Concrete implementation of the Chem::MolecularGraph interface that stores references to selectable Chem::Atom and Chem::Bond instances. More...

#include <Fragment.hpp>

Inheritance diagram for CDPL::Chem::Fragment:

Public Types
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 referenced `const` Chem::Atom instances. More...

typedef boost::indirect_iterator< AtomList::iterator, Atom >	AtomIterator
	A mutable random access iterator used to iterate over the referenced Chem::Atom instances. More...

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

typedef boost::indirect_iterator< BondList::iterator, Bond >	BondIterator
	A mutable random access iterator used to iterate over the referenced Chem::Bond instances. 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 instances. More...

typedef Util::IndexedElementIterator< Atom, AtomAccessor >	AtomIterator
	A mutable random access iterator used to iterate over the stored Chem::Atom instances. 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 instances. More...

typedef Util::IndexedElementIterator< Entity3D, EntityAccessor >	EntityIterator
	A mutable random access iterator used to iterate over the stored Chem::Entity3D instances. 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 instances. More...

typedef Util::IndexedElementIterator< Bond, BondAccessor >	BondIterator
	A mutable random access iterator used to iterate over the stored Chem::Bond instances. 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
	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 the atom sequence. More...

bool	containsBond (const Bond &bond) const
	Tells whether the specified bond is part of the bond sequence. 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 referenced `const` Chem::Atom instances. More...

AtomIterator	getAtomsBegin ()
	Returns a mutable iterator pointing to the beginning of the referenced Chem::Atom instances. More...

ConstAtomIterator	getAtomsEnd () const
	Returns a constant iterator pointing to the end of the referenced `const` Chem::Atom instances. More...

AtomIterator	getAtomsEnd ()
	Returns a mutable iterator pointing to the end of the referenced Chem::Atom instances. More...

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

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

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

BondIterator	getBondsEnd ()
	Returns a mutable iterator pointing to the end of the referenced Chem::Bond instances. 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 atoms according to criteria implemented by the provided atom comparison function. More...

void	orderBonds (const BondCompareFunction &func)
	Orders the 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 of 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 deep copy of the molecular graph. More...

void	reserveMemoryForAtoms (std::size_t num_atoms)
	Reserves storage for at least num_atoms atom references to avoid reallocations on subsequent additions. More...

void	reserveMemoryForBonds (std::size_t num_bonds)
	Reserves storage for at least num_bonds bond references to avoid reallocations on subsequent additions. 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 instances. More...

ConstAtomIterator	getAtomsEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Atom instances. More...

AtomIterator	getAtomsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Atom instances. More...

AtomIterator	getAtomsEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Atom instances. More...

ConstAtomIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Atom instances. More...

ConstAtomIterator	end () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Atom instances. More...

AtomIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Atom instances. More...

AtomIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Atom instances. More...

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

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

virtual Chem::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 instances. More...

ConstEntityIterator	getEntitiesEnd () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Entity3D instances. More...

EntityIterator	getEntitiesBegin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D instances. More...

EntityIterator	getEntitiesEnd ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D instances. More...

ConstEntityIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Entity3D instances. More...

ConstEntityIterator	end () const
	Returns a constant iterator pointing to the end of the stored `const` Chem::Entity3D instances. More...

EntityIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored Chem::Entity3D instances. More...

EntityIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Entity3D instances. 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 instances. More...

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

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

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

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

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

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

BondIterator	end ()
	Returns a mutable iterator pointing to the end of the stored Chem::Bond instances. 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 an entry 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)
	Removes the entry for the property specified by key. More...

void	clearProperties ()
	Erases all container entries. More...

void	addProperties (const PropertyContainer &cntnr)
	Adds the property entries of the `PropertyContainer` instance cntnr. More...

void	copyProperties (const PropertyContainer &cntnr)
	Replaces the current property entries by a copy of the entries in cntnr. More...

void	swap (PropertyContainer &cntnr)
	Exchanges the property entries of this container with the ones of 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)
	Replaces the current set of properties by a copy of the properties of the container cntnr. 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)
	Replaces the current set of properties by a copy of the properties of the container cntnr. 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

Concrete implementation of the Chem::MolecularGraph interface that stores references to selectable Chem::Atom and Chem::Bond instances.

