The Gnome Chemistry Utils
0.13.6
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GChemPaint molecule class. More...
#include <gcp/molecule.h>
Public Member Functions | |
Molecule (gcu::TypeId Type=gcu::MoleculeType) | |
Molecule (Atom *pAtom) | |
virtual | ~Molecule () |
void | AddChild (gcu::Object *object) |
void | AddAtom (gcu::Atom *pAtom) |
void | AddFragment (Fragment *pFragment) |
void | AddBond (gcu::Bond *pBond) |
void | Remove (gcu::Object *pObject) |
bool | Merge (Molecule *pMolecule, bool RemoveDuplicates=false) |
bool | Load (xmlNodePtr node) |
xmlNodePtr | Save (xmlDocPtr xml) const |
void | Clear () |
void | Transform2D (gcu::Matrix2D &m, double x, double y) |
Object * | GetAtomAt (double x, double y, double z=0.) |
double | GetYAlign () |
bool | BuildContextualMenu (gcu::UIManager *UIManager, gcu::Object *object, double x, double y) |
bool | OnSignal (gcu::SignalId Signal, gcu::Object *Child) |
void | SelectAlignmentItem (gcu::Object *child) |
std::string | GetAlignmentId () |
void | OpenCalc () |
void | CheckCrossings (Bond *pBond) |
std::string | GetRawFormula () const |
void | OnLoaded () |
unsigned | GetAtomsNumber () const |
GChemPaint molecule class.
Definition at line 45 of file gcp/molecule.h.
gcp::Molecule::Molecule | ( | gcu::TypeId | Type = gcu::MoleculeType | ) |
The default constructor. Builds a new empty molecule.
gcp::Molecule::Molecule | ( | Atom * | pAtom | ) |
pAtom | an atom. |
Constructs a new molecule containing pAtom and all atoms which might be bonded to it, and the corresponding bonds.
virtual gcp::Molecule::~Molecule | ( | ) | [virtual] |
The destructor.
Reimplemented from gcugtk::Molecule.
void gcp::Molecule::AddAtom | ( | gcu::Atom * | pAtom | ) | [virtual] |
void gcp::Molecule::AddBond | ( | gcu::Bond * | pBond | ) | [virtual] |
void gcp::Molecule::AddChild | ( | gcu::Object * | object | ) | [virtual] |
object | the object to add to the molecule. |
Adds an object (atom, bond, or fragment) to the molecule.
Reimplemented from gcu::Molecule.
void gcp::Molecule::AddFragment | ( | Fragment * | pFragment | ) |
pFragment | an atoms group. |
Adds a fragment to the molecule.
bool gcp::Molecule::BuildContextualMenu | ( | gcu::UIManager * | UIManager, |
gcu::Object * | object, | ||
double | x, | ||
double | y | ||
) | [virtual] |
UIManager | the gcu::UIManager to populate. |
object | the Object 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 the contextual menu for the molecule.
Reimplemented from gcu::Object.
void gcp::Molecule::CheckCrossings | ( | Bond * | pBond | ) |
pBond | a bond in the molecule. |
Checks if any other bond in the molecule crosses pBond, and notify both bonds that they are crossing.
void gcp::Molecule::Clear | ( | ) | [virtual] |
Removes all children from the molecule, resulting in a empty molecule.
Reimplemented from gcu::Molecule.
std::string gcp::Molecule::GetAlignmentId | ( | ) | [inline] |
Definition at line 176 of file gcp/molecule.h.
References gcu::Object::GetId().
Object* gcp::Molecule::GetAtomAt | ( | double | x, |
double | y, | ||
double | z = 0. |
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) | [virtual] |
x | the x coordinate |
y | the y coordinate |
z | the z coordinate (not used) |
Reimplemented from gcu::Object.
unsigned gcp::Molecule::GetAtomsNumber | ( | ) | const [virtual] |
Reimplemented from gcu::Molecule.
std::string gcp::Molecule::GetRawFormula | ( | ) | const [virtual] |
Reimplemented from gcu::Molecule.
double gcp::Molecule::GetYAlign | ( | ) | [virtual] |
Used to retrieve the y coordinate for alignment.
Reimplemented from gcu::Object.
bool gcp::Molecule::Load | ( | xmlNodePtr | node | ) | [virtual] |
node | a pointer to the xmlNode containing the serialized molecule. |
Used to load a molecule in memory. The Mlecule instance must already exist.
Reimplemented from gcu::Object.
bool gcp::Molecule::Merge | ( | Molecule * | pMolecule, |
bool | RemoveDuplicates = false |
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) |
pMolecule | a molecule. |
RemoveDuplicates | whether duplicate atoms should be unififed or not. |
Adds all children from pMolecule in this instance, and removes one of the atoms for each pair of duplicates (atoms with same atomic number and position) if RemoveDuplicates is true. This might fail when it would end with hypervalent atoms. On success pMolecule is deleted.
void gcp::Molecule::OnLoaded | ( | ) | [virtual] |
Updates all cycles after loading.
Reimplemented from gcu::Object.
bool gcp::Molecule::OnSignal | ( | gcu::SignalId | Signal, |
gcu::Object * | Child | ||
) | [virtual] |
Signal | the appropriate SignalId |
Child | the child which emitted the signal or NULL |
Signals the molecule that at least one of its children changed.
Reimplemented from gcu::Object.
void gcp::Molecule::OpenCalc | ( | ) |
Opens GChemCalc with the formula for the molecule. Molecules with fragments are not currently supported.
void gcp::Molecule::Remove | ( | gcu::Object * | pObject | ) | [virtual] |
pObject | an atom, a bond, or a fragment in the molecule. |
Removes an atom, a bond, or a fragment from a molecule.
Reimplemented from gcu::Molecule.
xmlNodePtr gcp::Molecule::Save | ( | xmlDocPtr | xml | ) | const [virtual] |
xml | the xmlDoc used to save the document. |
Used to save the molecule to the xmlDoc.
Reimplemented from gcu::Object.
void gcp::Molecule::SelectAlignmentItem | ( | gcu::Object * | child | ) |
child | the child used for alignment. |
Selects the child used for alignment, which might be an atom or group of atoms, or a bond. For bonds, the center of the bonds is used, a while for the others a call to their gcu::Object::GetYAlign() method will be used.
void gcp::Molecule::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. |
Used to move and/or transform the molecule taking care of hydrogen atoms positions around heteroatoms.
Reimplemented from gcu::Object.