#include <Molecule.hpp>

Inheritance diagram for CDPL::Chem::Molecule:

Public Types
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 atoms of the molecule. More...

typedef AtomContainer::AtomIterator	AtomIterator
	A mutable random access iterator used to iterate over the atoms of the molecule. More...

typedef BondContainer::ConstBondIterator	ConstBondIterator
	A constant random access iterator used to iterate over the bonds of the molecule. More...

typedef BondContainer::BondIterator	BondIterator
	A mutable random access iterator used to iterate over the bonds of the molecule. More...

typedef std::function< void(Molecule &, const MolecularGraph &)>	CopyPostprocessingFunction

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
virtual	~Molecule ()
	Virtual destructor. More...

virtual void	clear ()=0
	Removes all atoms and bonds and clears all properties of the molecule. More...

virtual std::size_t	getNumAtoms () const =0
	Returns the number of explicit atoms. More...

virtual std::size_t	getNumBonds () const =0
	Returns the number of explicit bonds. More...

virtual const Atom &	getAtom (std::size_t idx) const =0
	Returns a `const` reference to the atom at index idx. More...

virtual Atom &	getAtom (std::size_t idx)=0
	Returns a non-`const` reference to the atom at index idx. More...

virtual Atom &	addAtom ()=0
	Creates a new atom and adds it to the molecule. More...

virtual void	removeAtom (std::size_t idx)=0
	Removes the atom at the specified index. More...

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

virtual const Bond &	getBond (std::size_t idx) const =0
	Returns a `const` reference to the bond at index idx. More...

virtual Bond &	getBond (std::size_t idx)=0
	Returns a non-`const` reference to the bond at index idx. More...

virtual Bond &	addBond (std::size_t atom1_idx, std::size_t atom2_idx)=0
	Creates a new or returns an already existing bond between the atoms specified by atom1_idx and atom2_idx. More...

virtual void	removeBond (std::size_t idx)=0
	Removes the bond at the specified index. More...

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

virtual bool	containsAtom (const Atom &atom) const =0
	Tells whether the specified atom is part of this molecule. More...

virtual bool	containsBond (const Bond &bond) const =0
	Tells whether the specified bond is part of this molecule. More...

virtual std::size_t	getAtomIndex (const Atom &atom) const =0
	Returns the index of the specified atom. More...

virtual std::size_t	getBondIndex (const Bond &bond) const =0
	Returns the index of the specified bond. More...

virtual void	copy (const Molecule &mol)=0
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

virtual void	copy (const MolecularGraph &molgraph)=0
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecular graph molgraph. More...

virtual void	append (const Molecule &mol)=0
	Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol. More...

virtual void	append (const MolecularGraph &molgraph)=0
	Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecular graph molgraph. More...

virtual void	remove (const MolecularGraph &molgraph)=0
	Removes atoms and bonds referenced by the molecular graph molgraph that are part of this `Molecule` instance. More...

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

virtual 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 in 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 in 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...

virtual SharedPointer	clone () const =0
	Creates a copy of the molecular graph. More...

Public Member Functions inherited from CDPL::Chem::AtomContainer
ConstAtomIterator	getAtomsBegin () const
	Returns a constant iterator pointing to the beginning of the stored `const` Chem::Atom objects. More...

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

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

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

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

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

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

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

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

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

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

virtual void	orderAtoms (const AtomCompareFunction &func)=0
	Orders the stored atoms according to criteria implemented by the provided atom comparison function. 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...

virtual void	orderBonds (const BondCompareFunction &func)=0
	Orders the stored bonds according to criteria implemented by the provided bond comparison function. 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...

Static Public Member Functions
static void	registerCopyPostprocessingFunction (const CopyPostprocessingFunction &func)

Protected Member Functions
void	invokeCopyPostprocessingFunctions (const MolecularGraph &src_molgraph)

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

Molecule.

Member Typedef Documentation

◆ SharedPointer

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

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

◆ ConstAtomIterator

typedef AtomContainer::ConstAtomIterator CDPL::Chem::Molecule::ConstAtomIterator

A constant random access iterator used to iterate over the atoms of the molecule.

◆ AtomIterator

typedef AtomContainer::AtomIterator CDPL::Chem::Molecule::AtomIterator

A mutable random access iterator used to iterate over the atoms of the molecule.

◆ ConstBondIterator

typedef BondContainer::ConstBondIterator CDPL::Chem::Molecule::ConstBondIterator

A constant random access iterator used to iterate over the bonds of the molecule.

