from CDPL::Chem::AtomContainer
ConstAtomIterator	getAtomsBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Atom objects. More...

ConstAtomIterator	getAtomsEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Atom objects. More...

AtomIterator	getAtomsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects. More...

AtomIterator	getAtomsEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More...

ConstAtomIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Atom objects. More...

ConstAtomIterator	end () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Atom objects. More...

AtomIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects. More...

AtomIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Atom objects. More...

virtual std::size_t	getNumEntities () const
	Returns the number of stored Chem::Entity3D objects. More...

virtual const Entity3D &	getEntity (std::size_t idx) const
	Returns a `const` reference to the Chem::Entity3D instance at index idx. More...

virtual Entity3D &	getEntity (std::size_t idx)
	Returns a non-`const` reference to the entity at index idx. More...

virtual void	orderAtoms (const AtomCompareFunction &func)=0
	Orders the stored atoms according to criteria implemented by the provided atom comparison function. More...

const AtomContainer &	getAtoms () const
	Returns a `const` reference to itself. More...

AtomContainer &	getAtoms ()
	Returns a reference to itself. More...

Public Member Functions inherited from CDPL::Chem::Entity3DContainer
ConstEntityIterator	getEntitiesBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Entity3D objects. More...

ConstEntityIterator	getEntitiesEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Entity3D objects. More...

EntityIterator	getEntitiesBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D objects. More...

EntityIterator	getEntitiesEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D objects. More...

ConstEntityIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Entity3D objects. More...

ConstEntityIterator	end () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Entity3D objects. More...

EntityIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D objects. More...

EntityIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D objects. More...

const Entity3DContainer &	getEntities () const
	Returns a `const` reference to itself. More...

Entity3DContainer &	getEntities ()
	Returns a reference to itself. More...

Public Member Functions inherited from CDPL::Base::PropertyContainer
std::size_t	getNumProperties () const
	Returns the number of property entries. More...

template<typename T >
void	setProperty (const LookupKey &key, T &&val)
	Sets the value of the property specified by key to val. More...

template<typename T >
const T &	getProperty (const LookupKey &key) const
	Returns the value of the property specified by key as a `const` reference to an object of type T. More...

template<typename T >
const T &	getPropertyOrDefault (const LookupKey &key, const T &def_val) const
	Returns the value of the property specified by key as a `const` reference to an object of type T, or the default value def_val if a stored value does not exist. More...

const Any &	getProperty (const LookupKey &key, bool throw_=false) const
	Returns the value of the property specified by key. More...

bool	isPropertySet (const LookupKey &key) const
	Tells whether or not a value has been assigned to the property specified by key. More...

ConstPropertyIterator	getPropertiesBegin () const
	Returns a constant iterator pointing to the beginning of the property entries. More...

ConstPropertyIterator	getPropertiesEnd () const
	Returns a constant iterator pointing to the end of the property entries. More...

ConstPropertyIterator	begin () const
	Returns a constant iterator pointing to the beginning of the property entries. More...

ConstPropertyIterator	end () const
	Returns a constant iterator pointing to the end of the property entries. More...

bool	removeProperty (const LookupKey &key)
	Clears the value of the property specified by key. More...

void	clearProperties ()
	Clears all property values. More...

void	addProperties (const PropertyContainer &cntnr)
	Adds the property value entries in the `PropertyContainer` instance cntnr. More...

void	copyProperties (const PropertyContainer &cntnr)
	Replaces the current set of properties by a copy of the entries in cntnr. More...

void	swap (PropertyContainer &cntnr)
	Exchanges the properties of this container with the properties of the container cntnr. More...

const PropertyContainer &	getProperties () const
	Returns a `const` reference to itself. More...

Protected Member Functions
virtual	~Bond ()
	Virtual destructor. More...

Protected Member Functions inherited from CDPL::Chem::AtomContainer
virtual	~AtomContainer ()
	Virtual destructor. More...

AtomContainer &	operator= (const AtomContainer &cntnr)
	Assignment operator. More...

Protected Member Functions inherited from CDPL::Chem::Entity3DContainer
virtual	~Entity3DContainer ()
	Virtual destructor. More...

Entity3DContainer &	operator= (const Entity3DContainer &cntnr)
	Assignment operator. More...

Protected Member Functions inherited from CDPL::Base::PropertyContainer
	PropertyContainer ()
	Constructs an empty `PropertyContainer` instance. More...

	PropertyContainer (const PropertyContainer &cntnr)
	Constructs a copy of the `PropertyContainer` instance cntnr. More...

virtual	~PropertyContainer ()
	Virtual destructor. More...

PropertyContainer &	operator= (const PropertyContainer &cntnr)
	Assignment operator. More...

Detailed Description

Bond.

Member Typedef Documentation

◆ AtomIterator

typedef AtomContainer::AtomIterator CDPL::Chem::Bond::AtomIterator

A mutable random access iterator used to iterate over the connected atoms.

◆ ConstAtomIterator

typedef AtomContainer::ConstAtomIterator CDPL::Chem::Bond::ConstAtomIterator

A constant random access iterator used to iterate over the connected atoms.

Constructor & Destructor Documentation

◆ ~Bond()

virtual CDPL::Chem::Bond::~Bond ( )

inlineprotectedvirtual

Virtual destructor.

Member Function Documentation

◆ getMolecule() [1/2]

virtual const Molecule& CDPL::Chem::Bond::getMolecule ( ) const

pure virtual

Returns a const reference to the parent molecule.

Returns: A const reference to the parent molecule.

Implemented in CDPL::Chem::BasicBond.

◆ getMolecule() [2/2]

virtual Molecule& CDPL::Chem::Bond::getMolecule ( )

pure virtual

Returns a non-const reference to the parent molecule.

Returns: A non-const reference to the parent molecule.

Implemented in CDPL::Chem::BasicBond.

◆ getBegin() [1/2]

virtual const Atom& CDPL::Chem::Bond::getBegin ( ) const

pure virtual

Returns a const reference to the start atom of the bond.

Returns: A const reference to the start atom of the bond.

Implemented in CDPL::Chem::BasicBond.

◆ getBegin() [2/2]

virtual Atom& CDPL::Chem::Bond::getBegin ( )

pure virtual

Returns a non-const reference to the start atom of the bond.

Returns: A non-const reference to the start atom of the bond.

Implemented in CDPL::Chem::BasicBond.

◆ getEnd() [1/2]

virtual const Atom& CDPL::Chem::Bond::getEnd ( ) const

pure virtual

Returns a const reference to the end atom of the bond.

Returns: A const reference to the end atom of the bond.

Implemented in CDPL::Chem::BasicBond.

◆ getEnd() [2/2]

virtual Atom& CDPL::Chem::Bond::getEnd ( )

pure virtual

Returns a non-const reference to the end atom of the bond.

Returns: A non-const reference to the end atom of the bond.

Implemented in CDPL::Chem::BasicBond.

◆ getNeighbor() [1/2]

virtual const Atom& CDPL::Chem::Bond::getNeighbor ( const Atom & atom ) const

pure virtual

Returns a const reference to the connected neighbor of the argument atom.

Parameters

atom	The atom for which to return the connected neighbor atom.

Returns: A const reference to the connected neighbor of the argument atom.

Exceptions

Base::ItemNotFound if the bond is not incident to the specified atom.

Implemented in CDPL::Chem::BasicBond.

◆ getNeighbor() [2/2]

virtual Atom& CDPL::Chem::Bond::getNeighbor ( const Atom & atom )

pure virtual

Returns a non-const reference to the connected neighbor of the argument atom.

Parameters

atom	The atom for which to return the connected neighbor atom.

Returns: A non-const reference to the connected neighbor atom of the argument atom.

Exceptions

Base::ItemNotFound if the specified atom is not involved in the bond.

Implemented in CDPL::Chem::BasicBond.

◆ getIndex()

virtual std::size_t CDPL::Chem::Bond::getIndex ( ) const

pure virtual

Returns the index of the bond in its parent molecule.

Returns: The zero-based index of the bond.

Implemented in CDPL::Chem::BasicBond.