Atoms and bonds are added via addAtom() / addBond() and removed via removeAtom() / removeBond(). Adding a bond automatically adds its end atoms when needed and removing an atom automatically removes any referenced incident bonds. Unlike a Chem::Molecule instance, a Fragment instance does not own its atoms and bonds. It is typically used to represent substructures comprising atoms and bonds that live elsewhere.

Note: Since Fragment does not own the referenced atoms or bonds they must outlive any Fragment instance that references them!

Member Typedef Documentation

◆ SharedPointer

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

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

◆ ConstAtomIterator

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

A constant random access iterator used to iterate over the referenced const Chem::Atom instances.

◆ AtomIterator

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

A mutable random access iterator used to iterate over the referenced Chem::Atom instances.

◆ ConstBondIterator

typedef boost::indirect_iterator<BondList::const_iterator, const Bond> CDPL::Chem::Fragment::ConstBondIterator

A constant random access iterator used to iterate over the referenced const Chem::Bond instances.

◆ BondIterator

typedef boost::indirect_iterator<BondList::iterator, Bond> CDPL::Chem::Fragment::BondIterator

A mutable random access iterator used to iterate over the referenced Chem::Bond instances.

Constructor & Destructor Documentation

◆ Fragment() [1/3]

CDPL::Chem::Fragment::Fragment ( )

Constructs an empty Fragment instance.

◆ Fragment() [2/3]

CDPL::Chem::Fragment::Fragment ( const Fragment & frag )

Constructs a copy of the Fragment instance frag.

Parameters

frag	The other `Fragment` instance to copy.

◆ Fragment() [3/3]

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

explicit

Constructs a Fragment instance storing the atoms, bonds and properties of the molecular graph molgraph.

Parameters

molgraph The Chem::MolecularGraph instance providing the atoms, bonds and properties to store.

◆ ~Fragment()

CDPL::Chem::Fragment::~Fragment ( )

Destructor.

Destroys the Fragment instance and frees all allocated resources.

Member Function Documentation

◆ getNumAtoms()

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

virtual

Returns the number of atoms.

Returns: The number of atoms.

Implements CDPL::Chem::AtomContainer.

◆ getNumBonds()

std::size_t CDPL::Chem::Fragment::getNumBonds ( ) const

virtual

Returns the number of bonds.

Returns: The number of bonds.

Implements CDPL::Chem::BondContainer.

◆ containsAtom()

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

virtual

Tells whether the specified atom is part of the atom sequence.

Parameters

atom	The atom to look for.

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

Implements CDPL::Chem::AtomContainer.

◆ containsBond()

bool CDPL::Chem::Fragment::containsBond ( const Bond & bond ) const

virtual

Tells whether the specified bond is part of the bond sequence.

Parameters

bond	The bond to look for.

Returns: true if bond is part of the sequence, and false otherwise.

Implements CDPL::Chem::BondContainer.

◆ getAtomIndex()

std::size_t CDPL::Chem::Fragment::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 could not be found.

Implements CDPL::Chem::AtomContainer.

◆ getBondIndex()

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

virtual

Returns the index of the specified bond.

Parameters

bond	The bond for which to return the index.

Returns: The zero-based index of the specified bond.

Exceptions

Base::ItemNotFound if the specified bond could not be found.

Implements CDPL::Chem::BondContainer.

◆ getAtomsBegin() [1/2]

ConstAtomIterator CDPL::Chem::Fragment::getAtomsBegin ( ) const

Returns a constant iterator pointing to the beginning of the referenced const Chem::Atom instances.

Returns: A constant iterator pointing to the beginning of the referenced const Chem::Atom instances.

◆ getAtomsBegin() [2/2]

AtomIterator CDPL::Chem::Fragment::getAtomsBegin ( )

Returns a mutable iterator pointing to the beginning of the referenced Chem::Atom instances.

Returns: A mutable iterator pointing to the beginning of the referenced Chem::Atom instances.

◆ getAtomsEnd() [1/2]

ConstAtomIterator CDPL::Chem::Fragment::getAtomsEnd ( ) const

Returns a constant iterator pointing to the end of the referenced const Chem::Atom instances.

Returns: A constant iterator pointing to the end of the referenced const Chem::Atom instances.

◆ getAtomsEnd() [2/2]

AtomIterator CDPL::Chem::Fragment::getAtomsEnd ( )

Returns a mutable iterator pointing to the end of the referenced Chem::Atom instances.

Returns: A mutable iterator pointing to the end of the referenced Chem::Atom instances.

◆ getBondsBegin() [1/2]

ConstBondIterator CDPL::Chem::Fragment::getBondsBegin ( ) const

Returns a constant iterator pointing to the beginning of the referenced const Chem::Bond instances.

Returns: A constant iterator pointing to the beginning of the referenced const Chem::Bond instances.

◆ getBondsBegin() [2/2]

BondIterator CDPL::Chem::Fragment::getBondsBegin ( )

Returns a mutable iterator pointing to the beginning of the referenced Chem::Bond instances.

Returns: A mutable iterator pointing to the beginning of the referenced Chem::Bond instances.

◆ getBondsEnd() [1/2]

ConstBondIterator CDPL::Chem::Fragment::getBondsEnd ( ) const

Returns a constant iterator pointing to the end of the referenced const Chem::Bond instances.

Returns: A constant iterator pointing to the end of the referenced const Chem::Bond instances.

◆ getBondsEnd() [2/2]

BondIterator CDPL::Chem::Fragment::getBondsEnd ( )

Returns a mutable iterator pointing to the end of the referenced Chem::Bond instances.

Returns: A mutable iterator pointing to the end of the referenced Chem::Bond instances.

◆ getAtom() [1/2]

const Atom& CDPL::Chem::Fragment::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 idx is not in the range [0, getNumAtoms()).

Implements CDPL::Chem::AtomContainer.

◆ getAtom() [2/2]

Atom& CDPL::Chem::Fragment::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 idx is not in the range [0, getNumAtoms()).

Implements CDPL::Chem::AtomContainer.

◆ getBond() [1/2]

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

virtual

Returns a const reference to the bond at index idx.

Parameters

idx	The zero-based index of the bond to return.

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

Exceptions

Base::IndexError if idx is not in the range [0, getNumBonds()).

Implements CDPL::Chem::BondContainer.

◆ getBond() [2/2]

Bond& CDPL::Chem::Fragment::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 bond to return.

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

Exceptions

Base::IndexError if idx is not in the range [0, getNumBonds()).

Implements CDPL::Chem::BondContainer.

◆ addAtom()

bool CDPL::Chem::Fragment::addAtom ( const Atom & atom )

Extends the fragment by the specified atom.

Parameters

atom	The atom to add.

Returns: true if the atom was not already a part of the fragment, and false otherwise.

◆ addBond()

bool CDPL::Chem::Fragment::addBond ( const Bond & bond )

Extends the fragment by the specified bond.

If the atoms of the bond are not already part of the fragment, they will be added automatically.

Parameters

bond	The bond to add.

Returns: true if the bond was not already a part of the fragment, and false otherwise.

◆ removeAtom() [1/3]

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

Removes the atom at the specified index.

If the specified atom is connected to any other atoms of the fragment, the connecting bonds will also be removed.

Parameters

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

Exceptions

Base::IndexError if idx is not in the range [0, getNumAtoms()).

◆ removeAtom() [2/3]

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

Removes the atom specified by the iterator it.

If the specified atom is connected to any other atoms of the fragment, the connecting bonds will also be removed.

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 it is not in the range [getAtomsBegin(), getAtomsEnd()).

◆ removeAtom() [3/3]

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

Removes the specified atom.

If the specified atom is connected to any other atoms of the fragment, the connecting bonds will also be removed.

Parameters

atom	The atom to remove.

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

◆ removeBond() [1/3]

void CDPL::Chem::Fragment::removeBond ( std::size_t idx )

Removes the bond at the specified index.

Parameters

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

Exceptions

Base::IndexError if idx is not in the range [0, getNumBonds()).

◆ removeBond() [2/3]

BondIterator CDPL::Chem::Fragment::removeBond ( const BondIterator & it )

Removes the bond specified by the iterator it.

Parameters

it	An iterator that specifies the bond to remove.

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

Exceptions

Base::RangeError if it is not in the range [getBondsBegin(), getBondsEnd()).

◆ removeBond() [3/3]

bool CDPL::Chem::Fragment::removeBond ( const Bond & bond )

Removes the specified bond.

Parameters

bond	The bond to remove.

Returns: true if the bond was removed, and false otherwise.

◆ clear()

void CDPL::Chem::Fragment::clear ( )

Removes all atoms and bonds.

◆ swap()

void CDPL::Chem::Fragment::swap ( Fragment & frag )

Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag.

Parameters

frag	The fragment the atoms, bonds and properties get exchanged with.

◆ orderAtoms()

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

virtual

Orders the 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::Chem::Fragment::orderBonds ( const BondCompareFunction & func )

virtual

Orders the 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.

◆ operator=() [1/2]

Fragment& CDPL::Chem::Fragment::operator= ( const Fragment & frag )

Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag.

Parameters

frag	The fragment to copy.

Returns: A reference to itself.

◆ operator=() [2/2]

Fragment& CDPL::Chem::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.

Parameters

molgraph The molecular graph providing the atoms, bonds and properties to copy.

Returns: A reference to itself.

◆ operator+=()

Fragment& CDPL::Chem::Fragment::operator+= ( const MolecularGraph & molgraph )

Extends the current set of atoms and bonds by the atoms and bonds of the molecular graph molgraph.

Parameters

molgraph The molecular graph providing the atoms and bonds to add.

Returns: A reference to itself.

Note: Does not affect any properties.

◆ operator-=()

Fragment& CDPL::Chem::Fragment::operator-= ( const MolecularGraph & molgraph )

Removes the atoms and bonds referenced by the molecular graph molgraph from this Fragment instance.

Parameters

molgraph The molecular graph providing the atoms and bonds to remove.

Returns: A reference to itself.

Note: Does not affect any properties if this != &molgraph.

◆ clone()

MolecularGraph::SharedPointer CDPL::Chem::Fragment::clone ( ) const

virtual

Creates a deep copy of the molecular graph.

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

Implements CDPL::Chem::MolecularGraph.

◆ reserveMemoryForAtoms()

void CDPL::Chem::Fragment::reserveMemoryForAtoms ( std::size_t num_atoms )

Reserves storage for at least num_atoms atom references to avoid reallocations on subsequent additions.

Parameters

num_atoms The minimum number of atom references to accommodate.

◆ reserveMemoryForBonds()

void CDPL::Chem::Fragment::reserveMemoryForBonds ( std::size_t num_bonds )

Reserves storage for at least num_bonds bond references to avoid reallocations on subsequent additions.

Parameters

num_bonds The minimum number of bond references to accommodate.

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

Fragment.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstAtomIterator

◆ AtomIterator

◆ ConstBondIterator

◆ BondIterator

Constructor & Destructor Documentation

◆ Fragment() [1/3]

◆ Fragment() [2/3]

◆ Fragment() [3/3]

◆ ~Fragment()

Member Function Documentation

◆ getNumAtoms()

◆ getNumBonds()

◆ containsAtom()

◆ containsBond()

◆ getAtomIndex()

◆ getBondIndex()

◆ getAtomsBegin() [1/2]

◆ getAtomsBegin() [2/2]

◆ getAtomsEnd() [1/2]

◆ getAtomsEnd() [2/2]

◆ getBondsBegin() [1/2]

◆ getBondsBegin() [2/2]

◆ getBondsEnd() [1/2]

◆ getBondsEnd() [2/2]

◆ getAtom() [1/2]

◆ getAtom() [2/2]

◆ getBond() [1/2]

◆ getBond() [2/2]

◆ addAtom()

◆ addBond()

◆ removeAtom() [1/3]

◆ removeAtom() [2/3]

◆ removeAtom() [3/3]

◆ removeBond() [1/3]

◆ removeBond() [2/3]

◆ removeBond() [3/3]

◆ clear()

◆ swap()

◆ orderAtoms()

◆ orderBonds()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator+=()

◆ operator-=()

◆ clone()

◆ reserveMemoryForAtoms()

◆ reserveMemoryForBonds()