Molecule Class Reference
[Molecular Datastructures]

#include <molecule.h>

Inheritance diagram for Molecule:


Public Types
Enums
enum	Property { IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES, NUMBER_OF_PROPERTIES }
	Properties.
Public Member Functions
bool	operator== (const Molecule &molecule) const throw ()
	Equality operator.
bool	operator!= (const Molecule &molecule) const throw ()
	Inequality operator.
Constructors and Destructors
	Molecule () throw ()
	Default constructor.
	Molecule (const Molecule &molecule, bool deep=true) throw ()
	Copy constructor.
	Molecule (const String &name) throw ()
	Detailled constructor.
virtual	~Molecule () throw ()
	Destructor.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Writes a Molecule object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a Molecule object from a persistent stream.
Assignment
void	set (const Molecule &molecule, bool deep=true) throw ()
	Assign from another Molecule.
Molecule &	operator= (const Molecule &molecule) throw ()
	Assignment operator.
void	get (Molecule &molecule, bool deep=true) const throw ()
	Assign to another Molecule.
void	swap (Molecule &molecule) throw ()
	Swap the contents of two molecules.
Accessors
System *	getSystem () throw ()
	Access the parent System.
const System *	getSystem () const throw ()
	Get a const pointer to the parent System.
void	prepend (Atom &atom) throw ()
	Insert an atom as the first child.
void	append (Atom &atom) throw ()
	Insert an atom as the last child.
void	insert (Atom &atom) throw ()
	Insert an atom as the last child.
void	insertBefore (Atom &atom, Composite &before) throw ()
	Insert an atom before a Composite object.
void	insertAfter (Atom &atom, Composite &after) throw ()
	Insert an atom after a Composite object.
bool	remove (Atom &atom) throw ()
	Remove an atom.
void	prepend (AtomContainer &atom_container) throw ()
	Insert an AtomContainer as the first child.
void	append (AtomContainer &atom_container) throw ()
	Append an AtomContainer as the last child.
void	insert (AtomContainer &atom_container) throw ()
	Insert an AtomContainer as the last child.
void	insertBefore (AtomContainer &atom_container, Composite &before) throw ()
	Insert an AtomContainer before a given Composite object.
void	insertAfter (AtomContainer &atom_container, Composite &after) throw ()
	Insert an AtomContainer after a given Composite object.
void	spliceBefore (AtomContainer &atom_container) throw ()
	Cut all children of `atom_container` and prepend them before the children of this molecule.
void	spliceAfter (AtomContainer &atom_container) throw ()
	Cut all children of `atom_container` and append them after the children of this molecule.
void	splice (AtomContainer &atom_container) throw ()
	Move the children of atom_container into this molecule.
bool	remove (AtomContainer &atom_container) throw ()
	Remove an AtomContainer.
Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const throw ()
	Internal state dump.
Protected Member Functions
Molecule *	getMolecule () throw ()
const Molecule *	getMolecule () const throw ()
AtomContainer *	getSuperAtomContainer () throw ()
	Get a mutable pointer to the parent AtomContainer.
const AtomContainer *	getSuperAtomContainer () const throw ()
	Get a constant pointer to the parent AtomContainer.
void	prepend (Molecule &molecule) throw ()
void	append (Molecule &molecule) throw ()
void	insert (Molecule &molecule) throw ()
void	insertBefore (Molecule &molecule, Composite &composite) throw ()
void	insertAfter (Molecule &molecule, Composite &composite) throw ()
bool	remove (Molecule &molecule) throw ()
bool	isSubAtomContainerOf (const AtomContainer &atom_container) const throw ()
	Test if an AtomContainer is a child.

Detailed Description

Molecule class.

Used to represent general molecules without specific properties.

Constructor & Destructor Documentation

Molecule::Molecule ( ) throw ()

Default constructor.

Molecule::Molecule ( const Molecule & molecule,

bool deep = true

) throw ()

Copy constructor.

Molecule::Molecule ( const String & name ) throw ()

Detailled constructor.

virtual Molecule::~Molecule ( ) throw () [virtual]

Destructor.

Member Function Documentation

void Molecule::append ( AtomContainer & atom_container ) throw ()

Append an AtomContainer as the last child.

Parameters:

atom_container the AtomContainer to add

Reimplemented from AtomContainer.

void Molecule::append ( Atom & atom ) throw ()

Insert an atom as the last child.

Parameters:

atom the atom to add

Reimplemented from AtomContainer.

virtual void Molecule::dump ( std::ostream & s = std::cout,

Size depth = 0

) const throw () [virtual]

Internal state dump.
Dump the current internal state to the output ostream s with dumping depth depth .
Parameters:

s output stream where to output the internal state

depth the dumping depth

Reimplemented from AtomContainer.
Reimplemented in NucleicAcid, and Protein.

void Molecule::get ( Molecule & molecule,

bool deep = true

) const throw ()

Assign to another Molecule.

Parameters:

molecule the Molecule to be assigned to

deep make a deep (=true) or shallow (=false) copy

const AtomContainer* Molecule::getSuperAtomContainer ( ) const throw () [protected]

Get a constant pointer to the parent AtomContainer.
The pointer is 0 if this instance does not have a parent AtomContainer.
Returns:
AtomContainer* - constant pointer to the parent AtomContainer

Reimplemented from AtomContainer.

AtomContainer* Molecule::getSuperAtomContainer ( ) throw () [protected]

Get a mutable pointer to the parent AtomContainer.
The pointer is 0 if this instance does not have a parent AtomContainer.
Returns:
AtomContainer* - mutable pointer to the parent AtomContainer

Reimplemented from AtomContainer.

const System* Molecule::getSystem ( ) const throw ()

Get a const pointer to the parent System.

Returns:
System* pointer to the parent System

System* Molecule::getSystem ( ) throw ()

Access the parent System.

Returns:
System* pointer to the parent System

void Molecule::insert ( AtomContainer & atom_container ) throw ()

Insert an AtomContainer as the last child.

Parameters:

atom_container the AtomContainer to add

Reimplemented from AtomContainer.

void Molecule::insert ( Atom & atom ) throw ()

Insert an atom as the last child.

Parameters:

atom the atom to add

Reimplemented from AtomContainer.

void Molecule::insertAfter ( AtomContainer & atom_container,

Composite & after

) throw ()

Insert an AtomContainer after a given Composite object.

Parameters:

atom_container the AtomContainer to insert

after the Composite object to insert after

Reimplemented from AtomContainer.

void Molecule::insertAfter ( Atom & atom,

Composite & after

) throw ()

Insert an atom after a Composite object.

Parameters:

atom the atom to insert

after the Composite object to insert after

Reimplemented from AtomContainer.

void Molecule::insertBefore ( AtomContainer & atom_container,

Composite & before

) throw ()

Insert an AtomContainer before a given Composite object.

Parameters:

atom_container the AtomContainer to insert

before the Composite object to insert before

Reimplemented from AtomContainer.

void Molecule::insertBefore ( Atom & atom,

Composite & before

) throw ()

Insert an atom before a Composite object.

Parameters:

atom the atom to insert

before the Composite object to insert before

Reimplemented from AtomContainer.

bool Molecule::isSubAtomContainerOf ( const AtomContainer & atom_container ) const throw () [protected]

Test if an AtomContainer is a child.

Parameters:

atom_container the AtomContainer to test

Reimplemented from AtomContainer.

bool Molecule::operator!= ( const Molecule & molecule ) const throw ()

Inequality operator.

See also:
operator ==

Molecule& Molecule::operator= ( const Molecule & molecule ) throw ()

Assignment operator.

Parameters:

molecule the Molecule to assign from

bool Molecule::operator== ( const Molecule & molecule ) const throw ()

Equality operator.
Two molecules are equal if they have the same handle.
See also:
Object::operator ==.

void Molecule::persistentRead ( PersistenceManager & pm ) throw (Exception::GeneralException) [virtual]

Reads a Molecule object from a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from AtomContainer.
Reimplemented in NucleicAcid, and Protein.

void Molecule::persistentWrite ( PersistenceManager & pm,

const char * name = 0

) const throw (Exception::GeneralException) [virtual]

Writes a Molecule object to a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from AtomContainer.
Reimplemented in NucleicAcid, and Protein.

void Molecule::prepend ( AtomContainer & atom_container ) throw ()

Insert an AtomContainer as the first child.

Parameters:

atom_container the AtomContainer to add

Reimplemented from AtomContainer.

void Molecule::prepend ( Atom & atom ) throw ()

Insert an atom as the first child.

Parameters:

atom the atom to add

Reimplemented from AtomContainer.

bool Molecule::remove ( AtomContainer & atom_container ) throw ()

Remove an AtomContainer.

Parameters:

atom_container the AtomContainer to remove

Reimplemented from AtomContainer.

bool Molecule::remove ( Atom & atom ) throw ()

Remove an atom.

Parameters:

atom the atom to remove

Reimplemented from AtomContainer.

void Molecule::set ( const Molecule & molecule,

bool deep = true

) throw ()

Assign from another Molecule.

Parameters:

molecule the Molecule object to assign from

deep make a deep (=true) or shallow (=false) copy

void Molecule::splice ( AtomContainer & atom_container ) throw ()

Move the children of atom_container into this molecule.
The children of atom_container are inserted at the position of atom_container if it is a child of this. Otherwise the children are inserted using spliceBefore .
Reimplemented from AtomContainer.

void Molecule::spliceAfter ( AtomContainer & atom_container ) throw ()

Cut all children of atom_container and append them after the children of this molecule.

Parameters:

atom_container the AtomContainer to access

Reimplemented from AtomContainer.

void Molecule::spliceBefore ( AtomContainer & atom_container ) throw ()

Cut all children of atom_container and prepend them before the children of this molecule.

Parameters:

atom_container the AtomContainer to access

Reimplemented from AtomContainer.

void Molecule::swap ( Molecule & molecule ) throw ()

Swap the contents of two molecules.

Parameters:

molecule the Molecule to swap contents with

Molecule Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Molecule Class Reference
[Molecular Datastructures]