RWMolecule Class Reference

The RWMolecule class is an editable molecule class that automatically populates an undo stack. More...

#include <avogadro/qtgui/rwmolecule.h>

Inheritance diagram for RWMolecule:

Classes
class	UndoCommand

Public Types
typedef RWAtom	AtomType
typedef PersistentAtom< RWMolecule >	PersistentAtomType
typedef RWBond	BondType
typedef PersistentBond< RWMolecule >	PersistentBondType

Public Slots
void	emitChanged (unsigned int change)
	Force the molecule to emit the changed() signal. More...

Signals
void	changed (unsigned int change)
	Indicates that the molecule has changed. More...

Public Member Functions
	RWMolecule (Molecule &mol, QObject *parent=nullptr)
Molecule &	molecule ()
const Molecule &	molecule () const
AtomType	addAtom (unsigned char atomicNumber, bool usingPositions=true)
AtomType	addAtom (unsigned char atomicNumber, const Vector3 &position3d)
AtomType	atom (Index atomId) const
AtomType	atomByUniqueId (Index atomUId) const
Index	atomCount () const
Index	atomCount (unsigned char atomicNumber) const
void	clearAtoms ()
void	adjustHydrogens (Index atomId)
void	adjustHydrogens (const Core::Array< Index > &atomIds)
const Core::Array< unsigned char > &	atomicNumbers () const
unsigned char	atomicNumber (Index atomId) const
bool	setAtomicNumbers (const Core::Array< unsigned char > &nums)
bool	setAtomicNumber (Index atomId, unsigned char atomicNumber)
const Core::Array< Vector3 > &	atomPositions3d () const
Vector3	atomPosition3d (Index atomId) const
std::string	label (Index atomId) const
bool	setLabel (Index atomId, const std::string &label, const QString &undoText=QStringLiteral("Change Atom Label"))
bool	setAtomPositions3d (const Core::Array< Vector3 > &pos, const QString &undoText=QStringLiteral("Change Atom Positions"))
bool	setAtomPosition3d (Index atomId, const Vector3 &pos, const QString &undoText=QStringLiteral("Change Atom Position"))
void	setAtomSelected (Index atomId, bool selected)
bool	atomSelected (Index atomId) const
bool	setAtomPosition2d (Index, const Vector2 &)
Vector2	atomPosition2d (Index)
const Core::Array< Vector2 > &	atomPositions2d () const
Core::AtomHybridization	hybridization (Index atomId) const
bool	setHybridization (Index atomId, Core::AtomHybridization hyb)
signed char	formalCharge (Index atomId) const
bool	setFormalCharge (Index atomId, signed char charge)
Vector3ub	color (Index atomId) const
bool	setColor (Index atomId, Vector3ub color)
bool	setLayer (Index atomId, size_t layer)
size_t	layer (Index atomId) const
BondType	bond (Index bondId) const
BondType	bond (Index atom1, Index atom2) const
BondType	bond (const AtomType &atom1, const AtomType &atom2) const
BondType	bondByUniqueId (Index bondUid) const
Index	bondUniqueId (Index bondId) const
Index	bondUniqueId (const BondType &bond) const
Index	bondCount () const
void	clearBonds ()
Core::Array< BondType >	bonds (const AtomType &atom) const
Core::Array< BondType >	bonds (const Index &atomId) const
const Core::Array< unsigned char > &	bondOrders () const
unsigned char	bondOrder (Index bondId) const
bool	setBondOrders (const Core::Array< unsigned char > &orders)
bool	setBondOrder (Index bondId, unsigned char order)
const Core::Array< std::pair< Index, Index > > &	bondPairs () const
std::pair< Index, Index >	bondPair (Index bondId) const
bool	setBondPairs (const Core::Array< std::pair< Index, Index > > &pairs)
bool	setBondPair (Index bondId, const std::pair< Index, Index > &pair)
void	addUnitCell ()
void	removeUnitCell ()
void	modifyMolecule (const Molecule &newMolecule, Molecule::MoleculeChanges changes, const QString &undoText=QStringLiteral("Modify Molecule"))
void	appendMolecule (const Molecule &addMolecule, const QString &undoText=QStringLiteral("Append Molecule"))
void	editUnitCell (Matrix3 cellMatrix, Core::CrystalTools::Options opts)
void	wrapAtomsToCell ()
void	rotateCellToStandardOrientation ()
void	setCellVolume (double newVolume, Core::CrystalTools::Options options)
void	buildSupercell (unsigned int a, unsigned int b, unsigned int c)
void