Default implementation of the Chem::Molecule interface. More...

#include <BasicMolecule.hpp>

Inheritance diagram for CDPL::Chem::BasicMolecule:

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

typedef boost::indirect_iterator< AtomList::iterator, BasicAtom >	AtomIterator
	A mutable random access iterator used to iterate over the stored Chem::BasicAtom objects. More...

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

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

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

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

typedef AtomContainer::ConstAtomIterator	ConstAtomIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Atom objects. More...

typedef AtomContainer::AtomIterator	AtomIterator
	A mutable random access iterator used to iterate over the stored Chem::Atom objects. More...

typedef BondContainer::ConstBondIterator	ConstBondIterator
	A constant random access iterator used to iterate over the stored `const` Chem::Bond objects. More...

typedef BondContainer::BondIterator	BondIterator
	A mutable random access iterator used to iterate over the stored Chem::Bond objects. More...

typedef std::function< void(Molecule &, const MolecularGraph &)>	CopyPostprocessingFunction
	Type of function invoked after a molecule has been altered due to copying/appending a source 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
	BasicMolecule ()
	Constructs an empty `BasicMolecule` instance. More...

	BasicMolecule (const BasicMolecule &mol)
	Constructs a `BasicMolecule` instance that is a copy of the molecule mol. More...

	BasicMolecule (const Molecule &mol)
	Constructs a `BasicMolecule` instance that is a copy of the molecule mol. More...

	BasicMolecule (const MolecularGraph &molgraph)
	Constructs a `BasicMolecule` instance with copies of the atoms, bonds and properties provided by the molecular graph molgraph. More...

	~BasicMolecule ()
	Destructor. More...

void	clear ()
	Removes all atoms and bonds and clears all properties of the molecule. More...

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

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

ConstAtomIterator	getAtomsBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::BasicAtom objects. More...

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

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

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

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

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

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

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

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

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

BasicAtom &	addAtom ()
	Creates a new atom and adds it to the molecule. 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...

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

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

BasicBond &	addBond (std::size_t atom1_idx, std::size_t atom2_idx)
	Creates a new or returns an already existing bond between the atoms specified by atom1_idx and atom2_idx. 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	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...

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...

BasicMolecule &	operator= (const BasicMolecule &mol)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

BasicMolecule &	operator+= (const BasicMolecule &mol)
	Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More...

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

void	copy (const BasicMolecule &mol)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

void	copy (const Molecule &mol)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

void	copy (const MolecularGraph &molgraph)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecular graph molgraph. More...

void	append (const BasicMolecule &mol)
	Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More...

void	append (const Molecule &mol)
	Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More...

void	append (const MolecularGraph &molgraph)
	Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecular graph molgraph. More...

void	remove (const MolecularGraph &molgraph)
	Removes atoms and bonds referenced by the molecular graph molgraph that are part of this `Molecule` instance. More...

void	reserveMemoryForAtoms (std::size_t num_atoms)
	Reserves memory for num_atoms atoms. More...

void	reserveMemoryForBonds (std::size_t num_bonds)
	Reserves memory for num_bonds bonds. More...

Molecule &	operator= (const Molecule &mol)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

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

Molecule &	operator+= (const Molecule &mol)
	Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More...

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

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

AtomIterator	removeAtom (const AtomIterator &it)
	Removes the atom specified by the iterator it. More...

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

Molecule &	operator= (const Molecule &mol)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

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

Molecule &	operator+= (const Molecule &mol)
	Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol. More...

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

Molecule &	operator-= (const MolecularGraph &molgraph)
	Removes atoms and bonds referenced by the molecular graph molgraph that are part of this `Molecule` instance. 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 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 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 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 Chem::Bond objects. 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...

virtual std::size_t	getNumEntities () const
	Returns the number of stored Chem::Entity3D objects. 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 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
Static Public Member Functions inherited from CDPL::Chem::Molecule
static void	registerCopyPostprocessingFunction (const CopyPostprocessingFunction &func)
	Registers a new copy postprocessing function in the global registry. More...

Protected Member Functions inherited from CDPL::Chem::Molecule
void	invokeCopyPostprocessingFunctions (const MolecularGraph &src_molgraph)
	Invokes all registered copy postprocessing functions on this molecule with src_molgraph as the source molecular graph. More...

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

Default implementation of the Chem::Molecule interface.

BasicMolecule implements the full editing interface inherited from Chem::Molecule and is the standard concrete type used for the creation, manipulation and processing of molecule/molecular graph data throughout the CDPL.

Member Typedef Documentation

◆ SharedPointer

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

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

◆ AtomIterator

typedef boost::indirect_iterator<AtomList::iterator, BasicAtom> CDPL::Chem::BasicMolecule::AtomIterator

A mutable random access iterator used to iterate over the stored Chem::BasicAtom objects.

◆ ConstAtomIterator

typedef boost::indirect_iterator<AtomList::const_iterator, const BasicAtom> CDPL::Chem::BasicMolecule::ConstAtomIterator

A constant random access iterator used to iterate over the stored const Chem::BasicAtom objects.

◆ BondIterator

typedef boost::indirect_iterator<BondList::iterator, BasicBond> CDPL::Chem::BasicMolecule::BondIterator

A mutable random access iterator used to iterate over the stored Chem::BasicBond objects.

◆ ConstBondIterator

typedef boost::indirect_iterator<BondList::const_iterator, const BasicBond> CDPL::Chem::BasicMolecule::ConstBondIterator

A constant random access iterator used to iterate over the stored const Chem::BasicBond objects.

Constructor & Destructor Documentation

◆ BasicMolecule() [1/4]

CDPL::Chem::BasicMolecule::BasicMolecule ( )

Constructs an empty BasicMolecule instance.

◆ BasicMolecule() [2/4]

CDPL::Chem::BasicMolecule::BasicMolecule ( const BasicMolecule & mol )

Constructs a BasicMolecule instance that is a copy of the molecule mol.

Parameters

mol	The other molecule to copy.

◆ BasicMolecule() [3/4]

CDPL::Chem::BasicMolecule::BasicMolecule ( const Molecule & mol )

Constructs a BasicMolecule instance that is a copy of the molecule mol.

Parameters

mol	The other molecule to copy.

◆ BasicMolecule() [4/4]

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

explicit

Constructs a BasicMolecule instance with copies of the atoms, bonds and properties provided by the molecular graph molgraph.

Parameters

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

◆ ~BasicMolecule()

CDPL::Chem::BasicMolecule::~BasicMolecule ( )

Destructor.

Destroys the BasicMolecule instance and frees all allocated resources.

Member Function Documentation

◆ clear()

void CDPL::Chem::BasicMolecule::clear ( )

virtual

Removes all atoms and bonds and clears all properties of the molecule.

Implements CDPL::Chem::Molecule.

◆ getNumAtoms()

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

virtual

Returns the number of atoms.

Returns: The number of atoms.

Implements CDPL::Chem::AtomContainer.

◆ getNumBonds()

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

virtual

Returns the number of bonds.

Returns: The number of bonds.

Implements CDPL::Chem::BondContainer.

◆ getAtomsBegin() [1/2]

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

Returns a constant iterator pointing to the beginning of the stored const Chem::BasicAtom objects.

Returns: A constant iterator pointing to the beginning of the stored const Chem::BasicAtom objects.

◆ getAtomsBegin() [2/2]

AtomIterator CDPL::Chem::BasicMolecule::getAtomsBegin ( )

Returns a mutable iterator pointing to the beginning of the stored Chem::BasicAtom objects.

Returns: A mutable iterator pointing to the beginning of the stored Chem::BasicAtom objects.

◆ getAtomsEnd() [1/2]

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

Returns a constant iterator pointing to the end of the stored const Chem::BasicAtom objects.

Returns: A constant iterator pointing to the end of the stored const Chem::BasicAtom objects.

◆ getAtomsEnd() [2/2]

AtomIterator CDPL::Chem::BasicMolecule::getAtomsEnd ( )

Returns a mutable iterator pointing to the end of the stored Chem::BasicAtom objects.

Returns: A mutable iterator pointing to the end of the stored Chem::BasicAtom objects.

◆ getBondsBegin() [1/2]

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

Returns a constant iterator pointing to the beginning of the stored const Chem::BasicBond objects.

Returns: A constant iterator pointing to the beginning of the stored const Chem::BasicBond objects.

◆ getBondsBegin() [2/2]

BondIterator CDPL::Chem::BasicMolecule::getBondsBegin ( )

Returns a mutable iterator pointing to the beginning of the stored Chem::BasicBond objects.

Returns: A mutable iterator pointing to the beginning of the stored Chem::BasicBond objects.

◆ getBondsEnd() [1/2]

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

Returns a constant iterator pointing to the end of the stored const Chem::BasicBond objects.

Returns: A constant iterator pointing to the end of the stored const Chem::BasicBond objects.

◆ getBondsEnd() [2/2]

BondIterator CDPL::Chem::BasicMolecule::getBondsEnd ( )

Returns a mutable iterator pointing to the end of the stored Chem::BasicBond objects.

Returns: A mutable iterator pointing to the end of the stored Chem::BasicBond objects.

◆ getAtom() [1/2]

const BasicAtom& CDPL::Chem::BasicMolecule::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]

BasicAtom& CDPL::Chem::BasicMolecule::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.

◆ addAtom()

BasicAtom& CDPL::Chem::BasicMolecule::addAtom ( )

virtual

Creates a new atom and adds it to the molecule.

Note that this method does not create any bonds - the returned atom is always unconnected.

Returns: A reference to the newly created atom.

Implements CDPL::Chem::Molecule.

◆ removeAtom() [1/2]

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

virtual

Removes the atom at the specified index.

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

Parameters

idx	The index of the atom to remove.

Exceptions

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

Implements CDPL::Chem::Molecule.

◆ removeAtom() [2/2]

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

Removes the atom specified by the iterator it.

If the specified atom is connected to any other atoms of the molecule then 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()).

◆ getBond() [1/2]

const BasicBond& CDPL::Chem::BasicMolecule::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]

BasicBond& CDPL::Chem::BasicMolecule::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.

◆ addBond()

BasicBond& CDPL::Chem::BasicMolecule::addBond	(	std::size_t	atom1_idx,
		std::size_t	atom2_idx
	)

virtual

Creates a new or returns an already existing bond between the atoms specified by atom1_idx and atom2_idx.

If a bond between the specified atoms already exists then the existing bond will be returned. If a bond does not yet exist, a new bond will be created. The atom specified by atom1_idx becomes the start atom and the atom specified by atom2_idx the end atom of the newly created bond.

Parameters

atom1_idx	The zero-based index of the first atom of the bond.
atom2_idx	The zero-based index of the second atom of the bond.

Returns: A reference to the newly created or already existing bond between the specified atoms.

Exceptions

Base::IndexError if atom1_idx and/or atom2_idx is not in the range [0, getNumAtoms()).

Implements CDPL::Chem::Molecule.

◆ removeBond() [1/2]

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

virtual

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()).

Implements CDPL::Chem::Molecule.

◆ removeBond() [2/2]

BondIterator CDPL::Chem::BasicMolecule::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()).

◆ containsAtom()

bool CDPL::Chem::BasicMolecule::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::BasicMolecule::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::BasicMolecule::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::BasicMolecule::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.

◆ orderAtoms()

void CDPL::Chem::BasicMolecule::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::BasicMolecule::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=() [1/3]

BasicMolecule& CDPL::Chem::BasicMolecule::operator= ( const BasicMolecule & mol )

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Internally calls copy() to perform the actual work.

Parameters

mol	The molecule to copy.

Returns: A reference to itself.

◆ operator+=() [1/3]

BasicMolecule& CDPL::Chem::BasicMolecule::operator+= ( const BasicMolecule & mol )

Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.

Internally calls append() to perform the actual work.

Parameters

mol	The molecule providing the atoms and bonds to append.

Returns: A reference to itself.

◆ clone()

MolecularGraph::SharedPointer CDPL::Chem::BasicMolecule::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.

◆ copy() [1/3]

void CDPL::Chem::BasicMolecule::copy ( const BasicMolecule & mol )

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Parameters

mol	The molecule to copy.

◆ copy() [2/3]

void CDPL::Chem::BasicMolecule::copy ( const Molecule & mol )

virtual

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Parameters

mol	The molecule to copy.

Implements CDPL::Chem::Molecule.

◆ copy() [3/3]

void CDPL::Chem::BasicMolecule::copy ( const MolecularGraph & molgraph )

virtual

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecular graph molgraph.

Parameters

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

Implements CDPL::Chem::Molecule.

◆ append() [1/3]

void CDPL::Chem::BasicMolecule::append ( const BasicMolecule & mol )

Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.

Parameters

mol	The molecule providing the atoms and bonds to append.

Note: Does not affect any properties.

◆ append() [2/3]

void CDPL::Chem::BasicMolecule::append ( const Molecule & mol )

virtual

Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.

Parameters

mol	The molecule providing the atoms and bonds to append.

Note: Does not affect any properties.

Implements CDPL::Chem::Molecule.

◆ append() [3/3]

void CDPL::Chem::BasicMolecule::append ( const MolecularGraph & molgraph )

virtual

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

Parameters

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

Note: Does not affect any properties.

Implements CDPL::Chem::Molecule.

◆ remove()

void CDPL::Chem::BasicMolecule::remove ( const MolecularGraph & molgraph )

virtual

Removes atoms and bonds referenced by the molecular graph molgraph that are part of this Molecule instance.

Parameters

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

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

Implements CDPL::Chem::Molecule.

◆ reserveMemoryForAtoms()

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

virtual

Reserves memory for num_atoms atoms.

Allows implementors to speed up the creation of molecules with a known large number of atoms.

Parameters

num_atoms The expected number of atoms for which memory shall be allocated in advance.

Reimplemented from CDPL::Chem::Molecule.

◆ reserveMemoryForBonds()

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

virtual

Reserves memory for num_bonds bonds.

Allows implementors to speed up the creation of molecules with a known large number of bonds.

Parameters

num_bonds The expected number of bonds for which memory shall be allocated in advance.

Reimplemented from CDPL::Chem::Molecule.

◆ operator=() [2/3]

Molecule& CDPL::Chem::Molecule::operator=

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Internally calls copy() to perform the actual work.

Parameters

mol	The molecule to copy.

Returns: A reference to itself.

◆ operator=() [3/3]

Molecule& CDPL::Chem::Molecule::operator=

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecular graph molgraph.

Internally calls copy() to perform the actual work.

Parameters

molgraph The Chem::MolecularGraph instance providing the atoms and bonds to copy.

Returns: A reference to itself.

◆ operator+=() [2/3]

Molecule& CDPL::Chem::Molecule::operator+=

Extends the current set of atoms and bonds by a copy of the atoms and bonds of the molecule mol.

Internally calls append() to perform the actual work.

Parameters

mol	The molecule providing the atoms and bonds to append.

Returns: A reference to itself.

◆ operator+=() [3/3]

Molecule& CDPL::Chem::Molecule::operator+=

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

Internally calls append() to perform the actual work.

Parameters

molgraph The Chem::MolecularGraph instance providing the atoms and bonds to append.

Returns: A reference to itself.

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

BasicMolecule.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ AtomIterator

◆ ConstAtomIterator

◆ BondIterator

◆ ConstBondIterator

Constructor & Destructor Documentation

◆ BasicMolecule() [1/4]

◆ BasicMolecule() [2/4]

◆ BasicMolecule() [3/4]

◆ BasicMolecule() [4/4]

◆ ~BasicMolecule()

Member Function Documentation

◆ clear()

◆ getNumAtoms()

◆ getNumBonds()

◆ 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]

◆ addAtom()

◆ removeAtom() [1/2]

◆ removeAtom() [2/2]

◆ getBond() [1/2]

◆ getBond() [2/2]

◆ addBond()

◆ removeBond() [1/2]

◆ removeBond() [2/2]

◆ containsAtom()

◆ containsBond()

◆ getAtomIndex()

◆ getBondIndex()

◆ orderAtoms()

◆ orderBonds()

◆ operator=() [1/3]

◆ operator+=() [1/3]

◆ clone()

◆ copy() [1/3]

◆ copy() [2/3]

◆ copy() [3/3]

◆ append() [1/3]

◆ append() [2/3]

◆ append() [3/3]

◆ remove()

◆ reserveMemoryForAtoms()

◆ reserveMemoryForBonds()

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ operator+=() [2/3]

◆ operator+=() [3/3]