#include <atom.h>

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) |
| Bond * | GetBondAtAngle (double angle) |
| void | SetShowSymbol (bool val) |
| bool | GetShowSymbol (void) const |
| bool & | GetRefShowSymbol (void) |
| void | SetHPosStyle (HPos val) |
| HPos | GetHPosStyle (void) const |
| HPos & | GetRefHPosStyle (void) |
| void | SetChargeItem (gccv::Item *val) |
| gccv::Item * | GetChargeItem (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 |
Definition at line 113 of file gcp/atom.h.
| gcp::Atom::Atom | ( | ) |
Default construtor.
Reimplemented from gcu::Atom.
| gcp::Atom::Atom | ( | int | Z, | |
| double | x, | |||
| double | y, | |||
| double | z | |||
| ) |
| 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 | ) |
| virtual gcp::Atom::~Atom | ( | ) | [virtual] |
The destructor.
Reimplemented from gcu::Atom.
| virtual bool gcp::Atom::AcceptCharge | ( | int | charge | ) | [virtual] |
| charge | the charge that might be set. |
Reimplemented in gcp::FragmentAtom.
| virtual bool gcp::Atom::AcceptNewBonds | ( | int | nb = 1 |
) | [virtual] |
| nb | the number of bonds to add, taking orders into account. |
Reimplemented in gcp::FragmentAtom.
| void gcp::Atom::AddBond | ( | gcu::Bond * | pBond | ) | [virtual] |
| void gcp::Atom::AddElectron | ( | Electron * | electron | ) |
| 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] |
| Mol,: | a pointer to a molecule |
Reimplemented in gcp::FragmentAtom.
| bool gcp::Atom::BuildContextualMenu | ( | GtkUIManager * | UIManager, | |
| Object * | object, | |||
| double | x, | |||
| double | y | |||
| ) |
| 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. |
| void gcp::Atom::BuildSymbolGeometry | ( | double | width, | |
| double | height, | |||
| double | ascent | |||
| ) | [protected] |
| width | the witdh of the atomic symbol. | |
| height | the height of the atomic symbol. | |
| ascent | the ascent of the atomic symbol. |
| void gcp::Atom::ForceChanged | ( | ) | [inline] |
Forces an update.
Definition at line 347 of file gcp/atom.h.
| int gcp::Atom::GetAttachedHydrogens | ( | ) | const [inline] |
Definition at line 171 of file gcp/atom.h.
| virtual int gcp::Atom::GetAvailablePosition | ( | double & | x, | |
| double & | y | |||
| ) | [virtual] |
| x | the x position. | |
| y | the y position. |
Reimplemented in gcp::FragmentAtom.
| HPos gcp::Atom::GetBestSide | ( | ) |
| Bond* gcp::Atom::GetBondAtAngle | ( | double | angle | ) |
| angle | the angle from the east direction in the trigonometric convention. |
| int gcp::Atom::GetCharge | ( | ) | const [inline] |
Definition at line 343 of file gcp/atom.h.
References gcu::Atom::m_Charge.
| gcp::Atom::GetChargeItem | ( | void | ) | [inline] |
Definition at line 475 of file gcp/atom.h.
| char gcp::Atom::GetChargePosition | ( | double * | Angle, | |
| double * | Dist | |||
| ) | const |
| 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. |
| virtual gccv::Anchor gcp::Atom::GetChargePosition | ( | unsigned char & | Pos, | |
| double | Angle, | |||
| double & | x, | |||
| double & | y | |||
| ) | [virtual] |
| 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. |
Reimplemented in gcp::FragmentAtom.
| gcp::Atom::GetHPosStyle | ( | void | ) | const [inline] |
| virtual bool gcp::Atom::GetPosition | ( | double | angle, | |
| double & | x, | |||
| double & | y | |||
| ) | [virtual] |
| angle | the angle at which a charge sign or an electron should be displayed. | |
| x | the x position. | |
| y | the y position. |
Reimplemented in gcp::FragmentAtom.
| gcp::Atom::GetRefHPosStyle | ( | void | ) | [inline] |
Definition at line 463 of file gcp/atom.h.
| gcp::Atom::GetRefShowSymbol | ( | void | ) | [inline] |
Definition at line 450 of file gcp/atom.h.
| virtual bool gcp::Atom::GetRelativePosition | ( | double | angle, | |
| double & | x, | |||
| double & | y | |||
| ) | [virtual] |
| angle | the angle at which a charge sign or an electron should be displayed. | |
| x | the x position. | |
| y | the y position. |
| gcp::Atom::GetShowCharge | ( | void | ) | const [inline] |
whether the local charge is displayed as a reference.
Definition at line 487 of file gcp/atom.h.
| gcp::Atom::GetShowSymbol | ( | void | ) | const [inline] |
Definition at line 450 of file gcp/atom.h.
| void gcp::Atom::GetSymbolGeometry | ( | double & | width, | |
| double & | height, | |||
| double & | angle, | |||
| bool | up | |||
| ) | const |
| 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 |
| int gcp::Atom::GetTotalBondsNumber | ( | ) | const |
| virtual double gcp::Atom::GetYAlign | ( | ) | [virtual] |
Reimplemented from gcu::Object.
| bool gcp::Atom::HasAvailableElectrons | ( | bool | paired | ) |
| paired | whether to ask for a pair of electrons or a single electron. |
| bool gcp::Atom::HasImplicitElectronPairs | ( | ) |
| virtual bool gcp::Atom::Load | ( | xmlNodePtr | node | ) | [virtual] |
| node | a pointer to the xmlNode containing the serialized atom. |
Reimplemented from gcu::Atom.
Reimplemented in gcp::FragmentAtom, and gcp::FragmentResidue.
| virtual bool gcp::Atom::LoadNode | ( | xmlNodePtr | node | ) | [virtual] |
| bool gcp::Atom::Match | ( | gcu::Atom * | atom, | |
| gcu::AtomMatchState & | state | |||
| ) | [virtual] |
| atom | the atom to which the this instance is to be compared. | |
| state | the AtomMatchState representing the current comparison state. |
Reimplemented from gcu::Atom.
Reimplemented in gcp::FragmentAtom.
| bool gcp::Atom::MayHaveImplicitUnpairedElectrons | ( | ) |
| void gcp::Atom::NotifyPositionOccupation | ( | unsigned char | pos, | |
| bool | occupied | |||
| ) |
| pos | one of POSITION_E, POSITION_N,... | |
| occupied | true if occupied, false otherwise. |
| void gcp::Atom::RemoveBond | ( | gcu::Bond * | pBond | ) | [virtual] |
| void gcp::Atom::RemoveElectron | ( | Electron * | electron | ) |
| virtual xmlNodePtr gcp::Atom::Save | ( | xmlDocPtr | xml | ) | const [virtual] |
| xml | the xmlDoc used to save the document. |
Reimplemented from gcu::Atom.
Reimplemented in gcp::FragmentAtom, and gcp::FragmentResidue.
| void gcp::Atom::SetCharge | ( | int | charge | ) |
| charge | the charge to set. |
| gcp::Atom::SetChargeItem | ( | gccv::Item * | item | ) | [inline] |
| item | a gccv::Item. |
Definition at line 475 of file gcp/atom.h.
| void gcp::Atom::SetChargePosition | ( | unsigned char | Pos, | |
| bool | def, | |||
| double | angle = 0., |
|||
| double | distance = 0. | |||
| ) |
| 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. |
| gcp::Atom::SetHPosStyle | ( | HPos | val | ) | [inline] |
| val | the new position. |
Definition at line 463 of file gcp/atom.h.
| void gcp::Atom::SetSelected | ( | int | state | ) | [virtual] |
| state | the selection state of the atom. |
Reimplemented from gccv::ItemClient.
Reimplemented in gcp::FragmentAtom.
| gcp::Atom::SetShowCharge | ( | bool | show | ) | [inline] |
| show | whether to display the local charge. |
Definition at line 487 of file gcp/atom.h.
| gcp::Atom::SetShowSymbol | ( | bool | ShowSymbol | ) | [inline] |
| ShowSymbol | whether the symbol of a carbon atom is to be displayed or not. |
Definition at line 450 of file gcp/atom.h.
| virtual void gcp::Atom::SetZ | ( | int | Z | ) | [virtual] |
| Z | the new atomic number. |
Reimplemented from gcu::Atom.
Reimplemented in gcp::FragmentAtom.
| virtual void gcp::Atom::Transform2D | ( | gcu::Matrix2D & | m, | |
| double | x, | |||
| double | y | |||
| ) | [virtual] |
| 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. |
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.
double gcp::Atom::m_CHeight [protected] |
Half the height of the "C" character.
Definition at line 437 of file gcp/atom.h.
1.5.9