◆ BondIterator

typedef BondContainer::BondIterator CDPL::Chem::Molecule::BondIterator

A mutable random access iterator used to iterate over the bonds of the molecule.

◆ CopyPostprocessingFunction

typedef std::function<void(Molecule&, const MolecularGraph&)> CDPL::Chem::Molecule::CopyPostprocessingFunction

Constructor & Destructor Documentation

◆ ~Molecule()

virtual CDPL::Chem::Molecule::~Molecule ( )

inlinevirtual

Virtual destructor.

Destroys the Molecule instance and frees all allocated resources.

Member Function Documentation

◆ clear()

virtual void CDPL::Chem::Molecule::clear ( )

pure virtual

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

Implemented in CDPL::Chem::BasicMolecule.

◆ getNumAtoms()

virtual std::size_t CDPL::Chem::Molecule::getNumAtoms ( ) const

pure virtual

Returns the number of explicit atoms.

Returns: The number of explicit atoms.

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ getNumBonds()

virtual std::size_t CDPL::Chem::Molecule::getNumBonds ( ) const

pure virtual

Returns the number of explicit bonds.

Returns: The number of explicit bonds.

Implements CDPL::Chem::BondContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ getAtom() [1/2]

virtual const Atom& CDPL::Chem::Molecule::getAtom ( std::size_t idx ) const

pure 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 the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ getAtom() [2/2]

virtual Atom& CDPL::Chem::Molecule::getAtom ( std::size_t idx )

pure 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 the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ addAtom()

virtual Atom& CDPL::Chem::Molecule::addAtom ( )

pure 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.

Implemented in CDPL::Chem::BasicMolecule.

◆ removeAtom() [1/2]

virtual void CDPL::Chem::Molecule::removeAtom ( std::size_t idx )

pure virtual

Removes the atom at the specified index.

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

Parameters

idx	The index of the atom to remove.

Exceptions

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

Implemented in CDPL::Chem::BasicMolecule.

◆ removeAtom() [2/2]

AtomIterator CDPL::Chem::Molecule::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, 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 the number of atoms is zero or it is not in the range [getAtomsBegin(), getAtomsEnd() - 1].

◆ getBond() [1/2]

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

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

Implements CDPL::Chem::BondContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ getBond() [2/2]

virtual Bond& CDPL::Chem::Molecule::getBond ( std::size_t idx )

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

Implements CDPL::Chem::BondContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ addBond()

virtual Bond& CDPL::Chem::Molecule::addBond	(	std::size_t	atom1_idx,
		std::size_t	atom2_idx
	)

pure 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 the number of atoms is zero or atom1_idx and/or atom2_idx is not in the range [0, getNumAtoms() - 1].

Implemented in CDPL::Chem::BasicMolecule.

◆ removeBond() [1/2]

virtual void CDPL::Chem::Molecule::removeBond ( std::size_t idx )

pure virtual

Removes the bond at the specified index.

Parameters

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

Exceptions

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

Implemented in CDPL::Chem::BasicMolecule.

◆ removeBond() [2/2]

BondIterator CDPL::Chem::Molecule::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 the number of bonds is zero or it is not in the range [getBondsBegin(), getBondsEnd() - 1].

◆ containsAtom()

virtual bool CDPL::Chem::Molecule::containsAtom ( const Atom & atom ) const

pure virtual

Tells whether the specified atom is part of this molecule.

Parameters

atom	The atom to look for.

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

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ containsBond()

virtual bool CDPL::Chem::Molecule::containsBond ( const Bond & bond ) const

pure virtual

Tells whether the specified bond is part of this molecule.

Parameters

bond	The bond to look for.

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

Implements CDPL::Chem::BondContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ getAtomIndex()

virtual std::size_t CDPL::Chem::Molecule::getAtomIndex ( const Atom & atom ) const

pure 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 is not part of the molecule.

Implements CDPL::Chem::AtomContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ getBondIndex()

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

pure 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 is not part of the molecule.

Implements CDPL::Chem::BondContainer.

Implemented in CDPL::Chem::BasicMolecule.

◆ copy() [1/2]

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

pure 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.

Implemented in CDPL::Chem::BasicMolecule.

◆ copy() [2/2]

virtual void CDPL::Chem::Molecule::copy ( const MolecularGraph & molgraph )

pure 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 Chem::MolecularGraph instance providing the atoms, bonds and properties to copy.

Implemented in CDPL::Chem::BasicMolecule.

◆ append() [1/2]

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

pure virtual

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

Parameters

mol	The molecule providing the atoms and bonds to append.

Note: Does not affect any properties.

Implemented in CDPL::Chem::BasicMolecule.

◆ append() [2/2]

virtual void CDPL::Chem::Molecule::append ( const MolecularGraph & molgraph )

pure virtual

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

Parameters

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

Note: Does not affect any properties.

Implemented in CDPL::Chem::BasicMolecule.

◆ remove()

virtual void CDPL::Chem::Molecule::remove ( const MolecularGraph & molgraph )

pure virtual

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

Parameters

molgraph The Chem::MolecularGraph instance specifying the atoms and bonds to remove.

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

Implemented in CDPL::Chem::BasicMolecule.

◆ reserveMemoryForAtoms()

virtual void CDPL::Chem::Molecule::reserveMemoryForAtoms ( std::size_t num_atoms )

inlinevirtual

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 in CDPL::Chem::BasicMolecule.

◆ reserveMemoryForBonds()

virtual void CDPL::Chem::Molecule::reserveMemoryForBonds ( std::size_t num_bonds )

inlinevirtual

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 in CDPL::Chem::BasicMolecule.

◆ operator=() [1/2]

Molecule& CDPL::Chem::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.

Internally calls copy() to perform the actual work.

Parameters

mol	The molecule to copy.

Returns: A reference to itself.

◆ operator=() [2/2]

Molecule& CDPL::Chem::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.

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+=() [1/2]

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

Extends the current set of atoms and bonds by a copy of the atoms and bonds in 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+=() [2/2]

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

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

◆ operator-=()

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

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

Internally calls remove() to perform the actual work.

Parameters

molgraph The Chem::MolecularGraph instance specifying the atoms and bonds to remove.

Returns: A reference to itself.

◆ registerCopyPostprocessingFunction()

static void CDPL::Chem::Molecule::registerCopyPostprocessingFunction ( const CopyPostprocessingFunction & func )

static

◆ invokeCopyPostprocessingFunctions()

void CDPL::Chem::Molecule::invokeCopyPostprocessingFunctions ( const MolecularGraph & src_molgraph )

protected

◆ getAtomsBegin() [1/2]

ConstAtomIterator CDPL::Chem::AtomContainer::getAtomsBegin

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

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

◆ getAtomsBegin() [2/2]

AtomIterator CDPL::Chem::AtomContainer::getAtomsBegin

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

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

◆ getAtomsEnd() [1/2]

ConstAtomIterator CDPL::Chem::AtomContainer::getAtomsEnd

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

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

◆ getAtomsEnd() [2/2]

AtomIterator CDPL::Chem::AtomContainer::getAtomsEnd

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

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

◆ getBondsBegin() [1/2]

ConstBondIterator CDPL::Chem::BondContainer::getBondsBegin

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

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

◆ getBondsBegin() [2/2]

BondIterator CDPL::Chem::BondContainer::getBondsBegin

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

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

◆ getBondsEnd() [1/2]

ConstBondIterator CDPL::Chem::BondContainer::getBondsEnd

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

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

◆ getBondsEnd() [2/2]

BondIterator CDPL::Chem::BondContainer::getBondsEnd

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

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

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

Molecule.hpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstAtomIterator

◆ AtomIterator

◆ ConstBondIterator

◆ BondIterator

◆ CopyPostprocessingFunction

Constructor & Destructor Documentation

◆ ~Molecule()

Member Function Documentation

◆ clear()

◆ getNumAtoms()

◆ getNumBonds()

◆ 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()

◆ copy() [1/2]

◆ copy() [2/2]

◆ append() [1/2]

◆ append() [2/2]

◆ remove()

◆ reserveMemoryForAtoms()

◆ reserveMemoryForBonds()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator+=() [1/2]

◆ operator+=() [2/2]

◆ operator-=()

◆ registerCopyPostprocessingFunction()

◆ invokeCopyPostprocessingFunctions()

◆ getAtomsBegin() [1/2]

◆ getAtomsBegin() [2/2]

◆ getAtomsEnd() [1/2]

◆ getAtomsEnd() [2/2]

◆ getBondsBegin() [1/2]

◆ getBondsBegin() [2/2]

◆ getBondsEnd() [1/2]

◆ getBondsEnd() [2/2]