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

#include <BasicAtom.hpp>

Inheritance diagram for CDPL::Chem::BasicAtom:

Public Types
typedef boost::transform_iterator< AtomAccessor< BasicAtom >, NeighborList::iterator >	AtomIterator
	A mutable random access iterator used to iterate over the connected Chem::BasicAtom instances. More...

typedef boost::transform_iterator< AtomAccessor< const BasicAtom >, NeighborList::const_iterator >	ConstAtomIterator
	A constant random access iterator used to iterate over the connected `const` Chem::BasicAtom instances. More...

typedef boost::transform_iterator< BondAccessor< BasicBond >, NeighborList::iterator >	BondIterator
	A mutable random access iterator used to iterate over the incident Chem::BasicBond instances. More...

typedef boost::transform_iterator< BondAccessor< const BasicBond >, NeighborList::const_iterator >	ConstBondIterator
	A constant random access iterator used to iterate over the incident `const` Chem::BasicBond instances. More...

Public Types inherited from CDPL::Chem::Atom
typedef AtomContainer::AtomIterator	AtomIterator
	A mutable random access iterator used to iterate over the connected Chem::Atom instances. More...

typedef AtomContainer::ConstAtomIterator	ConstAtomIterator
	A constant random access iterator used to iterate over the connected `const` Chem::Atom instances. More...

typedef BondContainer::BondIterator	BondIterator
	A mutable random access iterator used to iterate over the incident Chem::Bond instances. More...

typedef BondContainer::ConstBondIterator	ConstBondIterator
	A constant random access iterator used to iterate over the incident `const` Chem::Bond instances. 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 instances. More...

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

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

Public Types inherited from CDPL::Chem::BondContainer
typedef Util::IndexedElementIterator< const Bond, ConstBondAccessor >	ConstBondIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Bond instances. More...

typedef Util::IndexedElementIterator< Bond, BondAccessor >	BondIterator
	A mutable random access iterator used to iterate over the stored Chem::Bond instances. 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
const Molecule &	getMolecule () const
	Returns a `const` reference to the parent molecule. More...

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

std::size_t	getNumAtoms () const
	Returns the number of connected atoms. More...

std::size_t	getNumBonds () const
	Returns the number of incident bonds. More...

const Bond &	getBond (std::size_t idx) const
	Returns a `const` reference to the incident bond at index idx. More...

Bond &	getBond (std::size_t idx)
	Returns a non-`const` reference to the incident bond at index idx. More...

const Bond &	getBondToAtom (const Atom &atom) const
	Returns a `const` reference to the bond that connects this atom to the argument atom. More...

Bond &	getBondToAtom (const Atom &atom)
	Returns a non-`const` reference to the bond that connects this atom to the argument atom. More...

const Bond *	findBondToAtom (const Atom &atom) const
	Returns a pointer to the `const` bond that connects this atom to the argument atom. More...

Bond *	findBondToAtom (const Atom &atom)
	Returns a pointer to the non-`const` bond that connects this atom to the argument atom. More...

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

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

ConstAtomIterator	getAtomsBegin () const
	Returns a constant iterator pointing to the beginning of the connected `const` Chem::BasicAtom instances. More...

AtomIterator	getAtomsBegin ()
	Returns a mutable iterator pointing to the end of the connected Chem::BasicAtom instances. More...

ConstAtomIterator	getAtomsEnd () const
	Returns a constant iterator pointing to the end of the connected `const` Chem::BasicAtom instances. More...

AtomIterator	getAtomsEnd ()
	Returns a mutable iterator pointing to the end of the connected Chem::BasicAtom instances. More...

ConstBondIterator	getBondsBegin () const
	Returns a constant iterator pointing to the beginning of the incident `const` Chem::BasicBond instances. More...

BondIterator	getBondsBegin ()
	Returns a mutable iterator pointing to the beginning of the incident Chem::BasicBond instances. More...

ConstBondIterator	getBondsEnd () const
	Returns a constant iterator pointing to the end of the incident `const` Chem::BasicBond instances. More...

BondIterator	getBondsEnd ()
	Returns a mutable iterator pointing to the end of the incident Chem::BasicBond instances. More...

bool	containsAtom (const Atom &atom) const
	Tells whether this atom and the specified atom are connected by a bond. More...

bool	containsBond (const Bond &bond) const
	Tells whether the specified bond is incident to this atom. More...

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

std::size_t	getBondIndex (const Bond &bond) const
	Returns the index of the specified incident bond. More...

std::size_t	getIndex () const
	Returns the index of the atom in its parent molecule. More...

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

void	orderBonds (const BondCompareFunction &func)
	Orders the bonds according to criteria implemented by the provided bond comparison function. More...

BasicAtom &	operator= (const BasicAtom &atom)
	Assignment operator that replaces the current set of properties with the properties of atom. More...

Atom &	operator= (const Atom &atom)
	Assignment operator that replaces the current set of properties with the properties of atom. More...

Public Member Functions inherited from CDPL::Chem::Atom
Atom &	operator= (const Atom &atom)
	Assignment operator that replaces the current set of properties with the properties of atom. More...

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

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

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

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

ConstBondIterator	getBondsBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Bond instances. More...

BondIterator	getBondsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Bond instances. More...

ConstBondIterator	getBondsEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Bond instances. More...

BondIterator	getBondsEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Bond instances. 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 instances. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

EntityIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D instances. 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::Chem::BondContainer
ConstBondIterator	getBondsBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Bond instances. More...

ConstBondIterator	getBondsEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Bond instances. More...

BondIterator	getBondsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Bond instances. More...

BondIterator	getBondsEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Bond instances. More...

ConstBondIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Bond instances. More...

ConstBondIterator	end () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Bond instances. More...

BondIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Bond instances. More...

BondIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Bond instances. More...

const BondContainer &	getBonds () const
	Returns a `const` reference to itself. More...

BondContainer &	getBonds ()
	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 an entry 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)
	Removes the entry for the property specified by key. More...

void	clearProperties ()
	Erases all container entries. More...

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

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

void	swap (PropertyContainer &cntnr)
	Exchanges the property entries of this container with the ones of cntnr. More...

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

Friends
class	BasicMolecule

Additional Inherited Members
Protected Member Functions inherited from CDPL::Chem::Atom
virtual	~Atom ()
	Virtual destructor. More...

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

AtomContainer &	operator= (const AtomContainer &cntnr)
	Replaces the current set of properties by a copy of the properties of the container cntnr. 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::Chem::BondContainer
virtual	~BondContainer ()
	Virtual destructor. More...

BondContainer &	operator= (const BondContainer &cntnr)
	Replaces the current set of properties by a copy of the properties of the container cntnr. More...

Protected Member Functions inherited from CDPL::Chem::Entity3D
	Entity3D ()
	Default constructor. More...

	Entity3D (const Entity3D &entity)
	Constructs a copy of the `Entity3D` instance entity. More...

virtual	~Entity3D ()
	Virtual destructor. More...

Entity3D &	operator= (const Entity3D &entity)
	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::Atom interface.

Provides constant-time access to connected atoms and incident bonds via the inherited Chem::Atom interface. BasicAtom instances are created, owned and managed exclusively by a Chem::BasicMolecule instance.

Member Typedef Documentation

◆ AtomIterator

typedef boost::transform_iterator<AtomAccessor<BasicAtom>, NeighborList::iterator> CDPL::Chem::BasicAtom::AtomIterator

A mutable random access iterator used to iterate over the connected Chem::BasicAtom instances.

◆ ConstAtomIterator

typedef boost::transform_iterator<AtomAccessor<const BasicAtom>, NeighborList::const_iterator> CDPL::Chem::BasicAtom::ConstAtomIterator

A constant random access iterator used to iterate over the connected const Chem::BasicAtom instances.

◆ BondIterator

typedef boost::transform_iterator<BondAccessor<BasicBond>, NeighborList::iterator> CDPL::Chem::BasicAtom::BondIterator

A mutable random access iterator used to iterate over the incident Chem::BasicBond instances.

◆ ConstBondIterator

typedef boost::transform_iterator<BondAccessor<const BasicBond>, NeighborList::const_iterator> CDPL::Chem::BasicAtom::ConstBondIterator

A constant random access iterator used to iterate over the incident const Chem::BasicBond instances.

Member Function Documentation

◆ getMolecule() [1/2]

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

virtual

Returns a const reference to the parent molecule.

Returns: A const reference to the parent molecule.

Implements CDPL::Chem::Atom.

◆ getMolecule() [2/2]

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

virtual

Returns a non-const reference to the parent molecule.

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

Implements CDPL::Chem::Atom.

◆ getNumAtoms()

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

virtual

Returns the number of connected atoms.

Equivalent to getNumBonds().

Returns: The number of connected atoms.

Implements CDPL::Chem::Atom.

◆ getNumBonds()

std::size_t CDPL::Chem::BasicAtom::getNumBonds ( ) const

virtual

Returns the number of incident bonds.

Equivalent to getNumAtoms().

Returns: The number of incident bonds.

Implements CDPL::Chem::Atom.

◆ getBond() [1/2]

const Bond& CDPL::Chem::BasicAtom::getBond ( std::size_t idx ) const

virtual

Returns a const reference to the incident bond at index idx.

Parameters

idx	The index of the incident bond to return.

Returns: A const reference to the incident bond at index idx.

Exceptions

Base::IndexError if idx is not in the range [0, getNumBonds()).

Note: The order of incident bonds corresponds to the order of the connected atoms.

Implements CDPL::Chem::Atom.

◆ getBond() [2/2]

Bond& CDPL::Chem::BasicAtom::getBond ( std::size_t idx )

virtual

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

Parameters

idx	The index of the incident bond to return.

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

Exceptions

Base::IndexError if idx is not in the range [0, getNumBonds()).

Note: The order of incident bonds corresponds to the order of connected atoms.

Implements CDPL::Chem::Atom.

◆ getBondToAtom() [1/2]

const Bond& CDPL::Chem::BasicAtom::getBondToAtom ( const Atom & atom ) const

virtual

Returns a const reference to the bond that connects this atom to the argument atom.

Parameters

atom	The adjacent atom for which to return the connecting bond.

Returns: A const reference to the bond connecting this atom and the argument atom.

Exceptions

Base::ItemNotFound if the argument atom is not connected to this atom.

Implements CDPL::Chem::Atom.

◆ getBondToAtom() [2/2]

Bond& CDPL::Chem::BasicAtom::getBondToAtom ( const Atom & atom )

virtual

Returns a non-const reference to the bond that connects this atom to the argument atom.

Parameters

atom	The adjacent atom for which to return the connecting bond.

Returns: A non-const reference to the bond connecting this atom and the argument atom.

Exceptions

Base::ItemNotFound if the argument atom is not connected to this atom.

Implements CDPL::Chem::Atom.

◆ findBondToAtom() [1/2]

const Bond* CDPL::Chem::BasicAtom::findBondToAtom ( const Atom & atom ) const

virtual

Returns a pointer to the const bond that connects this atom to the argument atom.

Parameters

atom	The adjacent atom for which to return a pointer to the connecting bond.

Returns: A pointer to the const bond that connects this atom to the argument atom, or nullptr if the argument atom is not connected.

Implements CDPL::Chem::Atom.

◆ findBondToAtom() [2/2]

Bond* CDPL::Chem::BasicAtom::findBondToAtom ( const Atom & atom )

virtual

Returns a pointer to the non-const bond that connects this atom to the argument atom.

Parameters

atom	The adjacent atom for which to return a pointer to the connecting bond.

Returns: A pointer to the non-const bond that connects this atom to the argument atom, or nullptr if the argument atom is not connected.

Implements CDPL::Chem::Atom.

◆ getAtom() [1/2]

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

virtual

Returns a const reference to the connected atom at index idx.

Parameters

idx	The index of the atom to return.

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

Exceptions

Base::IndexError if idx is not in the range [0, getNumAtoms()).

Note: The order of connected atoms corresponds to the order of connecting bonds.

Implements CDPL::Chem::Atom.

◆ getAtom() [2/2]

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

virtual

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

Parameters

idx	The index of the atom to return.

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

Exceptions

Base::IndexError if idx is not in the range [0, getNumAtoms()).

Note: The order of connected atoms corresponds to the order of connecting bonds.

Implements CDPL::Chem::Atom.

◆ getAtomsBegin() [1/2]

ConstAtomIterator CDPL::Chem::BasicAtom::getAtomsBegin ( ) const

Returns a constant iterator pointing to the beginning of the connected const Chem::BasicAtom instances.

Returns: A constant iterator pointing to the beginning of the connected const Chem::BasicAtom instances.

◆ getAtomsBegin() [2/2]

AtomIterator CDPL::Chem::BasicAtom::getAtomsBegin ( )

Returns a mutable iterator pointing to the end of the connected Chem::BasicAtom instances.

Returns: A mutable iterator pointing to the end of the connected Chem::BasicAtom instances.

◆ getAtomsEnd() [1/2]

ConstAtomIterator CDPL::Chem::BasicAtom::getAtomsEnd ( ) const

Returns a constant iterator pointing to the end of the connected const Chem::BasicAtom instances.

Returns: A constant iterator pointing to the end of the connected const Chem::BasicAtom instances.

◆ getAtomsEnd() [2/2]

AtomIterator CDPL::Chem::BasicAtom::getAtomsEnd ( )

Returns a mutable iterator pointing to the end of the connected Chem::BasicAtom instances.

Returns: A mutable iterator pointing to the end of the connected Chem::BasicAtom instances.

◆ getBondsBegin() [1/2]

ConstBondIterator CDPL::Chem::BasicAtom::getBondsBegin ( ) const

Returns a constant iterator pointing to the beginning of the incident const Chem::BasicBond instances.

Returns: A constant iterator pointing to the beginning of the incident const Chem::BasicBond instances.

◆ getBondsBegin() [2/2]

BondIterator CDPL::Chem::BasicAtom::getBondsBegin ( )

Returns a mutable iterator pointing to the beginning of the incident Chem::BasicBond instances.

Returns: A mutable iterator pointing to the beginning of the incident Chem::BasicBond instances.

◆ getBondsEnd() [1/2]

ConstBondIterator CDPL::Chem::BasicAtom::getBondsEnd ( ) const

Returns a constant iterator pointing to the end of the incident const Chem::BasicBond instances.

Returns: A constant iterator pointing to the end of the incident const Chem::BasicBond instances.

◆ getBondsEnd() [2/2]

BondIterator CDPL::Chem::BasicAtom::getBondsEnd ( )

Returns a mutable iterator pointing to the end of the incident Chem::BasicBond instances.

Returns: A mutable iterator pointing to the end of the incident Chem::BasicBond instances.

◆ containsAtom()

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

virtual

Tells whether this atom and the specified atom are connected by a bond.

Parameters

atom	The atom to test for adjacency.

Returns: true if the argument atom is connected to this atom, and false otherwise.

Implements CDPL::Chem::Atom.

◆ containsBond()

bool CDPL::Chem::BasicAtom::containsBond ( const Bond & bond ) const

virtual

Tells whether the specified bond is incident to this atom.

Parameters

bond	The bond to test for incidence.

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

Implements CDPL::Chem::Atom.

◆ getAtomIndex()

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

virtual

Returns the index of the specified connected atom.

Parameters

atom	The connected atom for which to return the index.

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

Exceptions

Base::ItemNotFound if the specified atom is not connected to this atom.

Implements CDPL::Chem::Atom.

◆ getBondIndex()

std::size_t CDPL::Chem::BasicAtom::getBondIndex ( const Bond & bond ) const

virtual

Returns the index of the specified incident bond.

Parameters

bond	The bond for which to return the index.

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

Exceptions

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

Implements CDPL::Chem::Atom.

◆ getIndex()

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

virtual

Returns the index of the atom in its parent molecule.

Returns: The zero-based index of the atom.

Implements CDPL::Chem::Atom.

◆ orderAtoms()

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

virtual

Orders the atoms according to criteria implemented by the provided atom comparison function.

Parameters

func	The atom comparison function implementing the applied ordering criteria.

Implements CDPL::Chem::AtomContainer.

◆ orderBonds()

void CDPL::Chem::BasicAtom::orderBonds ( const BondCompareFunction & func )

virtual

Orders the bonds according to criteria implemented by the provided bond comparison function.

Parameters

func	The bond comparison function implementing the applied ordering criteria.

Implements CDPL::Chem::BondContainer.

◆ operator=() [1/2]

BasicAtom& CDPL::Chem::BasicAtom::operator= ( const BasicAtom & atom )

Assignment operator that replaces the current set of properties with the properties of atom.

Parameters

atom	The atom whose properties get copied.

Returns: A reference to itself.

◆ operator=() [2/2]

Atom& CDPL::Chem::Atom::operator=

Assignment operator that replaces the current set of properties with the properties of atom.

Parameters

atom	The atom whose properties get copied.

Returns: A reference to itself.

Friends And Related Function Documentation

◆ BasicMolecule

friend class BasicMolecule

friend

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

BasicAtom.hpp

Public Types

Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AtomIterator

◆ ConstAtomIterator

◆ BondIterator

◆ ConstBondIterator

Member Function Documentation

◆ getMolecule() [1/2]

◆ getMolecule() [2/2]

◆ getNumAtoms()

◆ getNumBonds()

◆ getBond() [1/2]

◆ getBond() [2/2]

◆ getBondToAtom() [1/2]

◆ getBondToAtom() [2/2]

◆ findBondToAtom() [1/2]

◆ findBondToAtom() [2/2]

◆ getAtom() [1/2]

◆ getAtom() [2/2]

◆ getAtomsBegin() [1/2]

◆ getAtomsBegin() [2/2]

◆ getAtomsEnd() [1/2]

◆ getAtomsEnd() [2/2]

◆ getBondsBegin() [1/2]

◆ getBondsBegin() [2/2]

◆ getBondsEnd() [1/2]

◆ getBondsEnd() [2/2]

◆ containsAtom()

◆ containsBond()

◆ getAtomIndex()

◆ getBondIndex()

◆ getIndex()

◆ orderAtoms()

◆ orderBonds()

◆ operator=() [1/2]

◆ operator=() [2/2]

Friends And Related Function Documentation

◆ BasicMolecule