Describes an electron system of a molecule in terms of involved atoms and their electron contributions. More...

#include <ElectronSystem.hpp>

Inheritance diagram for CDPL::Chem::ElectronSystem:

Public Types
typedef std::shared_ptr< ElectronSystem >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `ElectronSystem` instances. More...

typedef boost::indirect_iterator< AtomList::const_iterator, const Atom >	ConstAtomIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Atom objects. More...

typedef boost::indirect_iterator< AtomList::iterator, Atom >	AtomIterator
	A mutable random access iterator used to iterate over the stored `const` Chem::Atom objects. 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 Member Functions
	ElectronSystem ()
	Constructs an empty `ElectronSystem` instance. More...

std::size_t	getNumAtoms () const
	Returns the number of atoms contributing to the electron system. More...

bool	containsAtom (const Atom &atom) const
	Tells whether the specified atom is part of the electron system. More...

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

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

Atom &	getAtom (std::size_t idx)
	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...

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

void	clear ()
	Removes all atoms. More...

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

bool	addAtom (const Chem::Atom &atom, std::size_t elec_contrib)
	Extends the electron system by the specified atom and its electron contributions. More...

bool	addAtoms (const ElectronSystem &elec_sys)
	Adds the atoms and associated electron contributions in the electron system elec_sys to this system. More...

void	removeAtom (std::size_t idx)
	Removes the atom at the specified index. More...

AtomIterator	removeAtom (const AtomIterator &it)
	Removes the atom specified by the iterator it. More...

bool	removeAtom (const Atom &atom)
	Removes the specified atom. More...

std::size_t	getNumElectrons () const
	Returns the total number of electrons contributed by the involved atoms. More...

std::size_t	getElectronContrib (const Atom &atom) const
	Returns the number of electrons contributed by the specified atom. More...

std::size_t	getElectronContrib (std::size_t idx) const
	Returns the number of electrons contributed by the atom at the specified index. More...

void	setElectronContrib (const Atom &atom, std::size_t elec_contrib)
	Changes the number of electrons that are contributed by the specified atom. More...

void	setElectronContrib (std::size_t idx, std::size_t elec_contrib)
	Changes the number of electrons that are contributed by the atom at the specified index. More...

void	merge (const ElectronSystem &elec_sys)
	Merges the atoms and associated electron contributions in the electron system elec_sys with this system. More...

bool	overlaps (const ElectronSystem &elec_sys) const
	Checks if the electron system shares at least one atom with the system elec_sys. More...

bool	contains (const ElectronSystem &elec_sys) const
	Checks if all atoms in the electron system elec_sys are also part of this electron system. More...

bool	connected (const ElectronSystem &elec_sys, const BondContainer &bonds) const
	Checks if the atom sets of the electron systems do not intersect but are linked by at least one bond. More...

void	swap (ElectronSystem &elec_sys)
	Exchanges the state of this electron system with the state of the system elec_sys. 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...

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...

Additional Inherited Members
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...

Detailed Description

Describes an electron system of a molecule in terms of involved atoms and their electron contributions.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<ElectronSystem> CDPL::Chem::ElectronSystem::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated ElectronSystem instances.

◆ ConstAtomIterator

typedef boost::indirect_iterator<AtomList::const_iterator, const Atom> CDPL::Chem::ElectronSystem::ConstAtomIterator

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

◆ AtomIterator

typedef boost::indirect_iterator<AtomList::iterator, Atom> CDPL::Chem::ElectronSystem::AtomIterator

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

Constructor & Destructor Documentation

◆ ElectronSystem()

CDPL::Chem::ElectronSystem::ElectronSystem ( )

Constructs an empty ElectronSystem instance.

Member Function Documentation

◆ getNumAtoms()

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

virtual

Returns the number of atoms contributing to the electron system.

Returns: The number of atoms.

Implements CDPL::Chem::AtomContainer.

◆ containsAtom()

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

virtual

Tells whether the specified atom is part of the electron system.

Parameters

atom	The atom to look for.

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

Implements CDPL::Chem::AtomContainer.

◆ getAtomIndex()

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

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 is not part of this electron system.

Implements CDPL::Chem::AtomContainer.

◆ getAtom() [1/2]

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

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 the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

Implements CDPL::Chem::AtomContainer.

◆ getAtom() [2/2]

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

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 the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

Implements CDPL::Chem::AtomContainer.

◆ getAtomsBegin() [1/2]

ConstAtomIterator CDPL::Chem::ElectronSystem::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.

◆ getAtomsBegin() [2/2]

AtomIterator CDPL::Chem::ElectronSystem::getAtomsBegin ( )

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

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

◆ getAtomsEnd() [1/2]

ConstAtomIterator CDPL::Chem::ElectronSystem::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.

◆ getAtomsEnd() [2/2]

AtomIterator CDPL::Chem::ElectronSystem::getAtomsEnd ( )

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

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

◆ clear()

void CDPL::Chem::ElectronSystem::clear ( )

Removes all atoms.

◆ orderAtoms()

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

virtual

Orders the stored 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.

◆ addAtom()

bool CDPL::Chem::ElectronSystem::addAtom	(	const Chem::Atom &	atom,
		std::size_t	elec_contrib
	)

Extends the electron system by the specified atom and its electron contributions.

Parameters

atom	The atom to add.
elec_contrib	The number of electrons contributed by the added atom.

Returns: true if the atom was not already involved in this electron system and false, otherwise.

Note: If the atom is already part of the system no changes will be made.

◆ addAtoms()

bool CDPL::Chem::ElectronSystem::addAtoms ( const ElectronSystem & elec_sys )

Adds the atoms and associated electron contributions in the electron system elec_sys to this system.

The method is equivalent to repeatedly calling addAtom() for each atom in elec_sys.

Parameters

elec_sys The electron system to add.

Returns: true if the electron system was extended by atoms from elec_sys and false, otherwise.

◆ removeAtom() [1/3]

void CDPL::Chem::ElectronSystem::removeAtom ( std::size_t idx )

Removes the atom at the specified index.

Parameters

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

Exceptions

Base::IndexError if the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

◆ removeAtom() [2/3]

AtomIterator CDPL::Chem::ElectronSystem::removeAtom ( const AtomIterator & it )

Removes the atom specified by the iterator it.

Parameters

it	An iterator that specifies the atom to remove.

Returns: A mutable iterator pointing to the next atom in the list.

Exceptions

Base::RangeError if the number of atoms is zero or it is not in the range [getAtomsBegin(), getAtomsEnd() - 1].

◆ removeAtom() [3/3]

bool CDPL::Chem::ElectronSystem::removeAtom ( const Atom & atom )

Removes the specified atom.

Parameters

atom	The atom to remove.

Returns: true if the atom was part of the electron system and has been removed, and false otherwise.

◆ getNumElectrons()

std::size_t CDPL::Chem::ElectronSystem::getNumElectrons ( ) const

Returns the total number of electrons contributed by the involved atoms.

Returns: The total electron count of this system.

◆ getElectronContrib() [1/2]

std::size_t CDPL::Chem::ElectronSystem::getElectronContrib ( const Atom & atom ) const

Returns the number of electrons contributed by the specified atom.

Parameters

atom	The atom for which to return the contributed electron count.

Returns: The number of electrons contributed by the specified atom.

Exceptions

Base::ItemNotFound if the specified atom is not part of the electron system.

◆ getElectronContrib() [2/2]

std::size_t CDPL::Chem::ElectronSystem::getElectronContrib ( std::size_t idx ) const

Returns the number of electrons contributed by the atom at the specified index.

Parameters

idx	The index of the atom for which to return the contributed electron count.

Returns: The number of electrons contributed by the specified atom.

Exceptions

Base::IndexError if the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

◆ setElectronContrib() [1/2]

void CDPL::Chem::ElectronSystem::setElectronContrib	(	const Atom &	atom,
		std::size_t	elec_contrib
	)

Changes the number of electrons that are contributed by the specified atom.

Parameters

atom	The atom for which to update the electron contribution.
elec_contrib	The number of electrons contributed by the specified atom.

Exceptions

Base::ItemNotFound if the specified atom is not part of the electron system.

◆ setElectronContrib() [2/2]

void CDPL::Chem::ElectronSystem::setElectronContrib	(	std::size_t	idx,
		std::size_t	elec_contrib
	)

Changes the number of electrons that are contributed by the atom at the specified index.

Parameters

idx	The index of the atom for which to update the electron contribution.
elec_contrib	The number of electrons contributed by the specified atom.

Exceptions

Base::IndexError if the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

◆ merge()

void CDPL::Chem::ElectronSystem::merge ( const ElectronSystem & elec_sys )

Merges the atoms and associated electron contributions in the electron system elec_sys with this system.

For atoms that are present in both electron systems, the resulting electron contribution will be the sum of their contributions to the respective systems!

Parameters

elec_sys The electron system to merge.

◆ overlaps()

bool CDPL::Chem::ElectronSystem::overlaps ( const ElectronSystem & elec_sys ) const

Checks if the electron system shares at least one atom with the system elec_sys.

Parameters

elec_sys The electron system to check for atom set intersection.

Returns: true if at least one atom in elec_sys is also part of this electron system and false, otherwise.

◆ contains()

bool CDPL::Chem::ElectronSystem::contains ( const ElectronSystem & elec_sys ) const

Checks if all atoms in the electron system elec_sys are also part of this electron system.

Parameters

elec_sys The electron system to check for atom set containment.

Returns: true if all atoms in elec_sys are also part of this electron system and false, otherwise.

◆ connected()

bool CDPL::Chem::ElectronSystem::connected	(	const ElectronSystem &	elec_sys,
		const BondContainer &	bonds
	)		const

Checks if the atom sets of the electron systems do not intersect but are linked by at least one bond.

Parameters

elec_sys	The electron system to check.
bonds	The set of available bonds.

Returns: true if the electron systems do not share any atoms but are linked by at least one bond and false, otherwise.

◆ swap()

void CDPL::Chem::ElectronSystem::swap ( ElectronSystem & elec_sys )

Exchanges the state of this electron system with the state of the system elec_sys.

Parameters

elec_sys The other ElectronSystem instance.

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

ElectronSystem.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstAtomIterator

◆ AtomIterator

Constructor & Destructor Documentation

◆ ElectronSystem()

Member Function Documentation

◆ getNumAtoms()

◆ containsAtom()

◆ getAtomIndex()

◆ getAtom() [1/2]

◆ getAtom() [2/2]

◆ getAtomsBegin() [1/2]

◆ getAtomsBegin() [2/2]

◆ getAtomsEnd() [1/2]

◆ getAtomsEnd() [2/2]

◆ clear()

◆ orderAtoms()

◆ addAtom()

◆ addAtoms()

◆ removeAtom() [1/3]

◆ removeAtom() [2/3]

◆ removeAtom() [3/3]

◆ getNumElectrons()

◆ getElectronContrib() [1/2]

◆ getElectronContrib() [2/2]

◆ setElectronContrib() [1/2]

◆ setElectronContrib() [2/2]

◆ merge()

◆ overlaps()

◆ contains()

◆ connected()

◆ swap()