gcp::Atom Class Reference

#include <atom.h>

Inheritance diagram for gcp::Atom:

gcu::Atom gcu::DialogOwner gccv::ItemClient gcu::Object gcp::FragmentAtom gcp::FragmentResidue

List of all members.

Public Member Functions

 Atom ()
 Atom (int Z, double x, double y, double z)
 Atom (OpenBabel::OBAtom *atom)
virtual ~Atom ()
virtual void SetZ (int Z)
void AddBond (gcu::Bond *pBond)
void RemoveBond (gcu::Bond *pBond)
virtual void Update ()
int GetTotalBondsNumber () const
int GetAttachedHydrogens () const
HPos GetBestSide ()
virtual gccv::Anchor GetChargePosition (unsigned char &Pos, double Angle, double &x, double &y)
virtual int GetAvailablePosition (double &x, double &y)
virtual bool GetRelativePosition (double angle, double &x, double &y)
virtual bool GetPosition (double angle, double &x, double &y)
virtual xmlNodePtr Save (xmlDocPtr xml) const
virtual bool Load (xmlNodePtr node)
virtual bool LoadNode (xmlNodePtr node)
void AddItem ()
void SetSelected (int state)
virtual bool AcceptNewBonds (int nb=1)
virtual bool AcceptCharge (int charge)
virtual double GetYAlign ()
virtual void Transform2D (gcu::Matrix2D &m, double x, double y)
bool BuildContextualMenu (GtkUIManager *UIManager, Object *object, double x, double y)
virtual void AddToMolecule (Molecule *Mol)
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 ()
bool Match (gcu::Atom *atom, gcu::AtomMatchState &state)
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

Protected Member Functions

void BuildSymbolGeometry (double width, double height, double ascent)

Protected Attributes

double m_CHeight


Detailed Description

Represents atoms in GChemPaint.

Definition at line 113 of file gcp/atom.h.


Constructor & Destructor Documentation

gcp::Atom::Atom (  ) 

Default construtor.

Reimplemented from gcu::Atom.

gcp::Atom::Atom ( int  Z,
double  x,
double  y,
double  z 
)

Parameters:
Z the atomic number.
x the x coordinate.
y the y coordinate.
z the z coordinate.

Reimplemented from gcu::Atom.

gcp::Atom::Atom ( OpenBabel::OBAtom *  atom  ) 

Parameters:
atom an OpenBabel Atom instance.
Builds an atom importing as many properties from an existing OpenBabel Atom instance.

virtual gcp::Atom::~Atom (  )  [virtual]

The destructor.

Reimplemented from gcu::Atom.


Member Function Documentation

virtual bool gcp::Atom::AcceptCharge ( int  charge  )  [virtual]

Parameters:
charge the charge that might be set.
Returns:
true if the charge is acceptable.

Reimplemented in gcp::FragmentAtom.

virtual bool gcp::Atom::AcceptNewBonds ( int  nb = 1  )  [virtual]

Parameters:
nb the number of bonds to add, taking orders into account.
Returns:
true if the operation is allowed, false if the new bonds would exceed the maximum valence for the element.

Reimplemented in gcp::FragmentAtom.

void gcp::Atom::AddBond ( gcu::Bond pBond  )  [virtual]

Parameters:
pBond a bond.
Adds a bond to the atom.

Reimplemented from gcu::Atom.

void gcp::Atom::AddElectron ( Electron electron  ) 

Parameters:
electron a pointer to an Electron instance.
Adds the Electron (representing either a single electron or a pair) to the Atom.

void gcp::Atom::AddItem (  )  [virtual]

Used to add a representation of the atom in the view.

Reimplemented from gccv::ItemClient.

Reimplemented in gcp::FragmentAtom.

virtual void gcp::Atom::AddToMolecule ( Molecule Mol  )  [virtual]

Parameters:
Mol,: a pointer to a molecule
Adds the atom to the molecule calling gcpMolecule::AddAtom()

Reimplemented in gcp::FragmentAtom.

bool gcp::Atom::BuildContextualMenu ( GtkUIManager *  UIManager,
Object *  object,
double  x,
double  y 
)

Parameters:
UIManager,: the GtkUIManager to populate.
object the atom on which occured the mouse click.
x x coordinate of the mouse click.
y y coordinate of the mouse click.
This method is called to build a contextual menu for the atom.

void gcp::Atom::BuildSymbolGeometry ( double  width,
double  height,
double  ascent 
) [protected]

Parameters:
width the witdh of the atomic symbol.
height the height of the atomic symbol.
ascent the ascent of the atomic symbol.
Evaluates where lines representing bonds should end to not overload the symbol.

void gcp::Atom::ForceChanged (  )  [inline]

Forces an update.

Definition at line 347 of file gcp/atom.h.

int gcp::Atom::GetAttachedHydrogens (  )  const [inline]

Returns:
the number of implicit hydrogens lnked to the atom.

Definition at line 171 of file gcp/atom.h.

virtual int gcp::Atom::GetAvailablePosition ( double &  x,
double &  y 
) [virtual]

Parameters:
x the x position.
y the y position.
This method finds an available position for drawing a charge sign or electrons and returns it as a symbolic value (see POSITION_E, POSITION_N,...). The x and y are updated so that they give the absolute position.
Returns:
an available position.

Reimplemented in gcp::FragmentAtom.

HPos gcp::Atom::GetBestSide (  ) 

Returns:
the position of the attached hydrogen atoms symbol when automatically arranged.

Bond* gcp::Atom::GetBondAtAngle ( double  angle  ) 

Parameters:
angle the angle from the east direction in the trigonometric convention.
Returns:
the bond at or near the direction given by angle.

int gcp::Atom::GetCharge (  )  const [inline]

Returns:
the current formal local charge.

Definition at line 343 of file gcp/atom.h.

References gcu::Atom::m_Charge.

gcp::Atom::GetChargeItem ( void   )  [inline]

Returns:
the gccv::Item used to represent the formal charge of the atom.

Definition at line 475 of file gcp/atom.h.

char gcp::Atom::GetChargePosition ( double *  Angle,
double *  Dist 
) const

Parameters:
Angle where to store the angle from east direction in the trigonometric convention.
Dist where to store the distance from the center of the atom.
Returns:
the charge position as one of POSITION_E, POSITION_N,...

virtual gccv::Anchor gcp::Atom::GetChargePosition ( unsigned char &  Pos,
double  Angle,
double &  x,
double &  y 
) [virtual]

Parameters:
Pos the approximate position of the charge.
Angle the angle from horizontal left.
x the x position of the charge symbol.
y the y position of the charge symbol.
On input Pos can be one of POSITION_E, POSITION_N,... or 0xff, in which case, it will be given a default value. x and y are set to the position where the charge sign should be displayed usding the alignment code returned by this method.
Returns:
the anchor for the charge symbol. On error, gccv::AnchorCenter is used as the returned value.

Reimplemented in gcp::FragmentAtom.

gcp::Atom::GetHPosStyle ( void   )  const [inline]

Returns:
the position of attached hydrogen atoms symbol.

Definition at line 463 of file gcp/atom.h.

virtual bool gcp::Atom::GetPosition ( double  angle,
double &  x,
double &  y 
) [virtual]

Parameters:
angle the angle at which a charge sign or an electron should be displayed.
x the x position.
y the y position.
Updates x and y so that they become the absolute position corresponding to the angle when the position is available.
Returns:
true on success, false otherwise.

Reimplemented in gcp::FragmentAtom.

gcp::Atom::GetRefHPosStyle ( void   )  [inline]

Returns:
the position of attached hydrogen atoms symbol as a reference.

Definition at line 463 of file gcp/atom.h.

gcp::Atom::GetRefShowSymbol ( void   )  [inline]

Returns:
whether the symbol of a carbon atom is displayed or not as a reference.

Definition at line 450 of file gcp/atom.h.

virtual bool gcp::Atom::GetRelativePosition ( double  angle,
double &  x,
double &  y 
) [virtual]

Parameters:
angle the angle at which a charge sign or an electron should be displayed.
x the x position.
y the y position.
Updates x and y so that they become the position corresponding to the angle when the position is available, the origin being the position of the atom.
Returns:
true on success, false otherwise.

gcp::Atom::GetShowCharge ( void   )  const [inline]

Returns:
whether the local charge is displayed.

whether the local charge is displayed as a reference.

Definition at line 487 of file gcp/atom.h.

gcp::Atom::GetShowSymbol ( void   )  const [inline]

Returns:
whether the symbol of a carbon atom is displayed or not.

Definition at line 450 of file gcp/atom.h.

void gcp::Atom::GetSymbolGeometry ( double &  width,
double &  height,
double &  angle,
bool  up 
) const

Parameters:
width where to store the width.
height where to store the height.
angle where to store the limit angle.
up whether considering the top half or the bottom half
Used to retrieve the size of the ink rectangle of the atom symbol (if displayed). angle is absolute value of the angle between an horizontal line and the line joining the center and the top left or the bottom left vertex. The returned width value is actually half the full width. Height is the height. This method is used to avoid bonds lines extyending over their atoms symbols.

int gcp::Atom::GetTotalBondsNumber (  )  const

Returns:
the bonds number for this atom taking bond order into account

virtual double gcp::Atom::GetYAlign (  )  [virtual]

Returns:
the y coordinate at half height of the atom symbol if it was carbon.

Reimplemented from gcu::Object.

bool gcp::Atom::HasAvailableElectrons ( bool  paired  ) 

Parameters:
paired whether to ask for a pair of electrons or a single electron.
Returns:
true if non-bonding valence electrons are available.

bool gcp::Atom::HasImplicitElectronPairs (  ) 

Returns:
true if the atom has implicit electron pairs, false otherwise.

virtual bool gcp::Atom::Load ( xmlNodePtr  node  )  [virtual]

Parameters:
node a pointer to the xmlNode containing the serialized atom.
Used to load an atom in memory. The Atom must already exist.
Returns:
true on succes, false otherwise.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom, and gcp::FragmentResidue.

virtual bool gcp::Atom::LoadNode ( xmlNodePtr  node  )  [virtual]

Parameters:
node a pointer to the xmlNode containing the serialized Atom.
Used in this class to correctly set the atomic number.

Reimplemented from gcu::Atom.

bool gcp::Atom::Match ( gcu::Atom atom,
gcu::AtomMatchState state 
) [virtual]

Parameters:
atom the atom to which the this instance is to be compared.
state the AtomMatchState representing the current comparison state.
Try to match atoms from two molecules which are compared. This function calls itself recursively until all atoms from the two molecules have been matched or until an difference is found. Overriden methods should call this base function and return its result.
Returns:
true if the atoms match, false otherwise.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom.

bool gcp::Atom::MayHaveImplicitUnpairedElectrons (  ) 

Returns:
true if the atom has implcit electrons that might be unpaired.

void gcp::Atom::NotifyPositionOccupation ( unsigned char  pos,
bool  occupied 
)

Parameters:
pos one of POSITION_E, POSITION_N,...
occupied true if occupied, false otherwise.
Notifies if a position is occupied or not.

void gcp::Atom::RemoveBond ( gcu::Bond pBond  )  [virtual]

Parameters:
pBond a bond.
Removes a bond from the atom.

Reimplemented from gcu::Atom.

void gcp::Atom::RemoveElectron ( Electron electron  ) 

Parameters:
electron a pointer to an Electron instance.
Removes the Electron (representing either a single electron or a pair) from the Atom.

virtual xmlNodePtr gcp::Atom::Save ( xmlDocPtr  xml  )  const [virtual]

Parameters:
xml the xmlDoc used to save the document.
Used to save the Atom to the xmlDoc.
Returns:
the xmlNode containing the serialized atom.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom, and gcp::FragmentResidue.

void gcp::Atom::SetCharge ( int  charge  ) 

Parameters:
charge the charge to set.
Sets the formal local charge of an atom.

gcp::Atom::SetChargeItem ( gccv::Item item  )  [inline]

Parameters:
item a gccv::Item.
Sets the gccv::Item used to represent the formal charge of the atom, might be NULL.

Definition at line 475 of file gcp/atom.h.

void gcp::Atom::SetChargePosition ( unsigned char  Pos,
bool  def,
double  angle = 0.,
double  distance = 0. 
)

Parameters:
Pos one of POSITION_E, POSITION_N,...
def true if the position is automatic.
angle the angle from the east direction in the trigonometric convention.
distance the distance from the center of the atom, or 0. if automatic.
Sets the relative position of a charge sign.

gcp::Atom::SetHPosStyle ( HPos  val  )  [inline]

Parameters:
val the new position.
Sets the position of attached hydrogen atoms symbol.

Definition at line 463 of file gcp/atom.h.

void gcp::Atom::SetSelected ( int  state  )  [virtual]

Parameters:
state the selection state of the atom.
Used to set the selection state of the atom inside the widget. The values of state might be gcp::SelStateUnselected, gcp::SelStateSelected, gcp::SelStateUpdating, or gcp::SelStateErasing.

Reimplemented from gccv::ItemClient.

Reimplemented in gcp::FragmentAtom.

gcp::Atom::SetShowCharge ( bool  show  )  [inline]

Parameters:
show whether to display the local charge.
Shows or hides the atom local charge.

Definition at line 487 of file gcp/atom.h.

gcp::Atom::SetShowSymbol ( bool  ShowSymbol  )  [inline]

Parameters:
ShowSymbol whether the symbol of a carbon atom is to be displayed or not.
Sets the visibility of a carbon atom symbol in a chain.

Definition at line 450 of file gcp/atom.h.

virtual void gcp::Atom::SetZ ( int  Z  )  [virtual]

Parameters:
Z the new atomic number.
Changes the atomic number of the atom.

Reimplemented from gcu::Atom.

Reimplemented in gcp::FragmentAtom.

virtual void gcp::Atom::Transform2D ( gcu::Matrix2D m,
double  x,
double  y 
) [virtual]

Parameters:
m the Matrix2D of the transformation.
x the x component of the center of the transformation.
y the y component of the center of the transformation.
Used to move and/or transform an object.

Reimplemented from gcu::Atom.

virtual void gcp::Atom::Update (  )  [virtual]

Updates the atom after changing its bonds, charge or explicit electrons.

Reimplemented in gcp::FragmentAtom.


Member Data Documentation

double gcp::Atom::m_CHeight [protected]

Half the height of the "C" character.

Definition at line 437 of file gcp/atom.h.


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

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