gcu::Residue Class Reference
#include <gcu/residue.h>
List of all members.
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 66 of file gcu/residue.h.
Constructor & Destructor Documentation
gcu::Residue::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] |
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.
static std::string const* gcu::Residue::GetFirstResidueSymbol |
( |
ResidueIterator & |
i |
) |
[static] |
- Parameters:
-
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.
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 110 of file gcu/residue.h.
static std::string const* gcu::Residue::GetNextResidueSymbol |
( |
ResidueIterator & |
i |
) |
[static] |
- Parameters:
-
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.
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;
...
cout << "the residue has " << residue->GetRawFormula ()[6] << " carbon atoms." << endl;
Definition at line 98 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 105 of file gcu/residue.h.
virtual void gcu::Residue::Load |
( |
xmlNodePtr |
node |
) |
[virtual] |
- Parameters:
-
| 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] |
- 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 170 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.
void gcu::Residue::SetName |
( |
char const * |
name |
) |
|
- Parameters:
-
| name | the name to give to the Residue. |
Member Data Documentation
- Returns:
- the maxium length of all known symbols. This is used by the framework when parsing a string formula.
Definition at line 177 of file gcu/residue.h.
The documentation for this class was generated from the following file: