The Gnome Chemistry Utils  0.13.90
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, char const *symbol=NULL)
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)
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 Move (double x, double y, double z=0.)
virtual void Transform2D (gcu::Matrix2D &m, double x, double y)
bool BuildContextualMenu (gcu::UIManager *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)
bool UpdateStereoBonds ()
bool HasStereoBond () const
BondGetNewmanBond () const
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)
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)
Bond const * GetFirstBond (std::map< Atom *, Bond * >::const_iterator &i) const
BondGetNextBond (std::map< Atom *, Bond * >::iterator &i)
Bond const * GetNextBond (std::map< Atom *, Bond * >::const_iterator &i) const
BondGetBond (Atom *pAtom) const
int GetBondsNumber () const
virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node) const
std::string GetProperty (unsigned property) const
bool IsInCycle (Cycle *pCycle)
std::string Name ()
void NetToCartesian (double a, double b, double c, double alpha, double beta, double gamma)
- Public Member Functions inherited from gcu::Object
 Object (TypeId Id=OtherType)
virtual ~Object ()
TypeId GetType () const
void SetId (gchar const *Id)
char const * GetId () const
virtual void AddChild (Object *object)
ObjectGetMolecule () const
ObjectGetReaction () const
ObjectGetGroup () const
DocumentGetDocument () const
ApplicationGetApplication () 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 char *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::set< Object * > const &Children) throw (std::invalid_argument)
virtual bool BuildContextualMenu (UIManager *uim, 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
virtual bool CanSelect () const
virtual void NotifyEmpty ()
void ShowPropertiesDialog ()
bool GetDirty (void) const
- Public Member Functions inherited from gcu::DialogOwner
 DialogOwner ()
virtual ~DialogOwner ()
DialogGetDialog (std::string name) const
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 90 of file fragment-residue.h.

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

Definition at line 86 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,
char const *  symbol = NULL 
)
Parameters:
resthe residue corresponding to the symbol.
symbolthe symbol to use, or NULL to use the default symbol.

Sets the associated residue.


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