◆ getNumAtoms()

virtual std::size_t CDPL::Chem::Bond::getNumAtoms ( ) const

pure virtual

Returns the number of atoms connected by the bond.

Since a bond connects exactly two atoms, the return value is always 2.

Returns: The number of atoms connected by the bond (always 2).

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicBond.

◆ getAtom() [1/2]

virtual const Atom& CDPL::Chem::Bond::getAtom ( std::size_t idx ) const

pure virtual

Returns a const reference to the atom at index idx.

The index 0 specifies the start atom (see getBegin() const) and 1 the end atom of the bond (see getEnd() const).

Parameters

idx	The index of the atom to return.

Returns: A const reference to the atom at index idx.

Exceptions

Base::IndexError if idx is not in the range [0, 1].

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicBond.

◆ getAtom() [2/2]

virtual Atom& CDPL::Chem::Bond::getAtom ( std::size_t idx )

pure virtual

Returns a non-const reference to the atom at index idx.

The index 0 specifies the start atom (see getBegin() const) and 1 the end atom of the bond (see getEnd() const).

Parameters

idx	The index of the atom to return.

Returns: A non-const reference to the atom at index idx.

Exceptions

Base::IndexError if idx is not in the range [0, 1].

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicBond.

◆ containsAtom()

virtual bool CDPL::Chem::Bond::containsAtom ( const Atom & atom ) const

pure virtual

Tells whether the bond is incident to the specified atom.

Parameters

atom	The atom to check.

Returns: true if the bond is incident to the specified atom, and false otherwise.

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicBond.

◆ getAtomIndex()

virtual std::size_t CDPL::Chem::Bond::getAtomIndex ( const Atom & atom ) const

pure virtual

Returns the index of the specified atom.

If the specified atom is the start atom of the bond, the index 0 is returned. For the end atom of the bond, the value 1 will be returned.

Parameters

atom	The atom for which to return the index.

Returns: The zero-based index of the specified atom.

Exceptions

Base::ItemNotFound if the bond is not incident to the specified atom.

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicBond.

◆ operator=()

Bond& CDPL::Chem::Bond::operator= ( const Bond & bond )

Assignment operator that replaces the current set of properties with the properties of bond;.

Parameters

bond	The bond whose properties get copied.

Returns: A reference to itself.

◆ getAtomsBegin() [1/2]

ConstAtomIterator CDPL::Chem::AtomContainer::getAtomsBegin

Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects.

Returns: A constant iterator pointing to the beginning of the stored const Chem::Atom objects.

◆ getAtomsBegin() [2/2]

AtomIterator CDPL::Chem::AtomContainer::getAtomsBegin

Returns a mutable iterator pointing to the beginning of the stored Chem::Atom objects.

Returns: A mutable iterator pointing to the beginning of the stored Chem::Atom objects.

◆ getAtomsEnd() [1/2]

ConstAtomIterator CDPL::Chem::AtomContainer::getAtomsEnd

Returns a constant iterator pointing to the end of the stored const Chem::Atom objects.

Returns: A constant iterator pointing to the end of the stored const Chem::Atom objects.

◆ getAtomsEnd() [2/2]

AtomIterator CDPL::Chem::AtomContainer::getAtomsEnd

Returns a mutable iterator pointing to the end of the stored Chem::Atom objects.

Returns: A mutable iterator pointing to the end of the stored Chem::Atom objects.

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

Bond.hpp

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ AtomIterator

◆ ConstAtomIterator

Constructor & Destructor Documentation

◆ ~Bond()

Member Function Documentation

◆ getMolecule() [1/2]

◆ getMolecule() [2/2]

◆ getBegin() [1/2]

◆ getBegin() [2/2]

◆ getEnd() [1/2]

◆ getEnd() [2/2]

◆ getNeighbor() [1/2]

◆ getNeighbor() [2/2]

◆ getIndex()

◆ getNumAtoms()

◆ getAtom() [1/2]

◆ getAtom() [2/2]

◆ containsAtom()

◆ getAtomIndex()

◆ operator=()

◆ getAtomsBegin() [1/2]

◆ getAtomsBegin() [2/2]

◆ getAtomsEnd() [1/2]

◆ getAtomsEnd() [2/2]