#include <gcu/residue.h>
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) |
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 |
Definition at line 66 of file gcu/residue.h.
gcu::Residue::Residue | ( | ) |
Creates a residue.
Reimplemented in gcp::Residue.
gcu::Residue::Residue | ( | char const * | name, | |
Document * | doc = NULL | |||
) |
name | the name of the residue. | |
doc | the document owning the residue when it does not have global scope. |
virtual gcu::Residue::~Residue | ( | ) | [virtual] |
The destructor.
Reimplemented in gcp::Residue.
void gcu::Residue::AddSymbol | ( | char const * | symbol | ) |
symbol | a chemical symbol. |
gcu::Residue::GetDocument | ( | void | ) | [inline] |
Returns the gcu::Document* used to store the molecule associated with the atoms group.
Definition at line 207 of file gcu/residue.h.
static std::string const* gcu::Residue::GetFirstResidueSymbol | ( | ResidueIterator & | i | ) | [static] |
i | an iterator. |
gcu::Residue::GetGeneric | ( | void | ) | const [inline] |
Definition at line 202 of file gcu/residue.h.
gcu::Residue::GetMolecule | ( | void | ) | [inline] |
Returns the gcu::Molecule* describing the structure of the atoms group.
Definition at line 212 of file gcu/residue.h.
gcu::Residue::GetName | ( | void | ) | const [inline] |
std::map<std::string, std::string> const& gcu::Residue::GetNames | ( | ) | const [inline] |
Definition at line 110 of file gcu/residue.h.
static std::string const* gcu::Residue::GetNextResidueSymbol | ( | ResidueIterator & | i | ) | [static] |
i | an iterator initialized by Residue::GetFirstResidueSymbol. |
gcu::Residue::GetOwner | ( | void | ) | const [inline] |
Definition at line 217 of file gcu/residue.h.
std::map<int,int> const& gcu::Residue::GetRawFormula | ( | ) | const [inline] |
Residue *residue; ... // initialize the residue cout << "the residue has " << residue->GetRawFormula ()[6] << " carbon atoms." << endl;
Definition at line 98 of file gcu/residue.h.
gcu::Residue::GetRefGeneric | ( | void | ) | [inline] |
Definition at line 202 of file gcu/residue.h.
static Residue const* gcu::Residue::GetResidue | ( | char const * | symbol, | |
bool * | ambiguous = NULL | |||
) | [static] |
symbol | the symbol for which a Residue* is searched. | |
ambiguous | where to store the boolean telling if the symbol is ambiguous or NULL. |
static Residue const* gcu::Residue::GetResiduebyName | ( | char const * | name | ) | [static] |
name | the name for which a Residue* is searched. |
std::map<std::string, bool> const& gcu::Residue::GetSymbols | ( | ) | const [inline] |
Definition at line 105 of file gcu/residue.h.
virtual void gcu::Residue::Load | ( | xmlNodePtr | node | ) | [virtual] |
node | a XMLNode* representing the residue. |
virtual bool gcu::Residue::operator== | ( | G_GNUC_UNUSED Molecule const & | mol | ) | const [inline, virtual] |
mol | a molecule to compare to the atoms group. |
Definition at line 170 of file gcu/residue.h.
void gcu::Residue::RemoveSymbol | ( | char const * | symbol | ) |
symbol | a chemical symbol. |
gcu::Residue::SetGeneric | ( | bool | Generic | ) | [inline] |
Generic | whether the symbol is a generic symbol or not. |
Definition at line 202 of file gcu/residue.h.
void gcu::Residue::SetName | ( | char const * | name | ) |
name | the name to give to the Residue. |
unsigned gcu::Residue::MaxSymbolLength [static] |
Definition at line 177 of file gcu/residue.h.