The Gnome Chemistry Utils 0.13.3
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#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, 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 |
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.
gcu::Residue::Residue | ( | ) |
Creates a residue.
Reimplemented in gcp::Residue.
gcu::Residue::Residue | ( | char const * | name, |
Document * | doc = NULL |
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) |
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.
void gcu::Residue::AddSymbol | ( | char const * | symbol | ) |
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 208 of file gcu/residue.h.
static std::string const* gcu::Residue::GetFirstResidueSymbol | ( | ResidueIterator & | i | ) | [static] |
i | an iterator. |
Used to iterate through all known atoms groups and their symbols. Initializes the iterator.
gcu::Residue::GetGeneric | ( | void | ) | const [inline] |
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] |
Definition at line 188 of file gcu/residue.h.
std::map<std::string, std::string> const& gcu::Residue::GetNames | ( | ) | const [inline] |
Definition at line 111 of file gcu/residue.h.
static std::string const* gcu::Residue::GetNextResidueSymbol | ( | ResidueIterator & | i | ) | [static] |
i | an iterator initialized by Residue::GetFirstResidueSymbol. |
Used to iterate through all known atoms groups and their symbols. Initializes the iterator.
gcu::Residue::GetOwner | ( | void | ) | const [inline] |
Definition at line 218 of file gcu/residue.h.
std::map<int,int> const& gcu::Residue::GetRawFormula | ( | ) | const [inline] |
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] |
Definition at line 203 of file gcu/residue.h.
static Residue const* gcu::Residue::GetResidue | ( | char const * | symbol, |
bool * | ambiguous = NULL |
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) | [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] |
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] |
node | a 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] |
mol | a molecule to compare to the atoms group. |
Definition at line 171 of file gcu/residue.h.
void gcu::Residue::RemoveSymbol | ( | char const * | symbol | ) |
symbol | a chemical symbol. |
Removes symbol from the list of valid symbols for the atoms group.
gcu::Residue::SetGeneric | ( | bool | Generic | ) | [inline] |
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 203 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 178 of file gcu/residue.h.