Data structure representing a canonicalized molecular fragment. More...

#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
	A mutable iterator over the contained atoms. More...

typedef Chem::BasicMolecule::ConstAtomIterator	ConstAtomIterator
	A constant iterator over the contained atoms. More...

typedef Chem::BasicMolecule::BondIterator	BondIterator
	A mutable iterator over the contained bonds. More...

typedef Chem::BasicMolecule::ConstBondIterator	ConstBondIterator
	A constant iterator over the contained bonds. More...

typedef std::vector< const Chem::Atom * >	AtomMapping
	Maps each atom of the fragment (in canonical order) to the corresponding atom of the parent molecular graph. 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
	CanonicalFragment ()
	Constructs an empty `CanonicalFragment` instance. More...

	CanonicalFragment (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &parent)
	Constructs a `CanonicalFragment` instance from the fragment molgraph of the parent molecular graph parent. More...

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

void	clear ()
	Removes all atoms and bonds and resets the hash code. More...

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

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

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

ConstAtomIterator	getAtomsBegin () const
	Returns a constant iterator pointing to the first atom. More...

ConstAtomIterator	getAtomsEnd () const
	Returns a constant iterator pointing one past the last atom. More...

AtomIterator	getAtomsBegin ()
	Returns a mutable iterator pointing to the first atom. More...

AtomIterator	getAtomsEnd ()
	Returns a mutable iterator pointing one past the last atom. More...

bool	containsAtom (const Chem::Atom &atom) const
	Tells whether the fragment contains atom. More...

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

std::size_t	getNumEntities () const
	Returns the number of 3D entities in the fragment. More...

const Chem::Entity3D &	getEntity (std::size_t idx) const
	Returns a `const` reference to the 3D entity at index idx. More...

Chem::Entity3D &	getEntity (std::size_t idx)
	Returns a reference to the 3D entity at index idx. More...

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

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

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

ConstBondIterator	getBondsBegin () const
	Returns a constant iterator pointing to the first bond. More...

ConstBondIterator	getBondsEnd () const
	Returns a constant iterator pointing one past the last bond. More...

BondIterator	getBondsBegin ()
	Returns a mutable iterator pointing to the first bond. More...

BondIterator	getBondsEnd ()
	Returns a mutable iterator pointing one past the last bond. More...

bool	containsBond (const Chem::Bond &bond) const
	Tells whether the fragment contains bond. More...

std::size_t	getBondIndex (const Chem::Bond &bond) const
	Returns the index of bond in the fragment. More...

void	orderAtoms (const Chem::AtomCompareFunction &func)
	Reorders the atoms of the fragment according to func. More...

void	orderBonds (const Chem::BondCompareFunction &func)
	Reorders the bonds of the fragment according to func. More...

std::uint64_t	getHashCode () const
	Returns the hash code of the fragment. More...

Chem::MolecularGraph::SharedPointer	clone () const
	Creates and returns a deep copy of the fragment. More...

CanonicalFragment &	operator= (const CanonicalFragment &frag)
	Replaces the contents of this fragment with a copy of frag. More...

void	create (const Chem::MolecularGraph &molgraph, const Chem::MolecularGraph &parent, bool modify=true, bool strip_aro_subst=true)
	Builds the canonical fragment from the fragment molgraph of the parent molecular graph parent. More...

const AtomMapping &	getAtomMapping () const
	Returns the atom mapping from this fragment to the parent molecular graph. More...

void	perceiveSSSR ()
	Perceives the smallest set of smallest rings of the fragment. More...

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

Data structure representing a canonicalized molecular fragment.

A CanonicalFragment is constructed from a fragment of a parent molecular graph and stores a canonicalized copy of the fragment's atoms and bonds. Canonicalization yields a stable atom ordering and an associated hash code that uniquely identifies the topology (and, optionally, the stereochemistry) of the fragment.

See also: ConfGen::FragmentLibrary

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

A mutable iterator over the contained atoms.

◆ ConstAtomIterator

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

A constant iterator over the contained atoms.

◆ BondIterator

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

A mutable iterator over the contained bonds.

◆ ConstBondIterator

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

A constant iterator over the contained bonds.

◆ AtomMapping

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

Maps each atom of the fragment (in canonical order) to the corresponding atom of the parent molecular graph.

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 from the fragment molgraph of the parent molecular graph parent.

Parameters

molgraph	The molecular graph defining the fragment to canonicalize.
parent	The parent molecular graph the fragment was derived from.

◆ CanonicalFragment() [3/3]

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

Constructs a copy of the CanonicalFragment instance frag.

Parameters

frag	The `CanonicalFragment` to copy.

Member Function Documentation

◆ clear()

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

Removes all atoms and bonds and resets the hash code.

◆ getNumAtoms()

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

virtual

Returns the number of atoms in the fragment.

Returns: The number of atoms.

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 atom at index idx.

Parameters

idx	The index of the atom.

Returns: A const reference to the atom.

Implements CDPL::Chem::AtomContainer.

◆ getAtom() [2/2]

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

virtual

Returns a reference to the atom at index idx.

Parameters

idx	The index of the atom.

Returns: A reference to the atom.

Implements CDPL::Chem::AtomContainer.

◆ getAtomsBegin() [1/2]

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

Returns a constant iterator pointing to the first atom.

Returns: A constant iterator pointing to the first atom.

◆ getAtomsEnd() [1/2]

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

Returns a constant iterator pointing one past the last atom.

Returns: A constant iterator pointing one past the last atom.

◆ getAtomsBegin() [2/2]

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

Returns a mutable iterator pointing to the first atom.

Returns: A mutable iterator pointing to the first atom.

◆ getAtomsEnd() [2/2]

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

Returns a mutable iterator pointing one past the last atom.

Returns: A mutable iterator pointing one past the last atom.

◆ containsAtom()

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

virtual

Tells whether the fragment contains atom.

Parameters

atom	The atom to look up.

Returns: true if the atom is part of the fragment, 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 atom in the fragment.

Parameters

atom	The atom whose index is requested.

Returns: The index of the atom.

Implements CDPL::Chem::AtomContainer.

◆ getNumEntities()

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

virtual

Returns the number of 3D entities in the fragment.

Returns: The number of 3D entities (equal to getNumAtoms()).

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 3D entity at index idx.

Parameters

idx	The index of the entity.

Returns: A const reference to the entity.

Reimplemented from CDPL::Chem::AtomContainer.

◆ getEntity() [2/2]

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

virtual

Returns a reference to the 3D entity at index idx.

Parameters

idx	The index of the entity.

Returns: A reference to the entity.

Reimplemented from CDPL::Chem::AtomContainer.

◆ getNumBonds()

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

virtual

Returns the number of bonds in the fragment.

Returns: The number of bonds.

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 bond at index idx.

Parameters

idx	The index of the bond.

Returns: A const reference to the bond.

Implements CDPL::Chem::BondContainer.

◆ getBond() [2/2]

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

virtual

Returns a reference to the bond at index idx.

Parameters

idx	The index of the bond.

Returns: A reference to the bond.

Implements CDPL::Chem::BondContainer.

◆ getBondsBegin() [1/2]

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

Returns a constant iterator pointing to the first bond.

Returns: A constant iterator pointing to the first bond.

◆ getBondsEnd() [1/2]

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

Returns a constant iterator pointing one past the last bond.

Returns: A constant iterator pointing one past the last bond.

◆ getBondsBegin() [2/2]

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

Returns a mutable iterator pointing to the first bond.

Returns: A mutable iterator pointing to the first bond.

◆ getBondsEnd() [2/2]

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

Returns a mutable iterator pointing one past the last bond.

Returns: A mutable iterator pointing one past the last bond.

◆ containsBond()

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

virtual

Tells whether the fragment contains bond.

Parameters

bond	The bond to look up.

Returns: true if the bond is part of the fragment, 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 bond in the fragment.

Parameters

bond	The bond whose index is requested.

Returns: The index of the bond.

Implements CDPL::Chem::BondContainer.

◆ orderAtoms()

void CDPL::ConfGen::CanonicalFragment::orderAtoms ( const Chem::AtomCompareFunction & func )

virtual

Reorders the atoms of the fragment according to func.

Parameters

func	The comparison function used to define the new atom order.

Implements CDPL::Chem::AtomContainer.

◆ orderBonds()

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

virtual

Reorders the bonds of the fragment according to func.

Parameters

func	The comparison function used to define the new bond order.

Implements CDPL::Chem::BondContainer.

◆ getHashCode()

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

Returns the hash code of the fragment.

Returns: The fragment hash code (0 if not yet computed).

◆ clone()

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

virtual

Creates and returns a deep copy of the fragment.

Returns: A smart pointer to the cloned fragment.

Implements CDPL::Chem::MolecularGraph.

◆ operator=()

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

Replaces the contents of this fragment with a copy of frag.

Parameters

frag	The source `CanonicalFragment`.

Returns: A reference to itself.

◆ create()

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

Builds the canonical fragment from the fragment molgraph of the parent molecular graph parent.

Parameters

molgraph	The molecular graph defining the fragment to canonicalize.
parent	The parent molecular graph the fragment was derived from.
modify	If `true`, the fragment is modified prior to canonicalization (e.g. ring perception, hydrogenization).
strip_aro_subst	If `true`, aromatic-ring substituents are stripped during fragment construction.

◆ getAtomMapping()

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

Returns the atom mapping from this fragment to the parent molecular graph.

Returns: A const reference to the atom mapping.

◆ perceiveSSSR()

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

Perceives the smallest set of smallest rings of the fragment.

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()