#include <gcu/residue.h>

Inheritance diagram for gcu::Residue:

Public Member Functions
	Residue ()
	Residue (char const name, Document doc=NULL)
virtual	~Residue ()
std::map< int, int > const &	GetRawFormula () const
std::map< std::string, bool > const &	GetSymbols () const
std::map< std::string, std::string > const &	GetNames () const
void	SetName (char const *name)
void	AddSymbol (char const *symbol)
void	RemoveSymbol (char const *symbol)
virtual void	Load (xmlNodePtr node, Application *app)
virtual bool	operator== (G_GNUC_UNUSED Molecule const &mol) const
char const *	GetName (void) const
void	SetGeneric (bool val)
bool	GetGeneric (void) const
bool &	GetRefGeneric (void)
Document *	GetDocument (void)
Molecule *	GetMolecule (void)
Document *	GetOwner (void) const

Static Public Member Functions
static Residue const *	GetResidue (char const symbol, bool ambiguous=NULL)
static Residue const *	GetResiduebyName (char const *name)
static std::string const *	GetFirstResidueSymbol (ResidueIterator &i)
static std::string const *	GetNextResidueSymbol (ResidueIterator &i)

Static Public Attributes
static unsigned	MaxSymbolLength

Detailed Description

Represents the meaning of group symbols, such as Me, Ph or Bz. They have one or more associated symbols and a molecule which atoms and bonds are represented by the symbol. The molecule starts from a pseudo-atom with Z = 0, which represents the atom linked to the group. Currently only one pseudo-atom with one single bond to the group is allowed.

Definition at line 67 of file gcu/residue.h.

Constructor & Destructor Documentation

gcu::Residue::Residue ( )

Creates a residue.

Reimplemented in gcp::Residue.

gcu::Residue::Residue	(	char const *	name,
		Document *	doc = `NULL`
	)

Parameters

name	the name of the residue.
doc	the document owning the residue when it does not have global scope.

Creates a residue and sets its name.

virtual gcu::Residue::~Residue ( )

virtual

The destructor.

Reimplemented in gcp::Residue.

Member Function Documentation

void gcu::Residue::AddSymbol ( char const * symbol )

Parameters

symbol a chemical symbol.

Adds symbol to the list of valid symbols for the atoms group.

gcu::Residue::GetDocument ( void )

inline

Returns the gcu::Document* used to store the molecule associated with the atoms group.

Definition at line 209 of file gcu/residue.h.

static std::string const* gcu::Residue::GetFirstResidueSymbol ( ResidueIterator & i )

static

Parameters

i	an iterator.

Used to iterate through all known atoms groups and their symbols. Initializes the iterator.

Returns: the first known symbol. If not NULL, the iterator gives access to the associated Residue througn a gcu::SymbolResidue structure.

gcu::Residue::GetGeneric ( void ) const

inline

Returns: whether the symbol is a generic symbol or not.

Definition at line 204 of file gcu/residue.h.

gcu::Residue::GetMolecule ( void )

inline

Returns the gcu::Molecule* describing the structure of the atoms group.

Definition at line 214 of file gcu/residue.h.

gcu::Residue::GetName ( void ) const

inline

Returns: the name of the Residue instance.

Definition at line 189 of file gcu/residue.h.

std::map<std::string, std::string> const& gcu::Residue::GetNames ( ) const

inline

Returns: the names of the atoms group, as a std::map indexed by the correspondig locale.

Definition at line 111 of file gcu/residue.h.

static std::string const* gcu::Residue::GetNextResidueSymbol ( ResidueIterator & i )

static

Parameters

i	an iterator initialized by Residue::GetFirstResidueSymbol.

Used to iterate through all known atoms groups and their symbols. Initializes the iterator.

Returns: the next known symbol. If not NULL, the iterator gives access to the associated Residue through a gcu::SymbolResidue structure.

gcu::Residue::GetOwner ( void ) const

inline

Returns: the Document for which the Residue is valid. If NULL, the Residue is of global scope.

Definition at line 219 of file gcu/residue.h.

std::map<int,int> const& gcu::Residue::GetRawFormula ( ) const

inline

Returns: the raw formula of the residue as a map of integers (number of atoms of an element) indexed by the atomic number of the element.

The following code gives the number of carbon atoms:

Residue *residue;
... // initialize the residue
cout << "the residue has " << residue->GetRawFormula ()[6] << " carbon atoms." << endl;

Definition at line 99 of file gcu/residue.h.

gcu::Residue::GetRefGeneric ( void )

inline

Returns: whether the symbol is a generic symbol or not as a reference to a boolean variable.

Definition at line 204 of file gcu/residue.h.

static Residue const* gcu::Residue::GetResidue	(	char const *	symbol,
		bool *	ambiguous = `NULL`
	)

static

Parameters

symbol	the symbol for which a Residue* is searched.
ambiguous	where to store the boolean telling if the symbol is ambiguous or NULL.

Returns: the Residue* found or NULL.

static Residue const* gcu::Residue::GetResiduebyName ( char const * name )

static

Parameters

name	the name for which a Residue* is searched.

Returns: the Residue* found or NULL.

std::map<std::string, bool> const& gcu::Residue::GetSymbols ( ) const

inline

Returns: the symbols of the atoms group as a std::map. The symbols index boolean values telling whether the symbol is ambiguous or not.

A symbol is ambiguous if it can also represent a single atom, such as Ac, or Pr.

Definition at line 106 of file gcu/residue.h.

virtual void gcu::Residue::Load	(	xmlNodePtr	node,
		Application *	app
	)

virtual

Parameters

node	a XMLNode* representing the residue.
app	the Application owning the residue.

loads the residu from an XML file.

virtual bool gcu::Residue::operator== ( G_GNUC_UNUSED Molecule const & mol ) const

inlinevirtual

Parameters

mol	a molecule to compare to the atoms group.

Returns: true if the molecule is the same as the one associated with this.

Definition at line 172 of file gcu/residue.h.

void gcu::Residue::RemoveSymbol ( char const * symbol )

Parameters

symbol a chemical symbol.

Removes symbol from the list of valid symbols for the atoms group.

gcu::Residue::SetGeneric ( bool Generic )

inline

Parameters

Generic whether the symbol is a generic symbol or not.

Generic symbols are such symbols as R, Ar, or X which might represent various atoms or groups of atoms. When expanded, they will be replaced by a default value, for example, R will expand to a methyl, and Ar to a phenyl group.

Definition at line 204 of file gcu/residue.h.

void gcu::Residue::SetName ( char const * name )

Parameters

name	the name to give to the Residue.

Member Data Documentation

unsigned gcu::Residue::MaxSymbolLength

static

Returns: the maxium length of all known symbols. This is used by the framework when parsing a string formula.

Definition at line 179 of file gcu/residue.h.

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

gcu/residue.h

Public Member Functions

Static Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation