gcp::Atom Class Reference
#include <atom.h>
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 |
void | SetShowSymbol (bool val) |
bool | GetShowSymbol (void) const |
bool & | GetRefShowSymbol (void) |
void | SetHPosStyle (HPos val) |
HPos | GetHPosStyle (void) const |
HPos & | GetRefHPosStyle (void) |
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
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:
-
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 |
( |
|
) |
|
Used to add a representation of the atom in the view.
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, |
|
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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, |
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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] |
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.
int gcp::Atom::GetCharge |
( |
|
) |
const [inline] |
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 452 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 452 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 439 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::GetShowSymbol |
( |
void |
|
) |
const [inline] |
- Returns:
- whether the symbol of a carbon atom is displayed or not.
Definition at line 439 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::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.
- 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:
-
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] |
void gcp::Atom::SetCharge |
( |
int |
charge |
) |
|
- Parameters:
-
| charge | the charge to set. |
Sets the formal local charge of an atom.
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:
-
Sets the position of attached hydrogen atoms symbol.
Definition at line 452 of file gcp/atom.h.
void gcp::Atom::SetSelected |
( |
int |
state |
) |
|
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 439 of file gcp/atom.h.
virtual void gcp::Atom::SetZ |
( |
int |
Z |
) |
[virtual] |
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
Half the height of the "C" character.
Definition at line 426 of file gcp/atom.h.
The documentation for this class was generated from the following file: