Implements the perception of aromatic atoms and bonds in a molecular graph. More...

#include <AromaticSubstructure.hpp>

Inheritance diagram for CDPL::Chem::AromaticSubstructure:

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

Public Types inherited from CDPL::Chem::Fragment
typedef std::shared_ptr< Fragment >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `Fragment` 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...

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

typedef boost::indirect_iterator< BondList::iterator, Bond >	BondIterator
	A mutable random access iterator used to iterate over the stored `const` Chem::Bond objects. More...

Public Types inherited from CDPL::Chem::MolecularGraph
typedef std::shared_ptr< MolecularGraph >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MolecularGraph` 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 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::Chem::BondContainer
typedef Util::IndexedElementIterator< const Bond, ConstBondAccessor >	ConstBondIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Bond objects. More...

typedef Util::IndexedElementIterator< Bond, BondAccessor >	BondIterator
	A mutable random access iterator used to iterate over the stored Chem::Bond 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
	AromaticSubstructure ()
	Constructs an empty `AromaticSubstructure` instance. More...

	AromaticSubstructure (const MolecularGraph &molgraph)
	Construct a `AromaticSubstructure` instance that consists of the aromatic atoms and bonds of the molecular graph molgraph. More...

void	perceive (const MolecularGraph &molgraph)
	Replaces the currently stored atoms and bonds by the set of aromatic atoms and bonds of the molecular graph molgraph. More...

Public Member Functions inherited from CDPL::Chem::Fragment
	Fragment ()
	Constructs an empty `Fragment` instance. More...

	Fragment (const Fragment &frag)
	Constructs a copy of the `Fragment` instance frag. More...

	Fragment (const MolecularGraph &molgraph)
	Constructs a `Fragment` instance storing the atoms, bonds and properties of the molecular graph molgraph. More...

	~Fragment ()
	Destructor. More...

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

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

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

bool	containsBond (const Bond &bond) const
	Tells whether the specified bond is part of this fragment. More...

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

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

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

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

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

BondIterator	getBondsEnd ()
	Returns a mutable iterator pointing to the end of the stored `const` Chem::Bond objects. 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...

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

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

bool	addAtom (const Atom &atom)
	Extends the fragment by the specified atom. More...

bool	addBond (const Bond &bond)
	Extends the fragment by the specified bond. 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...

void	removeBond (std::size_t idx)
	Removes the bond at the specified index. More...

BondIterator	removeBond (const BondIterator &it)
	Removes the bond specified by the iterator it. More...

bool	removeBond (const Bond &bond)
	Removes the specified bond. More...

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

void	swap (Fragment &frag)
	Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag. More...

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

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

Fragment &	operator= (const Fragment &frag)
	Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag. More...

Fragment &	operator= (const MolecularGraph &molgraph)
	Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph. More...

Fragment &	operator+= (const MolecularGraph &molgraph)
	Extends the current set of atoms and bonds by the atoms and bonds in the molecular graph molgraph. More...

Fragment &	operator-= (const MolecularGraph &molgraph)
	Removes the atoms and bonds referenced by the molecular graph molgraph from this `Fragment` instance. More...

MolecularGraph::SharedPointer	clone () const
	Creates a copy of the molecular graph. More...

void	reserveMemoryForAtoms (std::size_t num_atoms)

void	reserveMemoryForBonds (std::size_t num_bonds)

Public Member Functions inherited from CDPL::Chem::MolecularGraph
virtual	~MolecularGraph ()
	Virtual destructor. 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...

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 objects. More...

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

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

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

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

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

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

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

Additional Inherited Members
Protected Member Functions inherited from CDPL::Chem::MolecularGraph
MolecularGraph &	operator= (const MolecularGraph &molgraph)
	Assignment operator. 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::Chem::BondContainer
virtual	~BondContainer ()
	Virtual destructor. More...

BondContainer &	operator= (const BondContainer &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

Implements the perception of aromatic atoms and bonds in a molecular graph.

Member Typedef Documentation

◆ SharedPointer

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

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

Constructor & Destructor Documentation

◆ AromaticSubstructure() [1/2]

CDPL::Chem::AromaticSubstructure::AromaticSubstructure ( )

inline

Constructs an empty AromaticSubstructure instance.

◆ AromaticSubstructure() [2/2]

CDPL::Chem::AromaticSubstructure::AromaticSubstructure ( const MolecularGraph & molgraph )

Construct a AromaticSubstructure instance that consists of the aromatic atoms and bonds of the molecular graph molgraph.

Parameters

molgraph The molecular graph for which to perceive aromatic atoms and bonds.

Member Function Documentation

◆ perceive()

void CDPL::Chem::AromaticSubstructure::perceive ( const MolecularGraph & molgraph )

Replaces the currently stored atoms and bonds by the set of aromatic atoms and bonds of the molecular graph molgraph.