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The Gnome Chemistry Utils
0.14.17
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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.
| 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.
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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.
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inline |
Returns the gcu::Document* used to store the molecule associated with the atoms group.
Definition at line 209 of file gcu/residue.h.
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| i | an iterator. |
Used to iterate through all known atoms groups and their symbols. Initializes the iterator.
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Definition at line 204 of file gcu/residue.h.
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Returns the gcu::Molecule* describing the structure of the atoms group.
Definition at line 214 of file gcu/residue.h.
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Definition at line 189 of file gcu/residue.h.
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inline |
Definition at line 111 of file gcu/residue.h.
References gcu::Document::GetResidue(), and gcu::Object::Load().
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| i | an iterator initialized by Residue::GetFirstResidueSymbol. |
Used to iterate through all known atoms groups and their symbols. Initializes the iterator.
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inline |
Definition at line 219 of file gcu/residue.h.
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inline |
The following code gives the number of carbon atoms:
Definition at line 99 of file gcu/residue.h.
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Definition at line 204 of file gcu/residue.h.
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| symbol | the symbol for which a Residue* is searched. |
| ambiguous | where to store the boolean telling if the symbol is ambiguous or NULL. |
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| name | the name for which a Residue* is searched. |
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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.
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virtual |
| node | a XMLNode* representing the residue. |
| app | the Application owning the residue. |
loads the residu from an XML file.
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inlinevirtual |
| mol | a molecule to compare to the atoms group. |
Definition at line 172 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.
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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 204 of file gcu/residue.h.
| void gcu::Residue::SetName | ( | char const * | name | ) |
| name | the name to give to the Residue. |
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static |
Definition at line 179 of file gcu/residue.h.
1.8.13