Common interface for data structures that support a random access to stored Chem::Atom instances. More...

#include <AtomContainer.hpp>

Inheritance diagram for CDPL::Chem::AtomContainer:

Public Types
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 Member Functions
virtual std::size_t	getNumAtoms () const =0
	Returns the number of atoms. 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...

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 bool	containsAtom (const Atom &atom) const =0
	Tells whether the specified atom is part of the atom sequence. More...

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

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

virtual void	orderAtoms (const AtomCompareFunction &func)=0
	Orders the 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...

Protected Member Functions
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...

Detailed Description

Common interface for data structures that support a random access to stored Chem::Atom instances.

Implementations have to guarantee that a given Chem::Atom object is stored only once and its index is unique amongst all contained Chem::Atom instances. Otherwise algorithms that rely on this behaviour may not work correctly!

Member Typedef Documentation

◆ ConstAtomIterator

typedef Util::IndexedElementIterator<const Atom, ConstAtomAccessor> CDPL::Chem::AtomContainer::ConstAtomIterator

A constant random access iterator used to iterate over the stored const Chem::Atom objects.

◆ AtomIterator

typedef Util::IndexedElementIterator<Atom, AtomAccessor> CDPL::Chem::AtomContainer::AtomIterator

A mutable random access iterator used to iterate over the stored Chem::Atom objects.

Constructor & Destructor Documentation

◆ ~AtomContainer()

virtual CDPL::Chem::AtomContainer::~AtomContainer ( )

inlineprotectedvirtual

Virtual destructor.

Member Function Documentation

◆ getNumAtoms()

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

pure virtual

Returns the number of atoms.

Returns: The number of atoms.

Implemented in CDPL::Chem::Bond, CDPL::Chem::Atom, CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Fragment, CDPL::Chem::ElectronSystem, CDPL::Chem::BasicMolecule, CDPL::Chem::BasicBond, and CDPL::Chem::BasicAtom.

◆ getAtom() [1/2]

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

pure virtual

Returns a const reference to the atom at index idx.

Parameters

idx	The zero-based index of the atom to return.

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

Exceptions

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

Implemented in CDPL::Chem::Bond, CDPL::Chem::Atom, CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Fragment, CDPL::Chem::ElectronSystem, CDPL::Chem::BasicMolecule, CDPL::Chem::BasicBond, and CDPL::Chem::BasicAtom.

◆ getAtom() [2/2]

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

pure virtual

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

Parameters

idx	The zero-based index of the atom to return.

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

Exceptions

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

Implemented in CDPL::Chem::Bond, CDPL::Chem::Atom, CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Fragment, CDPL::Chem::ElectronSystem, CDPL::Chem::BasicMolecule, CDPL::Chem::BasicBond, and CDPL::Chem::BasicAtom.

◆ getAtomsBegin() [1/2]

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

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.

◆ getAtomsEnd() [1/2]

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

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.

◆ 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() [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.

◆ begin() [1/2]

ConstAtomIterator CDPL::Chem::AtomContainer::begin ( ) const

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.

◆ end() [1/2]

ConstAtomIterator CDPL::Chem::AtomContainer::end ( ) const

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.

◆ begin() [2/2]

AtomIterator CDPL::Chem::AtomContainer::begin ( )

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.

◆ end() [2/2]

AtomIterator CDPL::Chem::AtomContainer::end ( )

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.

◆ containsAtom()

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

pure virtual

Tells whether the specified atom is part of the atom sequence.

Parameters

atom	The atom to look for.

Returns: true if atom is part of the sequence, and false otherwise.

Implemented in CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Bond, CDPL::Chem::Atom, CDPL::Chem::Fragment, CDPL::Chem::ElectronSystem, CDPL::Chem::BasicMolecule, CDPL::Chem::BasicBond, and CDPL::Chem::BasicAtom.

◆ getAtomIndex()

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

pure virtual

Returns the index of the specified atom.

Parameters

atom	The atom for which to return the index.

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

Exceptions

Base::ItemNotFound if the specified atom could not be found.

Implemented in CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Bond, CDPL::Chem::Atom, CDPL::Chem::Fragment, CDPL::Chem::ElectronSystem, CDPL::Chem::BasicMolecule, CDPL::Chem::BasicBond, and CDPL::Chem::BasicAtom.

◆ getNumEntities()

virtual std::size_t CDPL::Chem::AtomContainer::getNumEntities ( ) const

virtual

Returns the number of stored Chem::Entity3D objects.

Forwards to getNumAtoms() and exists to satisfy the Chem::Entity3DContainer interface.

Returns: The number of contained atoms.

Implements CDPL::Chem::Entity3DContainer.

Reimplemented in CDPL::ConfGen::CanonicalFragment.

◆ getEntity() [1/2]

virtual const Chem::Entity3D& CDPL::Chem::AtomContainer::getEntity ( std::size_t idx ) const

virtual

Returns a const reference to the entity at index idx.

Forwards to getAtom() and exists to satisfy the Chem::Entity3DContainer interface.

Parameters

idx	The zero-based entity index.

Returns: A const reference to the entity at the specified index.

Exceptions

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

Implements CDPL::Chem::Entity3DContainer.

Reimplemented in CDPL::ConfGen::CanonicalFragment.

◆ getEntity() [2/2]

virtual Chem::Entity3D& CDPL::Chem::AtomContainer::getEntity ( std::size_t idx )

virtual

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

Forwards to getAtom() and exists to satisfy the Chem::Entity3DContainer interface.

Parameters

idx	The zero-based entity index.

Returns: A non-const reference to the entity at the specified index.

Exceptions

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

Implements CDPL::Chem::Entity3DContainer.

Reimplemented in CDPL::ConfGen::CanonicalFragment.

◆ orderAtoms()

virtual void CDPL::Chem::AtomContainer::orderAtoms ( const AtomCompareFunction & func )

pure 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.

Implemented in CDPL::ConfGen::CanonicalFragment, CDPL::Chem::Fragment, CDPL::Chem::ElectronSystem, CDPL::Chem::BasicMolecule, CDPL::Chem::BasicBond, and CDPL::Chem::BasicAtom.

◆ getAtoms() [1/2]

const AtomContainer& CDPL::Chem::AtomContainer::getAtoms ( ) const

inline

Returns a const reference to itself.

Returns: A const reference to itself.

◆ getAtoms() [2/2]

AtomContainer& CDPL::Chem::AtomContainer::getAtoms ( )

inline

Returns a reference to itself.

Returns: A reference to itself.

◆ operator=()

AtomContainer& CDPL::Chem::AtomContainer::operator= ( const AtomContainer & cntnr )

protected

Replaces the current set of properties by a copy of the properties of the container cntnr.

Parameters

cntnr The container to copy.

Returns: A reference to itself.

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

AtomContainer.hpp

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstAtomIterator

◆ AtomIterator

Constructor & Destructor Documentation

◆ ~AtomContainer()

Member Function Documentation

◆ getNumAtoms()

◆ getAtom() [1/2]

◆ getAtom() [2/2]

◆ getAtomsBegin() [1/2]

◆ getAtomsEnd() [1/2]

◆ getAtomsBegin() [2/2]

◆ getAtomsEnd() [2/2]

◆ begin() [1/2]

◆ end() [1/2]

◆ begin() [2/2]

◆ end() [2/2]

◆ containsAtom()

◆ getAtomIndex()

◆ getNumEntities()

◆ getEntity() [1/2]

◆ getEntity() [2/2]

◆ orderAtoms()

◆ getAtoms() [1/2]

◆ getAtoms() [2/2]

◆ operator=()