CDPL::Chem::BasicMolecule Class Reference

Concrete Chem::Molecule implementation that owns Chem::BasicAtom and Chem::BasicBond instances. 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
	Mutable random-access iterator over the atoms of the molecule. More...
typedef boost::indirect_iterator< AtomList::const_iterator, const BasicAtom >	ConstAtomIterator
	Constant random-access iterator over the atoms of the molecule. More...
typedef boost::indirect_iterator< BondList::iterator, BasicBond >	BondIterator
	Mutable random-access iterator over the bonds of the molecule. More...
typedef boost::indirect_iterator< BondList::const_iterator, const BasicBond >	ConstBondIterator
	Constant random-access iterator over the bonds of the molecule. 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 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
	Type of a callback invoked after a molecule has been copied from a source molecular graph (first argument: the freshly populated destination molecule; second argument: the source 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 copy of the BasicMolecule instance mol. More...
	BasicMolecule (const Molecule &mol)
	Constructs a copy of the Chem::Molecule instance mol. More...
	BasicMolecule (const MolecularGraph &molgraph)
	Constructs a BasicMolecule instance with copies of the atoms and bonds of the Chem::MolecularGraph instance molgraph. More...
	~BasicMolecule ()
	Destructor. More...
void	clear ()
	Removes all atoms, bonds, and properties of the molecule. More...
std::size_t	getNumAtoms () const
	Returns the number of atoms in the molecule. More...
std::size_t	getNumBonds () const
	Returns the number of bonds in the molecule. More...
ConstAtomIterator	getAtomsBegin () const
	Returns a constant iterator pointing to the beginning of the atoms. More...
AtomIterator	getAtomsBegin ()
	Returns a mutable iterator pointing to the beginning of the atoms. More...
ConstAtomIterator	getAtomsEnd () const
	Returns a constant iterator pointing to the end of the atoms. More...
AtomIterator	getAtomsEnd ()
	Returns a mutable iterator pointing to the end of the atoms. More...
ConstBondIterator	getBondsBegin () const
	Returns a constant iterator pointing to the beginning of the bonds. More...
BondIterator	getBondsBegin ()
	Returns a mutable iterator pointing to the beginning of the bonds. More...
ConstBondIterator	getBondsEnd () const
	Returns a constant iterator pointing to the end of the bonds. More...
BondIterator	getBondsEnd ()
	Returns a mutable iterator pointing to the end of the bonds. 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 mutable reference to the atom at index idx. More...
BasicAtom &	addAtom ()
	Creates and appends a new atom and returns a reference to it. More...
void	removeAtom (std::size_t idx)
	Removes the atom at index idx (along with any incident bonds). 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 mutable reference to the bond at index idx. More...
BasicBond &	addBond (std::size_t atom1_idx, std::size_t atom2_idx)
	Creates a new bond between the atoms at indices atom1_idx and atom2_idx and returns a reference to it. More...
void	removeBond (std::size_t idx)
	Removes the bond at index idx. More...
BondIterator	removeBond (const BondIterator &it)
	Removes the bond specified by the iterator it. More...
bool	containsAtom (const Atom &atom) const
	Tells whether atom is part of this molecule. More...
bool	containsBond (const Bond &bond) const
	Tells whether bond is part of this molecule. More...
std::size_t	getAtomIndex (const Atom &atom) const
	Returns the index of atom atom in this molecule. More...
std::size_t	getBondIndex (const Bond &bond) const
	Returns the index of bond bond in this molecule. More...
void	orderAtoms (const AtomCompareFunction &func)
	Reorders the atom list using the binary comparator func. More...
void	orderBonds (const BondCompareFunction &func)
	Reorders the bond list using the binary comparator func. 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 in the molecule mol. More...
MolecularGraph::SharedPointer	clone () const
	Creates a 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 mol. More...
void	copy (const MolecularGraph &molgraph)
	Replaces the current set of atoms, bonds and properties by a copy of molgraph. More...
void	append (const BasicMolecule &mol)
	Extends the current set of atoms and bonds by a copy of the atoms and bonds in the molecule mol. More...
void	append (const Molecule &mol)
	Extends the current set of atoms and bonds by a copy of those in mol. More...
void	append (const MolecularGraph &molgraph)
	Extends the current set of atoms and bonds by a copy of those in molgraph. More...
void	remove (const MolecularGraph &molgraph)
	Removes the atoms and bonds of molgraph from this molecule. More...
void	reserveMemoryForAtoms (std::size_t num_atoms)
	Reserves storage for at least num_atoms atoms to avoid reallocations on subsequent additions. More...
void	reserveMemoryForBonds (std::size_t num_bonds)
	Reserves storage for at least num_bonds bonds to avoid reallocations on subsequent additions. 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...
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 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...
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 (equivalent to getNumAtoms()). More...
virtual const Entity3D &	getEntity (std::size_t idx) const
	Returns a const reference to the Chem::Entity3D instance at index idx (equivalent to getAtom(idx)). More...
virtual Entity3D &	getEntity (std::size_t idx)
	Returns a non-const reference to the Chem::Entity3D instance at index idx (equivalent to getAtom(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. 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)
	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

Concrete Chem::Molecule implementation that owns Chem::BasicAtom and Chem::BasicBond instances.

BasicMolecule provides the default in-memory representation of a molecular graph: atoms and bonds are allocated from internal object pools and accessed through random-access iterators. The class implements the full editing interface inherited from Chem::Molecule (addAtom, addBond, removeAtom, removeBond, copy, append, remove, reserveMemoryForAtoms, reserveMemoryForBonds) and is the standard concrete type used by readers and downstream algorithms throughout CDPKit.

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

Mutable random-access iterator over the atoms of the molecule.

ConstAtomIterator

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

Constant random-access iterator over the atoms of the molecule.

BondIterator

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

Mutable random-access iterator over the bonds of the molecule.

ConstBondIterator

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

Constant random-access iterator over the bonds of the molecule.

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 copy of the BasicMolecule instance mol.

Parameters

mol	The other BasicMolecule instance to copy.

BasicMolecule() [3/4]

CDPL::Chem::BasicMolecule::BasicMolecule

(

const Molecule &

mol

)

Constructs a copy of the Chem::Molecule instance mol.

Parameters

mol	The other Chem::Molecule instance to copy.

BasicMolecule() [4/4]

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

explicit

Constructs a BasicMolecule instance with copies of the atoms and bonds of the Chem::MolecularGraph instance molgraph.

Parameters

molgraph

The Chem::MolecularGraph instance providing the atoms and bonds 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, bonds, and properties of the molecule.

Implements CDPL::Chem::Molecule.

getNumAtoms()

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

virtual

Returns the number of atoms in the molecule.

Returns

The atom count.

Implements CDPL::Chem::Molecule.

getNumBonds()

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

virtual

Returns the number of bonds in the molecule.

Returns

The bond count.

Implements CDPL::Chem::Molecule.

getAtomsBegin() [1/2]

ConstAtomIterator CDPL::Chem::BasicMolecule::getAtomsBegin

(

)

const

Returns a constant iterator pointing to the beginning of the atoms.

Returns

A constant iterator pointing to the beginning of the atoms.

getAtomsBegin() [2/2]

AtomIterator CDPL::Chem::BasicMolecule::getAtomsBegin

(

)

Returns a mutable iterator pointing to the beginning of the atoms.

Returns

A mutable iterator pointing to the beginning of the atoms.

getAtomsEnd() [1/2]

ConstAtomIterator CDPL::Chem::BasicMolecule::getAtomsEnd

(

)

const

Returns a constant iterator pointing to the end of the atoms.

Returns

A constant iterator pointing to the end of the atoms.

getAtomsEnd() [2/2]

AtomIterator CDPL::Chem::BasicMolecule::getAtomsEnd

(

)

Returns a mutable iterator pointing to the end of the atoms.

Returns

A mutable iterator pointing to the end of the atoms.

getBondsBegin() [1/2]

ConstBondIterator CDPL::Chem::BasicMolecule::getBondsBegin

(

)

const

Returns a constant iterator pointing to the beginning of the bonds.

Returns

A constant iterator pointing to the beginning of the bonds.

getBondsBegin() [2/2]

BondIterator CDPL::Chem::BasicMolecule::getBondsBegin

(

)

Returns a mutable iterator pointing to the beginning of the bonds.

Returns

A mutable iterator pointing to the beginning of the bonds.

getBondsEnd() [1/2]

ConstBondIterator CDPL::Chem::BasicMolecule::getBondsEnd

(

)

const

Returns a constant iterator pointing to the end of the bonds.

Returns

A constant iterator pointing to the end of the bonds.

getBondsEnd() [2/2]

BondIterator CDPL::Chem::BasicMolecule::getBondsEnd

(

)

Returns a mutable iterator pointing to the end of the bonds.

Returns

A mutable iterator pointing to the end of the bonds.

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 atom index.

Returns

A const reference to the atom.

Exceptions

Base::IndexError

if idx is not less than getNumAtoms().

Implements CDPL::Chem::Molecule.

getAtom() [2/2]

BasicAtom& CDPL::Chem::BasicMolecule::getAtom ( std::size_t  idx )

virtual

Returns a mutable reference to the atom at index idx.

Parameters

idx	The zero-based atom index.

Returns

A mutable reference to the atom.

Exceptions

Base::IndexError

if idx is not less than getNumAtoms().

Implements CDPL::Chem::Molecule.

addAtom()

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

virtual

Creates and appends a new atom and returns a reference to it.

Returns

A reference to the newly added atom.

Implements CDPL::Chem::Molecule.

removeAtom() [1/2]

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

virtual

Removes the atom at index idx (along with any incident bonds).

Parameters

idx	The zero-based atom index.

Exceptions

Base::IndexError

if idx is not less than 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, 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]

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 bond index.

Returns

A const reference to the bond.

Exceptions

Base::IndexError

if idx is not less than getNumBonds().

Implements CDPL::Chem::Molecule.

getBond() [2/2]

BasicBond& CDPL::Chem::BasicMolecule::getBond ( std::size_t  idx )

virtual

Returns a mutable reference to the bond at index idx.

Parameters

idx	The zero-based bond index.

Returns

A mutable reference to the bond.

Exceptions

Base::IndexError

if idx is not less than getNumBonds().

Implements CDPL::Chem::Molecule.

addBond()

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

virtual

Creates a new bond between the atoms at indices atom1_idx and atom2_idx and returns a reference to it.

Parameters

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

Returns

A reference to the newly added bond.

Exceptions

Base::IndexError

if either index is not less than getNumAtoms().

Implements CDPL::Chem::Molecule.

removeBond() [1/2]

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

virtual

Removes the bond at index idx.

Parameters

idx	The zero-based bond index.

Exceptions

Base::IndexError

if idx is not less than 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 the number of bonds is zero or it is not in the range [getBondsBegin(), getBondsEnd() - 1].

containsAtom()

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

virtual

Tells whether atom is part of this molecule.

Parameters

atom	The atom to look up.

Returns

true if atom is in the molecule, and false otherwise.

Implements CDPL::Chem::Molecule.

containsBond()

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

virtual

Tells whether bond is part of this molecule.

Parameters

bond	The bond to look up.

Returns

true if bond is in the molecule, and false otherwise.

Implements CDPL::Chem::Molecule.

getAtomIndex()

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

virtual

Returns the index of atom atom in this molecule.

Parameters

atom	The atom to look up.

Returns

The zero-based atom index.

Exceptions

Base::ItemNotFound

if atom is not part of the molecule.

Implements CDPL::Chem::Molecule.

getBondIndex()

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

virtual

Returns the index of bond bond in this molecule.

Parameters

bond	The bond to look up.

Returns

The zero-based bond index.

Exceptions

Base::ItemNotFound

if bond is not part of the molecule.

Implements CDPL::Chem::Molecule.

orderAtoms()

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

virtual

Reorders the atom list using the binary comparator func.

Parameters

func	The strict-weak-ordering comparator used to sort the atoms.

Implements CDPL::Chem::AtomContainer.

orderBonds()

void CDPL::Chem::BasicMolecule::orderBonds ( const BondCompareFunction &  func )

virtual

Reorders the bond list using the binary comparator func.

Parameters

func	The strict-weak-ordering comparator used to sort the bonds.

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 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.

clone()

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

virtual

Creates a copy of the molecular graph.

Returns

A smart pointer to the copy of the molecular graph.

Implements CDPL::Chem::MolecularGraph.

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 mol.

Parameters

mol	The source molecule.

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 molgraph.

Parameters

molgraph

The source molecular graph.

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 in 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 those in mol.

Parameters

mol	The source molecule.

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 those in molgraph.

Parameters

molgraph

The source molecular graph.

Note

Does not affect any properties.

Implements CDPL::Chem::Molecule.

remove()

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

virtual

Removes the atoms and bonds of molgraph from this molecule.

Parameters

molgraph

The molecular graph specifying the atoms and bonds to remove.

Implements CDPL::Chem::Molecule.

reserveMemoryForAtoms()

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

virtual

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

Parameters

num_atoms

The minimum number of atoms to accommodate.

Reimplemented from CDPL::Chem::Molecule.

reserveMemoryForBonds()

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

virtual

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

Parameters

num_bonds

The minimum number of bonds to accommodate.

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 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+=() [3/3]

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

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.

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

• BasicMolecule.hpp