Default implementation of the Chem::Bond interface. More...

#include <BasicBond.hpp>

Inheritance diagram for CDPL::Chem::BasicBond:

Public Member Functions
std::size_t	getNumAtoms () const
	Returns the number of atoms incident to this bond (always 2). More...

const Molecule &	getMolecule () const
	Returns the parent molecule. More...

Molecule &	getMolecule ()
	Returns the parent molecule. More...

const Atom &	getBegin () const
	Returns the first atom of the bond. More...

Atom &	getBegin ()
	Returns the first atom of the bond. More...

const Atom &	getEnd () const
	Returns the second atom of the bond. More...

Atom &	getEnd ()
	Returns the second atom of the bond. More...

const Atom &	getAtom (std::size_t idx) const
	Returns the bond atom at index idx. More...

Atom &	getAtom (std::size_t idx)
	Returns the bond atom at index idx. More...

bool	containsAtom (const Atom &atom) const
	Tells whether atom is one of the two bonded atoms. More...

std::size_t	getAtomIndex (const Atom &atom) const
	Returns the index of atom within this bond. More...

const Atom &	getNeighbor (const Atom &atom) const
	Returns the atom on the opposite side of atom. More...

Atom &	getNeighbor (const Atom &atom)
	Returns the atom on the opposite side of atom. More...

std::size_t	getIndex () const
	Returns the zero-based index of this bond within the parent molecule. More...

void	orderAtoms (const AtomCompareFunction &func)
	Reorders the begin/end atoms of this bond according to the comparison function func. More...

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

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

Public Member Functions inherited from CDPL::Chem::Bond
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 (equivalent to getNumAtoms()). More...

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

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

Friends
class	BasicMolecule

class	BasicAtom

Additional Inherited Members
Public Types inherited from CDPL::Chem::Bond
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...

Protected Member Functions inherited from CDPL::Chem::Bond
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

Default implementation of the Chem::Bond interface.

Instances of BasicBond are owned and constructed exclusively by a Chem::BasicMolecule instance and reference two Chem::BasicAtom instances that represent the bonded atoms.

Member Function Documentation

◆ getNumAtoms()

std::size_t CDPL::Chem::BasicBond::getNumAtoms ( ) const

virtual

Returns the number of atoms incident to this bond (always 2).

Returns: The atom count (2).

Implements CDPL::Chem::Bond.

◆ getMolecule() [1/2]

const Molecule& CDPL::Chem::BasicBond::getMolecule ( ) const

virtual

Returns the parent molecule.

Returns: A const reference to the parent molecule.

Implements CDPL::Chem::Bond.

◆ getMolecule() [2/2]

Molecule& CDPL::Chem::BasicBond::getMolecule ( )

virtual

Returns the parent molecule.

Returns: A reference to the parent molecule.

Implements CDPL::Chem::Bond.

◆ getBegin() [1/2]

const Atom& CDPL::Chem::BasicBond::getBegin ( ) const

virtual

Returns the first atom of the bond.

Returns: A const reference to the first atom.

Implements CDPL::Chem::Bond.

◆ getBegin() [2/2]

Atom& CDPL::Chem::BasicBond::getBegin ( )

virtual

Returns the first atom of the bond.

Returns: A reference to the first atom.

Implements CDPL::Chem::Bond.

◆ getEnd() [1/2]

const Atom& CDPL::Chem::BasicBond::getEnd ( ) const

virtual

Returns the second atom of the bond.

Returns: A const reference to the second atom.

Implements CDPL::Chem::Bond.

◆ getEnd() [2/2]

Atom& CDPL::Chem::BasicBond::getEnd ( )

virtual

Returns the second atom of the bond.

Returns: A reference to the second atom.

Implements CDPL::Chem::Bond.

◆ getAtom() [1/2]

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

virtual

Returns the bond atom at index idx.

Parameters

idx	The zero-based atom index (0 = begin, 1 = end).

Returns: A const reference to the atom.

Exceptions

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

Implements CDPL::Chem::Bond.

◆ getAtom() [2/2]

Atom& CDPL::Chem::BasicBond::getAtom ( std::size_t idx )

virtual

Returns the bond atom at index idx.

Parameters

idx	The zero-based atom index (0 = begin, 1 = end).

Returns: A reference to the atom.

Exceptions

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

Implements CDPL::Chem::Bond.

◆ containsAtom()

bool CDPL::Chem::BasicBond::containsAtom ( const Atom & atom ) const

virtual

Tells whether atom is one of the two bonded atoms.

Parameters

atom	The atom to test.

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

Implements CDPL::Chem::Bond.

◆ getAtomIndex()

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

virtual

Returns the index of atom within this bond.

Parameters

atom	The atom whose index is requested.

Returns: The atom index (0 for the begin atom, 1 for the end atom).

Exceptions

Base::ItemNotFound if atom is not incident to this bond.

Implements CDPL::Chem::Bond.

◆ getNeighbor() [1/2]

const Atom& CDPL::Chem::BasicBond::getNeighbor ( const Atom & atom ) const

virtual

Returns the atom on the opposite side of atom.

Parameters

atom	One of the two bonded atoms.

Returns: A const reference to the other bonded atom.

Exceptions

Base::ItemNotFound if atom is not incident to this bond.

Implements CDPL::Chem::Bond.

◆ getNeighbor() [2/2]

Atom& CDPL::Chem::BasicBond::getNeighbor ( const Atom & atom )

virtual

Returns the atom on the opposite side of atom.

Parameters

atom	One of the two bonded atoms.

Returns: A reference to the other bonded atom.

Exceptions

Base::ItemNotFound if atom is not incident to this bond.

Implements CDPL::Chem::Bond.

◆ getIndex()

std::size_t CDPL::Chem::BasicBond::getIndex ( ) const

virtual

Returns the zero-based index of this bond within the parent molecule.

Returns: The bond index.

Implements CDPL::Chem::Bond.

◆ orderAtoms()

void CDPL::Chem::BasicBond::orderAtoms ( const AtomCompareFunction & func )

virtual

Reorders the begin/end atoms of this bond according to the comparison function func.

Parameters

func	The comparison function defining the desired order.

Implements CDPL::Chem::AtomContainer.

◆ operator=() [1/2]

BasicBond& CDPL::Chem::BasicBond::operator= ( const BasicBond & 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.

◆ operator=() [2/2]

Bond& CDPL::Chem::Bond::operator=

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.

Friends And Related Function Documentation

◆ BasicMolecule

friend class BasicMolecule

friend

◆ BasicAtom

friend class BasicAtom

friend

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

BasicBond.hpp

Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ getNumAtoms()

◆ getMolecule() [1/2]

◆ getMolecule() [2/2]

◆ getBegin() [1/2]

◆ getBegin() [2/2]

◆ getEnd() [1/2]

◆ getEnd() [2/2]

◆ getAtom() [1/2]

◆ getAtom() [2/2]

◆ containsAtom()

◆ getAtomIndex()

◆ getNeighbor() [1/2]

◆ getNeighbor() [2/2]

◆ getIndex()

◆ orderAtoms()

◆ operator=() [1/2]

◆ operator=() [2/2]

Friends And Related Function Documentation

◆ BasicMolecule

◆ BasicAtom