KDE 4.2 API Reference kalzium
Avogadro::Molecule Class Reference
#include <primitive.h>
Detailed Description
Molecule Class.The Molecule class implements the OpenBabel::OBMol virtual functions in order to not only use our primitive objects but also to provide signals based on internal OpenBabel actions. In terms of a Model-View architecture, this is our model class and is used by our various views to hold all required data.
Definition at line 269 of file src/primitive.h.
Signals | |
| void | primitiveAdded (Primitive *primitive) |
| void | primitiveRemoved (Primitive *primitive) |
| void | primitiveUpdated (Primitive *primitive) |
Public Member Functions | |
| const Eigen::Vector3d & | center () const |
| Atom * | CreateAtom (void) |
| Bond * | CreateBond (void) |
| Residue * | CreateResidue (void) |
| void | DestroyAtom (OpenBabel::OBAtom *atom) |
| void | DestroyBond (OpenBabel::OBBond *bond) |
| void | DestroyResidue (OpenBabel::OBResidue *residue) |
| const Atom * | farthestAtom () const |
| Atom * | getAtomById (unsigned long id) const |
| Bond * | getBondById (unsigned long id) const |
| Molecule (const Molecule &other) | |
| Molecule (QObject *parent=0) | |
| Atom * | newAtom (unsigned long id) |
| Atom * | newAtom () |
| Bond * | newBond (unsigned long id) |
| Bond * | newBond () |
| const Eigen::Vector3d & | normalVector () const |
| Molecule & | operator+= (const Molecule &other) |
| Molecule & | operator= (const Molecule &other) |
| const double & | radius () const |
| void | update () |
| virtual | ~Molecule () |
Constructor & Destructor Documentation
| Avogadro::Molecule::Molecule | ( | QObject * | parent = 0 |
) |
| Avogadro::Molecule::Molecule | ( | const Molecule & | other | ) |
Definition at line 137 of file primitive.cpp.
| Avogadro::Molecule::~Molecule | ( | ) | [virtual] |
Definition at line 143 of file primitive.cpp.
Member Function Documentation
| const Eigen::Vector3d & Avogadro::Molecule::center | ( | ) | const |
Definition at line 315 of file primitive.cpp.
| Atom * Avogadro::Molecule::CreateAtom | ( | void | ) |
Virtual function inherited from OpenBabel::OBMol.
Creates a new Atom object.
- Returns:
- pointer to a newly allocated Atom object
Definition at line 147 of file primitive.cpp.
| Bond * Avogadro::Molecule::CreateBond | ( | void | ) |
Virtual function inherited from OpenBabel::OBMol.
Creates a new Bond object.
- Returns:
- pointer to a newly allocated Bond object
Definition at line 168 of file primitive.cpp.
| Residue * Avogadro::Molecule::CreateResidue | ( | void | ) |
Virtual function inherited from OpenBabel::OBMol.
Creates a new Residue object.
- Returns:
- pointer to a newly allocated Residue object
Definition at line 189 of file primitive.cpp.
| void Avogadro::Molecule::DestroyAtom | ( | OpenBabel::OBAtom * | atom | ) |
Virtual function inherited from OpenBabel::OBMol.
Deletes an Atom object.
- Parameters:
-
atom the atom to delete
Definition at line 224 of file primitive.cpp.
| void Avogadro::Molecule::DestroyBond | ( | OpenBabel::OBBond * | bond | ) |
Virtual function inherited from OpenBabel::OBMol.
Deletes an Bond object.
- Parameters:
-
atom the bond to delete
Definition at line 270 of file primitive.cpp.
| void Avogadro::Molecule::DestroyResidue | ( | OpenBabel::OBResidue * | residue | ) |
Virtual function inherited from OpenBabel::OBMol.
Deletes an Residue object.
- Parameters:
-
atom the residue to delete
Definition at line 291 of file primitive.cpp.
| const Atom * Avogadro::Molecule::farthestAtom | ( | ) | const |
Definition at line 336 of file primitive.cpp.
| Atom * Avogadro::Molecule::getAtomById | ( | unsigned long | id | ) | const |
Definition at line 235 of file primitive.cpp.
| Bond * Avogadro::Molecule::getBondById | ( | unsigned long | id | ) | const |
Definition at line 281 of file primitive.cpp.
| Atom * Avogadro::Molecule::newAtom | ( | unsigned long | id | ) |
Definition at line 203 of file primitive.cpp.
| Atom * Avogadro::Molecule::newAtom | ( | ) |
These are new functions to replace OBMol::NewAtom to use our new unique identifier functionality.
Definition at line 197 of file primitive.cpp.
| Bond * Avogadro::Molecule::newBond | ( | unsigned long | id | ) |
Definition at line 250 of file primitive.cpp.
| Bond * Avogadro::Molecule::newBond | ( | ) |
These are new functions to replace OBMol::NewBond to use our new unique identifier functionality.
Definition at line 245 of file primitive.cpp.
| const Eigen::Vector3d & Avogadro::Molecule::normalVector | ( | ) | const |
Definition at line 322 of file primitive.cpp.
Definition at line 391 of file primitive.cpp.
Definition at line 343 of file primitive.cpp.
| void Avogadro::Molecule::primitiveAdded | ( | Primitive * | primitive | ) | [signal] |
Emitted when a child primitive is added.
- Parameters:
-
primitive pointer to the primitive that was added
| void Avogadro::Molecule::primitiveRemoved | ( | Primitive * | primitive | ) | [signal] |
Emitted when a child primitive is deleted.
- Parameters:
-
primitive pointer to the primitive that was updated before it is free'd
| void Avogadro::Molecule::primitiveUpdated | ( | Primitive * | primitive | ) | [signal] |
Emitted when a child primitive is updated.
- Parameters:
-
primitive pointer to the primitive that was updated
| const double & Avogadro::Molecule::radius | ( | ) | const |
Definition at line 329 of file primitive.cpp.
| void Avogadro::Molecule::update | ( | ) |
Function used to push changes to a primitive to the rest of the system.
At this time there is no way (other than this) to generate a signal when properties of a primitive change.
In the case of the Atom primitive, this should be called when changes to coordinates have been made.
Reimplemented from Avogadro::Primitive.
Definition at line 308 of file primitive.cpp.
The documentation for this class was generated from the following files:
