The Gnome Chemistry Utils  0.12.11
Public Member Functions
gcp::FragmentResidue Class Reference

#include <gcp/fragment-residue.h>

Inheritance diagram for gcp::FragmentResidue:
gcp::FragmentAtom gcp::Atom gcu::Atom gcu::DialogOwner gccv::ItemClient gcu::Object

List of all members.

Public Member Functions

 FragmentResidue ()
 FragmentResidue (Fragment *fragment, char const *symbol)
virtual ~FragmentResidue ()
xmlNodePtr Save (xmlDocPtr xml) const
bool Load (xmlNodePtr node)
void SetResidue (Residue const *res)
const gchar * GetSymbol () const
Residue const * GetResidue (void) const
std::string GetAbbrev (void) const
- Public Member Functions inherited from gcp::FragmentAtom
 FragmentAtom ()
 FragmentAtom (Fragment *fragment, int Z)
virtual ~FragmentAtom ()
void SetZ (int Z)
bool AcceptNewBonds (int nb)
void Update ()
void AddItem ()
void UpdateItem ()
void SetSelected (int state)
gccv::Anchor GetChargePosition (unsigned char &Pos, double Angle, double &x, double &y)
int GetAvailablePosition (double &x, double &y)
bool GetPosition (double angle, double &x, double &y)
bool AcceptCharge (int charge)
void AddToMolecule (Molecule *Mol)
bool Match (gcu::Atom *atom, gcu::AtomMatchState &state)
void DoBuildSymbolGeometry (View *pView)
Fragment const * GetFragment (void) const
- Public Member Functions inherited from gcp::Atom
 Atom ()
 Atom (int Z, double x, double y, double z)
 Atom (OpenBabel::OBAtom *atom)
virtual ~Atom ()
void AddBond (gcu::Bond *pBond)
void RemoveBond (gcu::Bond *pBond)
int GetTotalBondsNumber () const
int GetAttachedHydrogens () const
HPos GetBestSide ()
virtual bool GetRelativePosition (double angle, double &x, double &y)
virtual bool LoadNode (xmlNodePtr node)
virtual double GetYAlign ()
virtual void Transform2D (gcu::Matrix2D &m, double x, double y)
bool BuildContextualMenu (GtkUIManager *UIManager, Object *object, double x, double y)
bool HasImplicitElectronPairs ()
bool MayHaveImplicitUnpairedElectrons ()
void AddElectron (Electron *electron)
void RemoveElectron (Electron *electron)
void NotifyPositionOccupation (unsigned char pos, bool occupied)
void SetChargePosition (unsigned char Pos, bool def, double angle=0., double distance=0.)
char GetChargePosition (double *Angle, double *Dist) const
void SetCharge (int charge)
int GetCharge () const
void ForceChanged ()
void GetSymbolGeometry (double &width, double &height, double &angle, bool up) const
bool HasAvailableElectrons (bool paired)
BondGetBondAtAngle (double angle)
void SetShowSymbol (bool val)
bool GetShowSymbol (void) const
bool & GetRefShowSymbol (void)
void SetHPosStyle (HPos val)
HPos GetHPosStyle (void) const
HPosGetRefHPosStyle (void)
void SetChargeItem (gccv::Item *val)
gccv::ItemGetChargeItem (void)
void SetShowCharge (bool val)
bool GetShowCharge (void) const
- Public Member Functions inherited from gcu::Atom
 Atom (Atom &a)
Atomoperator= (Atom &a)
double Distance (Atom *pAtom)
void zoom (double ZoomFactor)
virtual bool GetCoords (double *x, double *y, double *z=NULL) const
void SetCoords (double x, double y, double z=0)
int GetZ () const
virtual void SetCharge (char Charge)
char GetCharge ()
double x () const
double y () const
double z () const
Vector GetVector () const
BondGetFirstBond (std::map< Atom *, Bond * >::iterator &i)
BondGetNextBond (std::map< Atom *, Bond * >::iterator &i)
BondGetBond (Atom *pAtom) const
int GetBondsNumber () const
virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const
virtual void Move (double x, double y, double z=0.)
bool SetProperty (unsigned property, char const *value)
std::string GetProperty (unsigned property) const
bool IsInCycle (Cycle *pCycle)
std::string Name ()
- Public Member Functions inherited from gcu::Object
 Object (TypeId Id=OtherType)
virtual ~Object ()
TypeId GetType () const
void SetId (gchar const *Id)
gchar const * GetId () const
virtual void AddChild (Object *object)
ObjectGetMolecule () const
ObjectGetReaction () const
ObjectGetGroup () const
DocumentGetDocument () const
ObjectGetParentOfType (TypeId Id) const
ObjectGetChild (const gchar *Id) const
ObjectGetFirstChild (std::map< std::string, Object * >::iterator &i)
ObjectGetNextChild (std::map< std::string, Object * >::iterator &i)
ObjectGetDescendant (const gchar *Id) const
ObjectGetParent () const
void SetParent (Object *Parent)
bool SaveChildren (xmlDocPtr xml, xmlNodePtr node) const
void SaveId (xmlNodePtr node) const
xmlNodePtr GetNodeByProp (xmlNodePtr node, char const *Property, char const *Id)
xmlNodePtr GetNextNodeByProp (xmlNodePtr node, char const *Property, char const *Id)
xmlNodePtr GetNodeByName (xmlNodePtr node, char const *Name)
xmlNodePtr GetNextNodeByName (xmlNodePtr node, char const *Name)
bool HasChildren () const
unsigned GetChildrenNumber () const
virtual ObjectGetAtomAt (double x, double y, double z=0.)
virtual bool Build (std::list< Object * > &Children) throw (std::invalid_argument)
virtual bool BuildContextualMenu (GtkUIManager *UIManager, Object *object, double x, double y)
void EmitSignal (SignalId Signal)
virtual bool OnSignal (SignalId Signal, Object *Child)
void Lock (bool state=true)
bool IsLocked ()
ObjectGetFirstLink (std::set< Object * >::iterator &i)
ObjectGetNextLink (std::set< Object * >::iterator &i)
void Link (Object *object)
void Unlink (Object *object)
virtual void OnUnlink (Object *object)
void GetPossibleAncestorTypes (std::set< TypeId > &types) const
virtual void OnLoaded ()
void SetDirty (bool dirty=true)
virtual void Clear ()
std::string Identity ()
virtual char const * HasPropertiesDialog () const
void ShowPropertiesDialog ()
bool GetDirty (void) const
- Public Member Functions inherited from gcu::DialogOwner
 DialogOwner ()
virtual ~DialogOwner ()
DialogGetDialog (std::string name)
void ClearDialogs ()
- Public Member Functions inherited from gccv::ItemClient
 ItemClient ()
virtual ~ItemClient ()
ItemGetItem (void)

Detailed Description

Represents a residue inside a atoms group (see gcp::Fragment class).

Definition at line 38 of file fragment-residue.h.


Constructor & Destructor Documentation

gcp::FragmentResidue::FragmentResidue ( )

The default constructor.

gcp::FragmentResidue::FragmentResidue ( Fragment fragment,
char const *  symbol 
)
Parameters:
fragmentthe fragment containing the residue symbol.
symbolthe residue symbol.

Constructs a FragmentResidue as a child of fragment.

virtual gcp::FragmentResidue::~FragmentResidue ( )
virtual

The destructor.


Member Function Documentation

gcp::FragmentResidue::GetAbbrev ( void  ) const
inline
Returns:
the used symbol for the residue.

Definition at line 89 of file fragment-residue.h.

gcp::FragmentResidue::GetResidue ( void  ) const
inline
Returns:
the associated residue.

Definition at line 85 of file fragment-residue.h.

const gchar* gcp::FragmentResidue::GetSymbol ( ) const
virtual
Returns:
the symbol of this Residue.

Reimplemented from gcu::Atom.

bool gcp::FragmentResidue::Load ( xmlNodePtr  node)
virtual
Parameters:
nodean XML node.

Loads the symbol and associated resdue from node.

Returns:
true on success, false otherwise.

Reimplemented from gcp::FragmentAtom.

xmlNodePtr gcp::FragmentResidue::Save ( xmlDocPtr  xml) const
virtual
Parameters:
xmlthe xmlDoc used to save the document.

Builds an XML node representing this instance.

Returns:
the new XML node or NULL on error.

Reimplemented from gcp::FragmentAtom.

void gcp::FragmentResidue::SetResidue ( Residue const *  res)
Parameters:
resthe residue correspondig to the symbol.

Sets the associated residue.


The documentation for this class was generated from the following file: