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The Gnome Chemistry Utils 0.12.8
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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) |
| 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 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 |
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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 207 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 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] |
Definition at line 187 of file gcu/residue.h.
| 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. |
Used to iterate through all known atoms groups and their symbols. Initializes the iterator.
| 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] |
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 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 |
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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 105 of file gcu/residue.h.
| virtual void gcu::Residue::Load | ( | xmlNodePtr | node | ) | [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 170 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 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.
1.7.4