A QObject derived molecule object with signals/slots.

#include <avogadro/qtgui/molecule.h>

Inheritance diagram for Molecule:

Public Types
enum	MoleculeChange { NoChange = 0 , Atoms = 1 , Bonds = 2 , UnitCell = 4 , Selection = 8 , Layers = 16 , Properties = 32 , Constraints = 64 , Added = 1024 , Removed = 2048 , Modified = 4096 }
typedef Core::Molecule::AtomType	AtomType
typedef PersistentAtom< Molecule >	PersistentAtomType
typedef Core::Molecule::BondType	BondType
typedef PersistentBond< Molecule >	PersistentBondType
Public Types inherited from Molecule
using	AtomType = Atom
using	BondType = Bond
using	CustomElementMap = std::map<unsigned char, std::string>
using	ElementMask = std::bitset<element_count>

Public Slots
void	emitChanged (unsigned int change)
	Force the molecule to emit the changed() signal.
void	emitUpdate () const
	Request an update through the update() signal.

Signals
void	changed (unsigned int change) const
	Indicates that the molecule has changed.
void	update () const
	Request an update of the molecule. (e.g., re-compute properties).

Public Member Functions
	Molecule (QObject *parent_=nullptr)
	~Molecule () override
	Molecule (const Molecule &other)
	Molecule (const Core::Molecule &other)
Molecule &	operator= (const Molecule &other)
Molecule &	operator= (const Core::Molecule &other)
AtomType	addAtom (unsigned char atomicNumber) override
virtual AtomType	addAtom (unsigned char atomicNumber, Index uniqueId)
AtomType	addAtom (unsigned char number, Vector3 position3d, Index uniqueId=MaxIndex)
bool	removeAtom (Index index) override
	Remove the specified atom from the molecule.
bool	removeAtom (const AtomType &atom) override
	Remove the specified atom from the molecule.
AtomType	atomByUniqueId (Index uniqueId)
	Get the atom referenced by the `uniqueId`, the isValid method should be queried to ensure the id still referenced a valid atom.
Core::Array< Index > &	atomUniqueIds ()
BondType	addBond (const AtomType &a, const AtomType &b, unsigned char bondOrder=1) override
	Add a bond between the specified atoms.
BondType	addBond (Index atomId1, Index atomId2, unsigned char bondOrder=1) override
	Add a bond between the specified atoms.
void	addBonds (const Core::Array< std::pair< Index, Index > > &bonds, const Core::Array< unsigned char > &orders)
virtual BondType	addBond (const AtomType &a, const AtomType &b, unsigned char bondOrder, Index uniqueId)
	Add a bond between the specified atoms.
virtual BondType	addBond (Index atomId1, Index atomId2, unsigned char bondOrder, Index uniqueId)
	Add a bond between the specified atoms.
bool	removeBond (Index index) override
	Remove the specified bond.
bool	removeBond (const BondType &bond) override
	Remove the specified bond.
BondType	bondByUniqueId (Index uniqueId)
	Get the bond referenced by the `uniqueId`, the isValid method should be queried to ensure the id still referenced a valid bond.
Core::Array< Index > &	bondUniqueIds ()
Index	findAtomUniqueId (Index index) const
Index	findBondUniqueId (Index index) const
RWMolecule *	undoMolecule ()
QString	formattedFormula () const
	Get the formatted chemical formula for the molecule.
bool	isInteractive () const
void	swapBond (Index a, Index b)
void	swapAtom (Index a, Index b)

Index	atomUniqueId (const AtomType &atom) const
	Get the unique ID of the atom, this will uniquely reference the atom as long as it exists.
Index	atomUniqueId (Index atom) const
	Get the unique ID of the atom, this will uniquely reference the atom as long as it exists.

bool	removeBond (const AtomType &atom1, const AtomType &atom2) override
	Remove the specified bond.
bool	removeBond (Index atom1, Index atom2) override
	Remove the specified bond.

Index	bondUniqueId (const BondType &bond) const
	Get the unique ID of the bond, this will uniquely reference the bond as long as it exists.
Index	bondUniqueId (Index bond) const
	Get the unique ID of the bond, this will uniquely reference the bond as long as it exists.
Public Member Functions inherited from Molecule
	Molecule ()
	Molecule (const Molecule &other)
	Molecule (Molecule &&other) noexcept
Molecule &	operator= (const Molecule &other)
Molecule &	operator= (Molecule &&other) noexcept
void	readProperties (const Molecule &other)
void	setData (const std::string &name, const Variant &value)
Variant	data (const std::string &name) const
bool	hasData (const std::string &name) const
void	setDataMap (const VariantMap &map)
const VariantMap &	dataMap () const
VariantMap &	dataMap ()
MatrixX	spectra (const std::string &name) const
void	setSpectra (const std::string &name, const MatrixX &value)
std::set< std::string >	spectraTypes () const
void	setPartialCharges (const std::string &type, const MatrixX &value)
MatrixX	partialCharges (const std::string &type) const
std::set< std::string >	partialChargeTypes () const
Array< AtomHybridization > &	hybridizations ()
const Array< AtomHybridization > &	hybridizations () const
AtomHybridization	hybridization (Index atomId) const
bool	setHybridizations (const Core::Array< AtomHybridization > &hybs)
bool	setHybridization (Index atomId, AtomHybridization hybridization)
Array< signed char > &	formalCharges ()
const Array< signed char > &	formalCharges () const
signed char	totalCharge () const
char	totalSpinMultiplicity () const
signed char	formalCharge (Index atomId) const
bool	setFormalCharges (const Core::Array< signed char > &charges)
bool	setFormalCharge (Index atomId, signed char charge)
Array< Vector3ub > &	colors ()
const Array< Vector3ub > &	colors () const
Vector3ub	color (Index atomId) const
bool	setColors (const Core::Array< Vector3ub > &colors)
bool	setColor (Index atomId, Vector3ub color)
bool	setLayer (Index atomId, size_t layer)
size_t	layer (Index atomId) const
const Array< Vector2 > &	atomPositions2d () const
Array< Vector2 > &	atomPositions2d ()
Vector2	atomPosition2d (Index atomId) const
bool	setAtomPositions2d (const Core::Array< Vector2 > &pos)
bool	setAtomPosition2d (Index atomId, const Vector2 &pos)
const Array< Vector3 > &	atomPositions3d () const
Array< Vector3 > &	atomPositions3d ()
Vector3	atomPosition3d (Index atomId) const
bool	setAtomPositions3d (const Core::Array< Vector3 > &pos)
bool	setAtomPosition3d (Index atomId, const Vector3 &pos)
std::string	atomLabel (Index atomId) const
bool	setAtomLabel (Index atomId, const std::string &label)
const Core::Array< std::string >	atomLabels () const
bool	setAtomLabels (const Core::Array< std::string > &label)
void	setAtomSelected (Index atomId, bool selected)
bool	atomSelected (Index atomId) const
bool	isSelectionEmpty () const
const ElementMask	elements () const
AtomType	addAtom (unsigned char atomicNumber, Vector3 position3d)
virtual void	clearAtoms ()
AtomType	atom (Index index) const
virtual void	clearBonds ()
BondType	bond (Index index) const
BondType	bond (const AtomType &a, const AtomType &b) const
BondType	bond (Index atomId1, Index atomId2) const
std::string	bondLabel (Index bondIndex) const
bool	setBondLabel (Index bondIndex, const std::string &label)
const Core::Array< std::string >	bondLabels () const
bool	setBondLabels (const Core::Array< std::string > &label)
Mesh *	addMesh ()
	Add a mesh to the molecule.
Mesh *	mesh (Index index)
const Mesh *	mesh (Index index) const
Index	meshCount () const
void	clearMeshes ()
Cube *	addCube ()
	Add a cube to the molecule.
Cube *	cube (Index index)
const Cube *	cube (Index index) const
Index	cubeCount () const
void	clearCubes ()
std::vector< Cube * >	cubes ()
	Get the cubes vector set (if present) for the molecule.
const std::vector< Cube * >	cubes () const
std::string	formula (const std::string &delimiter="", int showCountsOver=1) const
double	mass () const
Vector3	centerOfGeometry () const
Vector3	centerOfMass () const
double	radius () const
std::pair< Vector3, Vector3 >	bestFitPlane () const
void	setBasisSet (BasisSet *basis)
BasisSet *	basisSet ()
const BasisSet *	basisSet () const
Array< double >	vibrationFrequencies () const
void	setVibrationFrequencies (const Array< double > &freq)
Array< double >	vibrationIRIntensities () const
void	setVibrationIRIntensities (const Array< double > &intensities)
Array< double >	vibrationRamanIntensities () const
void	setVibrationRamanIntensities (const Array< double > &intensities)
Array< Vector3 >	vibrationLx (int mode) const
void	setVibrationLx (const Array< Array< Vector3 > > &lx)
void	perceiveBondsSimple (const double tolerance=0.45, const double minDistance=0.32)
void	perceiveBondsFromResidueData ()
void	perceiveBondOrders ()
void	perceiveSubstitutedCations ()
size_t	coordinate3dCount () const
bool	setCoordinate3d (int coord)
Array< Vector3 >	coordinate3d (size_t index) const
bool	setCoordinate3d (const Array< Vector3 > &coords, size_t index)
void	clearCoordinate3d ()
bool	setTimeStep (double timestep, int index)
double	timeStep (int index, bool &status)
const Array< Vector3 > &	forceVectors () const
Array< Vector3 > &	forceVectors ()
Vector3	forceVector (Index atomId) const
bool	setForceVectors (const Core::Array< Vector3 > &forces)
bool	setForceVector (Index atomId, const Vector3 &force)
Residue &	addResidue (std::string &name, Index &number, char &id)
void	addResidue (Residue &residue)
Residue &	residue (Index index)
Array< Residue > &	residues ()
const Array< Residue > &	residues () const
Index	residueCount () const
Index	atomCount () const
Index	atomCount (unsigned char atomicNumber) const
	Get the number of atoms in the molecule that match atomicNumber.
Index	bondCount () const
std::pair< Index, Index >	bondPair (Index bondId) const
bool	setBondPairs (const Array< std::pair< Index, Index > > &pairs)
const Array< std::pair< Index, Index > > &	bondPairs () const
const Array< unsigned char > &	bondOrders () const
const Graph &	graph () const
const Array< unsigned char > &	atomicNumbers () const
unsigned char	atomicNumber (Index atomId) const
bool	setBondOrders (const Array< unsigned char > &orders)
bool	setBondOrder (Index bondId, unsigned char order)
bool	hasCustomElements () const
bool	setBondPair (Index bondId, const std::pair< Index, Index > &pair)
unsigned char	bondOrder (Index bondId) const
bool	setAtomicNumbers (const Core::Array< unsigned char > &nums)
bool	setAtomicNumber (Index atomId, unsigned char atomicNumber)
std::map< unsigned char, size_t >	composition () const
Array< std::pair< Index, Index > >	getAtomBonds (Index index) const
Array< unsigned char >	getAtomOrders (Index index) const
bool	removeBonds (Index atom)
void	addBonds (const Array< std::pair< Index, Index > > &bonds, const Array< unsigned char > &orders)
void	swapBond (Index a, Index b)
void	swapAtom (Index a, Index b)
std::list< Index >	getAtomsAtLayer (size_t layer)
Layer &	layer ()
const Layer &	layer () const
void	boundingBox (Vector3 &boxMin, Vector3 &boxMax, const double radius=1.0) const
const CustomElementMap &	customElementMap () const
void	setCustomElementMap (const CustomElementMap &map)
Array< BondType >	bonds (const AtomType &a)
	Get all bonds to `a`.
Array< BondType >	bonds (Index a)
	Get all bonds to `a`.
Array< const BondType * >	bonds (Index a) const
	Get all bonds to `a`.
void	setUnitCell (UnitCell *uc)
UnitCell *	unitCell ()
const UnitCell *	unitCell () const
void	setHallNumber (unsigned short hallNumber)
unsigned short	hallNumber () const
void	addConstraint (Real Value, Index a, Index b, Index c=MaxIndex, Index d=MaxIndex)
void	addConstraint (Constraint &c)
void	removeConstraint (Index a, Index b, Index c=MaxIndex, Index d=MaxIndex)
void	clearConstraints ()
void	setConstraints (const std::vector< Core::Constraint > &constraints)
std::vector< Core::Constraint > &	constraints ()
const std::vector< Core::Constraint > &	constraints () const
void	setFrozenAtom (Index atomId, bool frozen)
bool	frozenAtom (Index atomId) const
void	setFrozenAtomAxis (Index atomId, int axis, bool frozen)
Eigen::VectorXd	frozenAtomMask () const

Additional Inherited Members
Static Public Member Functions inherited from Molecule
static std::pair< Vector3, Vector3 >	bestFitPlane (const Array< Vector3 > &pos)
static std::pair< Index, Index >	makeBondPair (const Index &a, const Index &b)
Protected Attributes inherited from Molecule
VariantMap	m_data
std::map< std::string, MatrixX >	m_partialCharges
	Sets of atomic partial charges.
std::map< std::string, MatrixX >	m_spectra
	Sets of spectra.
CustomElementMap	m_customElementMap
ElementMask	m_elements
Array< Vector2 >	m_positions2d
Array< Vector3 >	m_positions3d
Array< std::string >	m_atomLabels
Array< std::string >	m_bondLabels
Array< Array< Vector3 > >	m_coordinates3d
	Store conformers/trajectories.
Array< double >	m_timesteps
Array< AtomHybridization >	m_hybridizations
Array< signed char >	m_formalCharges
Array< Vector3 >	m_forceVectors
Array< Vector3ub >	m_colors
Array< double >	m_vibrationFrequencies
Array< double >	m_vibrationIRIntensities
Array< double >	m_vibrationRamanIntensities
Array< Array< Vector3 > >	m_vibrationLx
std::vector< bool >	m_selectedAtoms
std::vector< Mesh * >	m_meshes
std::vector< Cube * >	m_cubes
BasisSet *	m_basisSet
UnitCell *	m_unitCell
Array< Residue >	m_residues
unsigned short	m_hallNumber = 0
std::vector< Core::Constraint >	m_constraints
Eigen::VectorXd	m_frozenAtomMask

