The Gnome Chemistry Utils 0.13.3
Public Member Functions | Static Public Member Functions | Static Public Attributes
gcu::Residue Class Reference

#include <gcu/residue.h>

Inheritance diagram for gcu::Residue:
gcp::Residue

List of all members.

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)
DocumentGetDocument (void)
MoleculeGetMolecule (void)
DocumentGetOwner (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:
namethe name of the residue.
docthe 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:
symbola 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 208 of file gcu/residue.h.

static std::string const* gcu::Residue::GetFirstResidueSymbol ( ResidueIterator &  i) [static]
Parameters:
ian 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 203 of file gcu/residue.h.

gcu::Residue::GetMolecule ( void  ) [inline]

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

Definition at line 213 of file gcu/residue.h.

gcu::Residue::GetName ( void  ) const [inline]
Returns:
the name of the Residue instance.

Definition at line 188 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:
ian 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 218 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 203 of file gcu/residue.h.

static Residue const* gcu::Residue::GetResidue ( char const *  symbol,
bool *  ambiguous = NULL 
) [static]
Parameters:
symbolthe symbol for which a Residue* is searched.
ambiguouswhere 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:
namethe 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:
nodea XMLNode* representing the residue.

loads the residu from an XML file.

virtual bool gcu::Residue::operator== ( G_GNUC_UNUSED Molecule const &  mol) const [inline, virtual]
Parameters:
mola molecule to compare to the atoms group.
Returns:
true if the molecule is the same as the one associated with this.

Definition at line 171 of file gcu/residue.h.

void gcu::Residue::RemoveSymbol ( char const *  symbol)
Parameters:
symbola chemical symbol.

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

gcu::Residue::SetGeneric ( bool  Generic) [inline]
Parameters:
Genericwhether 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 203 of file gcu/residue.h.

void gcu::Residue::SetName ( char const *  name)
Parameters:
namethe 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 178 of file gcu/residue.h.


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