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

#include <CyclicSubstructure.hpp>

Inheritance diagram for CDPL::Chem::CyclicSubstructure:

Public Types
typedef std::shared_ptr< CyclicSubstructure >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `CyclicSubstructure` 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
	CyclicSubstructure ()
	Constructs an empty `CyclicSubstructure` instance. More...

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

	CyclicSubstructure (const CyclicSubstructure &)=delete

CyclicSubstructure &	operator= (const CyclicSubstructure &)=delete

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

Member Typedef Documentation

◆ SharedPointer

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

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

Constructor & Destructor Documentation

◆ CyclicSubstructure() [1/3]

CDPL::Chem::CyclicSubstructure::CyclicSubstructure ( )

inline

Constructs an empty CyclicSubstructure instance.

◆ CyclicSubstructure() [2/3]

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

Construct a CyclicSubstructure instance that consists of the ring atoms and bonds of the molecular graph molgraph.

Parameters

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

◆ CyclicSubstructure() [3/3]

CDPL::Chem::CyclicSubstructure::CyclicSubstructure ( const CyclicSubstructure & )

delete

Member Function Documentation

◆ operator=()

CyclicSubstructure& CDPL::Chem::CyclicSubstructure::operator= ( const CyclicSubstructure & )

delete

◆ perceive()

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

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