Member Typedef Documentation

◆ AtomType

typedef Core::Molecule::AtomType AtomType

Typedef for Atom class.

◆ PersistentAtomType

typedef PersistentAtom<Molecule> PersistentAtomType

Typedef for PersistentAtom class.

◆ BondType

typedef Core::Molecule::BondType BondType

Typedef for Bond class.

◆ PersistentBondType

typedef PersistentBond<Molecule> PersistentBondType

Typedef for PersistentBond class.

Member Enumeration Documentation

◆ MoleculeChange

enum MoleculeChange

Enumeration of change types that can be given.

Enumerator
NoChange	Useful for initializing MoleculeChange variables.
Atoms	Object types that can be changed.
Added	Operations that can affect the above types.

Constructor & Destructor Documentation

◆ ~Molecule()

~Molecule ( )

overridevirtual

Destroys the molecule object.

Reimplemented from Molecule.

◆ Molecule() [1/2]

Molecule ( const Molecule & other )

copy constructor

◆ Molecule() [2/2]

Molecule ( const Core::Molecule & other )

copy constructor to copy data from base instance

Member Function Documentation

◆ operator=() [1/2]

Molecule & operator= ( const Molecule & other )

Assignment operator

◆ operator=() [2/2]

Molecule & operator= ( const Core::Molecule & other )

Assignment operator to copy data from base instance

◆ addAtom() [1/2]

AtomType addAtom ( unsigned char atomicNumber )

overridevirtual

Add an atom with atomicNumber to the molecule.

Returns: The atom created.

Reimplemented from Molecule.

◆ addAtom() [2/2]

virtual AtomType addAtom	(	unsigned char	atomicNumber,
		Index	uniqueId )

virtual

Add an atom with atomicNumber and uniqueId to the molecule.

Returns: The atom created. This can be invalid if the unique ID was already in use.

◆ removeAtom() [1/2]

bool removeAtom ( Index index )

overridevirtual

Parameters

index The index of the atom to be removed.

Returns: True on success, false if the atom was not found.

Reimplemented from Molecule.

◆ removeAtom() [2/2]

bool removeAtom ( const AtomType & atom )

overridevirtual

Parameters

atom	The atom to be removed.

Returns: True on success, false if the atom was not found. This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Reimplemented from Molecule.

◆ atomByUniqueId()

AtomType atomByUniqueId ( Index uniqueId )

Parameters

uniqueId The unique identifier for the atom.

Returns: An Atom object, check it is valid before using it.

◆ atomUniqueId() [1/2]

Index atomUniqueId ( const AtomType & atom ) const

Parameters

atom	The atom to obtain the unique ID of.

Returns: The unique identifier for the atom, MaxIndex if the atom is invalid or does not belong to this molecule.

◆ atomUniqueId() [2/2]

Index atomUniqueId ( Index atom ) const

Parameters

atom	The atom to obtain the unique ID of.

Returns: The unique identifier for the atom, MaxIndex if the atom is invalid or does not belong to this molecule.

◆ addBond() [1/4]

BondType addBond	(	const AtomType &	a,
		const AtomType &	b,
		unsigned char	bondOrder = 1 )

overridevirtual

Parameters

a	The first atom in the bond.
b	The second atom in the bond.
bondOrder	The order of the bond.

Returns: The bond created.

Reimplemented from Molecule.

◆ addBond() [2/4]

BondType addBond	(	Index	atomId1,
		Index	atomId2,
		unsigned char	bondOrder = 1 )

overridevirtual

Parameters

atomId1	The index of the first atom in the bond.
atomId2	The index of the second atom in the bond.
bondOrder	The order of the bond.

