#include <CanonicalFragment.hpp>

Inheritance diagram for CDPL::ConfGen::CanonicalFragment:

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

typedef Chem::BasicMolecule::AtomIterator	AtomIterator

typedef Chem::BasicMolecule::ConstAtomIterator	ConstAtomIterator

typedef Chem::BasicMolecule::BondIterator	BondIterator

typedef Chem::BasicMolecule::ConstBondIterator	ConstBondIterator

typedef std::vector< const Chem::Atom * >	AtomMapping

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
	CanonicalFragment ()
	Constructs an empty `CanonicalFragment` instance. More...

	CanonicalFragment (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &parent)
	Constructs a `CanonicalFragment` instance that contains the relevant atoms and bonds of the molecular graph molgraph. More...

	CanonicalFragment (const CanonicalFragment &frag)

void	clear ()

std::size_t	getNumAtoms () const
	Returns the number of stored Chem::Atom objects. More...

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

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

ConstAtomIterator	getAtomsBegin () const

ConstAtomIterator	getAtomsEnd () const

AtomIterator	getAtomsBegin ()

AtomIterator	getAtomsEnd ()

bool	containsAtom (const Chem::Atom &atom) const
	Tells whether the specified Chem::Atom instance is stored in this container. More...

std::size_t	getAtomIndex (const Chem::Atom &atom) const
	Returns the index of the specified Chem::Atom instance in this container. More...

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

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

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

std::size_t	getNumBonds () const
	Returns the number of stored Chem::Bond objects. More...

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

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

ConstBondIterator	getBondsBegin () const

ConstBondIterator	getBondsEnd () const

BondIterator	getBondsBegin ()

BondIterator	getBondsEnd ()

bool	containsBond (const Chem::Bond &bond) const
	Tells whether the specified Chem::Bond instance is stored in this container. More...

std::size_t	getBondIndex (const Chem::Bond &bond) const
	Returns the index of the specified Chem::Bond instance in this container. More...

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

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

std::uint64_t	getHashCode () const

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

CanonicalFragment &	operator= (const CanonicalFragment &frag)

void	create (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &parent, bool modify=true, bool strip_aro_subst=true)

const AtomMapping &	getAtomMapping () const

void	perceiveSSSR ()

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...

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

CanonicalFragment.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<CanonicalFragment> CDPL::ConfGen::CanonicalFragment::SharedPointer

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

◆ AtomIterator

typedef Chem::BasicMolecule::AtomIterator CDPL::ConfGen::CanonicalFragment::AtomIterator

◆ ConstAtomIterator

typedef Chem::BasicMolecule::ConstAtomIterator CDPL::ConfGen::CanonicalFragment::ConstAtomIterator

◆ BondIterator

typedef Chem::BasicMolecule::BondIterator CDPL::ConfGen::CanonicalFragment::BondIterator

◆ ConstBondIterator

typedef Chem::BasicMolecule::ConstBondIterator CDPL::ConfGen::CanonicalFragment::ConstBondIterator

◆ AtomMapping

typedef std::vector<const Chem::Atom*> CDPL::ConfGen::CanonicalFragment::AtomMapping

Constructor & Destructor Documentation

◆ CanonicalFragment() [1/3]

CDPL::ConfGen::CanonicalFragment::CanonicalFragment ( )

Constructs an empty CanonicalFragment instance.

◆ CanonicalFragment() [2/3]

CDPL::ConfGen::CanonicalFragment::CanonicalFragment	(	const Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph &	parent
	)

Constructs a CanonicalFragment instance that contains the relevant atoms and bonds of the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to generate the fragments.
parent	The parent molecular graph the fragment is coming from.

◆ CanonicalFragment() [3/3]

CDPL::ConfGen::CanonicalFragment::CanonicalFragment ( const CanonicalFragment & frag )

Member Function Documentation

◆ clear()

void CDPL::ConfGen::CanonicalFragment::clear ( )

◆ getNumAtoms()

std::size_t CDPL::ConfGen::CanonicalFragment::getNumAtoms ( ) const

virtual

Returns the number of stored Chem::Atom objects.

Returns: The number of stored Chem::Atom objects.

Implements CDPL::Chem::AtomContainer.

◆ getAtom() [1/2]

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

virtual

Returns a const reference to the Chem::Atom instance at index idx.

Parameters

idx	The zero-based index of the Chem::Atom instance to return.

Returns: A const reference to the Chem::Atom instance at the specified index.

Exceptions

Base::IndexError if the container is empty or idx is not in the range [0, getNumAtoms() - 1].

Implements CDPL::Chem::AtomContainer.

◆ getAtom() [2/2]

Chem::Atom& CDPL::ConfGen::CanonicalFragment::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 Chem::Atom instance 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::ConfGen::CanonicalFragment::getAtomsBegin ( ) const

◆ getAtomsEnd() [1/2]

ConstAtomIterator CDPL::ConfGen::CanonicalFragment::getAtomsEnd ( ) const

◆ getAtomsBegin() [2/2]

AtomIterator CDPL::ConfGen::CanonicalFragment::getAtomsBegin ( )

◆ getAtomsEnd() [2/2]

AtomIterator CDPL::ConfGen::CanonicalFragment::getAtomsEnd ( )

◆ containsAtom()

bool CDPL::ConfGen::CanonicalFragment::containsAtom ( const Chem::Atom & atom ) const

virtual

Tells whether the specified Chem::Atom instance is stored in this container.

Parameters

atom	The Chem::Atom instance to look for.

Returns: true if atom is stored in the container, and false otherwise.

Implements CDPL::Chem::AtomContainer.

◆ getAtomIndex()

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

virtual

Returns the index of the specified Chem::Atom instance in this container.

Parameters

atom	The Chem::Atom instance for which to return the index.

Returns: The zero-based index of the specified Chem::Atom instance.

Exceptions

Base::ItemNotFound if the specified Chem::Atom instance could not be found.

Implements CDPL::Chem::AtomContainer.

◆ getNumEntities()

std::size_t CDPL::ConfGen::CanonicalFragment::getNumEntities ( ) const

virtual

Returns the number of stored Chem::Entity3D objects.

Returns: The number of stored Chem::Entity3D objects.

Reimplemented from CDPL::Chem::AtomContainer.

◆ getEntity() [1/2]

const Chem::Entity3D& CDPL::ConfGen::CanonicalFragment::getEntity ( std::size_t idx ) const

virtual

Returns a const reference to the Chem::Entity3D instance at index idx.

Parameters

idx	The zero-based index of the Chem::Entity3D instance to return.

Returns: A const reference to the Chem::Entity3D instance at the specified index.

Exceptions

Base::IndexError if the container is empty or idx is not in the range [0, getNumEntities() - 1].

Reimplemented from CDPL::Chem::AtomContainer.

◆ getEntity() [2/2]

Chem::Entity3D& CDPL::ConfGen::CanonicalFragment::getEntity ( std::size_t idx )

virtual

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

Parameters

idx	The zero-based index of the Chem::Entity3D instance to return.

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

Exceptions

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

Reimplemented from CDPL::Chem::AtomContainer.

◆ getNumBonds()

std::size_t CDPL::ConfGen::CanonicalFragment::getNumBonds ( ) const

virtual

Returns the number of stored Chem::Bond objects.

Returns: The number of stored Chem::Bond objects.

Implements CDPL::Chem::BondContainer.

◆ getBond() [1/2]

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

virtual

Returns a const reference to the Chem::Bond instance at index idx.

Parameters

idx	The zero-based index of the Chem::Bond instance to return.

Returns: A const reference to the Chem::Bond instance at the specified index.

Exceptions

Base::IndexError if the container is empty or idx is not in the range [0, getNumBonds() - 1].

Implements CDPL::Chem::BondContainer.

◆ getBond() [2/2]

Chem::Bond& CDPL::ConfGen::CanonicalFragment::getBond ( std::size_t idx )

virtual

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

Parameters

idx	The zero-based index of the Chem::Bond instance to return.

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

Exceptions

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

Implements CDPL::Chem::BondContainer.

◆ getBondsBegin() [1/2]

ConstBondIterator CDPL::ConfGen::CanonicalFragment::getBondsBegin ( ) const

◆ getBondsEnd() [1/2]

ConstBondIterator CDPL::ConfGen::CanonicalFragment::getBondsEnd ( ) const

◆ getBondsBegin() [2/2]

BondIterator CDPL::ConfGen::CanonicalFragment::getBondsBegin ( )

◆ getBondsEnd() [2/2]

BondIterator CDPL::ConfGen::CanonicalFragment::getBondsEnd ( )

◆ containsBond()

bool CDPL::ConfGen::CanonicalFragment::containsBond ( const Chem::Bond & bond ) const

virtual

Tells whether the specified Chem::Bond instance is stored in this container.

Parameters

bond	The Chem::Bond instance to look for.

Returns: true if bond is stored in the container, and false otherwise.

Implements CDPL::Chem::BondContainer.

◆ getBondIndex()

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

virtual

Returns the index of the specified Chem::Bond instance in this container.

Parameters

bond	The Chem::Bond instance for which to return the index.

Returns: The zero-based index of the specified Chem::Bond instance.

Exceptions

Base::ItemNotFound if the specified Chem::Bond instance could not be found.

Implements CDPL::Chem::BondContainer.

◆ orderAtoms()

void CDPL::ConfGen::CanonicalFragment::orderAtoms ( const Chem::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.

◆ orderBonds()

void CDPL::ConfGen::CanonicalFragment::orderBonds ( const Chem::BondCompareFunction & func )

virtual

Orders the stored 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.

◆ getHashCode()

std::uint64_t CDPL::ConfGen::CanonicalFragment::getHashCode ( ) const

◆ clone()

Chem::MolecularGraph::SharedPointer CDPL::ConfGen::CanonicalFragment::clone ( ) const

virtual

Creates a copy of the molecular graph.

Returns: A smart pointer to the copy of the molecular graph.

Implements CDPL::Chem::MolecularGraph.

◆ operator=()

CanonicalFragment& CDPL::ConfGen::CanonicalFragment::operator= ( const CanonicalFragment & frag )

◆ create()

void CDPL::ConfGen::CanonicalFragment::create	(	const Chem::MolecularGraph &	molgraph,
		const Chem::MolecularGraph &	parent,
		bool	modify = `true`,
		bool	strip_aro_subst = `true`
	)

◆ getAtomMapping()

const AtomMapping& CDPL::ConfGen::CanonicalFragment::getAtomMapping ( ) const

◆ perceiveSSSR()

void CDPL::ConfGen::CanonicalFragment::perceiveSSSR ( )

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

CanonicalFragment.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ AtomIterator

◆ ConstAtomIterator

◆ BondIterator

◆ ConstBondIterator

◆ AtomMapping

Constructor & Destructor Documentation

◆ CanonicalFragment() [1/3]

◆ CanonicalFragment() [2/3]

◆ CanonicalFragment() [3/3]

Member Function Documentation

◆ clear()

◆ getNumAtoms()

◆ getAtom() [1/2]

◆ getAtom() [2/2]

◆ getAtomsBegin() [1/2]

◆ getAtomsEnd() [1/2]

◆ getAtomsBegin() [2/2]

◆ getAtomsEnd() [2/2]

◆ containsAtom()

◆ getAtomIndex()

◆ getNumEntities()

◆ getEntity() [1/2]

◆ getEntity() [2/2]

◆ getNumBonds()

◆ getBond() [1/2]

◆ getBond() [2/2]

◆ getBondsBegin() [1/2]

◆ getBondsEnd() [1/2]

◆ getBondsBegin() [2/2]

◆ getBondsEnd() [2/2]

◆ containsBond()

◆ getBondIndex()

◆ orderAtoms()

◆ orderBonds()

◆ getHashCode()

◆ clone()

◆ operator=()

◆ create()

◆ getAtomMapping()

◆ perceiveSSSR()