Returns: The bond created.

Reimplemented from Molecule.

◆ addBond() [3/4]

virtual BondType addBond	(	const AtomType &	a,
		const AtomType &	b,
		unsigned char	bondOrder,
		Index	uniqueId )

virtual

Parameters

a	The first atom in the bond.
b	The second atom in the bond.
bondOrder	The order of the bond.
uniqueId	The unique ID to use for the bond.

Returns: The bond created. This can be invalid if the unique ID was already in use.

◆ addBond() [4/4]

virtual BondType addBond	(	Index	atomId1,
		Index	atomId2,
		unsigned char	bondOrder,
		Index	uniqueId )

virtual

Parameters

a	The index of the first atom in the bond.
b	The index of the second atom in the bond.
bondOrder	The order of the bond.
uniqueId	The unique ID to use for the bond.

Returns: The bond created. This can be invalid if the unique ID was already in use.

◆ removeBond() [1/4]

bool removeBond ( Index index )

overridevirtual

Parameters

index The index of the bond to be removed.

Returns: True on success, false if the bond was not found.

Reimplemented from Molecule.

◆ removeBond() [2/4]

bool removeBond ( const BondType & bond )

overridevirtual

Parameters

bond	The bond to be removed.

Returns: True on success, false if the bond was not found. This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Reimplemented from Molecule.

◆ removeBond() [3/4]

bool removeBond	(	const AtomType &	atom1,
		const AtomType &	atom2 )

overridevirtual

Parameters

atom1	One atom in the bond.
atom2	The other atom in the bond.

Returns: True on success, false if the bond was not found. This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Reimplemented from Molecule.

◆ removeBond() [4/4]

bool removeBond	(	Index	atom1,
		Index	atom2 )

overridevirtual

Parameters

atom1	One atom in the bond.
atom2	The other atom in the bond.

Returns: True on success, false if the bond was not found. This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Reimplemented from Molecule.

◆ bondByUniqueId()

BondType bondByUniqueId ( Index uniqueId )

Parameters

uniqueId The unique identifier for the bond.

Returns: A Bond object, check it is valid before using it.

◆ bondUniqueId() [1/2]

Index bondUniqueId ( const BondType & bond ) const

Parameters

bond	The bond to obtain the unique ID of.

Returns: The unique identifier for the bond, MaxIndex if the bond is invalid or does not belong to this molecule.

◆ bondUniqueId() [2/2]

Index bondUniqueId ( Index bond ) const

Parameters

bond	The bond to obtain the unique ID of.

Returns: The unique identifier for the bond, MaxIndex if the bond is invalid or does not belong to this molecule.

◆ formattedFormula()

QString formattedFormula ( ) const

Returns: The formatted chemical formula in HTML format. This will include subscripts for atom counts and superscripts for charge and spin multiplicity.

◆ emitChanged

void emitChanged ( unsigned int change )

slot

Parameters

change See changed().

◆ changed

void changed ( unsigned int change ) const

signal

Parameters

change Use the MoleculeChange enum to check what has changed.

The change variable indicates what has changed, i.e. if change & Atoms == true then atoms were changed in some way, and if change & Removed == true then one or more atoms were removed.

The documentation for this class was generated from the following file:

qtgui/molecule.h

Public Types

Public Slots

Signals

Public Member Functions

Additional Inherited Members

Member Typedef Documentation

◆ AtomType

◆ PersistentAtomType

◆ BondType

◆ PersistentBondType

Member Enumeration Documentation

◆ MoleculeChange

Constructor & Destructor Documentation

◆ ~Molecule()

◆ Molecule() [1/2]

◆ Molecule() [2/2]

Member Function Documentation

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ addAtom() [1/2]

◆ addAtom() [2/2]

◆ removeAtom() [1/2]

◆ removeAtom() [2/2]

◆ atomByUniqueId()

◆ atomUniqueId() [1/2]

◆ atomUniqueId() [2/2]

◆ addBond() [1/4]

◆ addBond() [2/4]

◆ addBond() [3/4]

◆ addBond() [4/4]

◆ removeBond() [1/4]

◆ removeBond() [2/4]

◆ removeBond() [3/4]

◆ removeBond() [4/4]

◆ bondByUniqueId()

◆ bondUniqueId() [1/2]

◆ bondUniqueId() [2/2]

◆ formattedFormula()

◆ emitChanged

◆ changed