The Molecule class represents a chemical molecule.

#include <avogadro/core/molecule.h>

Inheritance diagram for Molecule:

Classes
struct	VibrationData

Public Types
using	AtomType = Atom
using	BondType = Bond
using	CustomElementMap = std::map<unsigned char, std::string>
using	ElementMask = std::bitset<element_count>

Public Member Functions
	Molecule ()
	Molecule (const Molecule &other)
	Molecule (Molecule &&other) noexcept
Molecule &	operator= (const Molecule &other)
Molecule &	operator= (Molecule &&other) noexcept
virtual	~Molecule ()
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)
void	removePartialCharges (const std::string &type)
MatrixX	partialCharges (const std::string &type) const
std::set< std::string >	partialChargeTypes () const
PropertyMap &	atomProperties ()
const PropertyMap &	atomProperties () const
PropertyMap &	bondProperties ()
const PropertyMap &	bondProperties () const
PropertyMap &	residueProperties ()
const PropertyMap &	residueProperties () const
PropertyMap &	conformerProperties ()
const PropertyMap &	conformerProperties () 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	formalCharge (Index atomId) const
bool	setFormalCharges (const Core::Array< signed char > &charges)
bool	setFormalCharge (Index atomId, signed char charge)
signed char	totalCharge () const
char	totalSpinMultiplicity () const
Array< unsigned short > &	isotopes ()
const Array< unsigned short > &	isotopes () const
unsigned short	isotope (Index atomId) const
bool	setIsotopes (const Core::Array< unsigned short > &isotopes)
bool	setIsotope (Index atomId, unsigned short isotope)
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
virtual AtomType	addAtom (unsigned char atomicNumber)
AtomType	addAtom (unsigned char atomicNumber, Vector3 position3d)
virtual bool	removeAtom (Index index)
	Remove the specified atom from the molecule.
virtual bool	removeAtom (const AtomType &atom)
	Remove the specified atom from the molecule.
virtual void	clearAtoms ()
AtomType	atom (Index index) const
virtual bool	removeBond (Index index)
	Remove the specified bond.
virtual bool	removeBond (const BondType &bond)
	Remove the specified bond.
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 ()
bool	setActiveCubeIndex (Index index)
	Set the active cube index for volume rendering.
Index	activeCubeIndex () const
	Get the index of the active cube.
Cube *	activeCube ()
	Get the active cube for volume rendering.
const Cube *	activeCube () const
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
double	monoisotopicMass () 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
bool	hasVibrations (size_t conformerIndex) const
bool	hasVibrations () const
size_t	vibrationConformerCount () const
Array< size_t >	vibrationConformers () const
void	clearVibrations ()
const VibrationData *	vibrationData (size_t conformerIndex) const
void	setVibrationData (const VibrationData &data, size_t conformerIndex)
void	perceiveBondsSimple (const double tolerance=0.45, const double minDistance=0.32)
void	perceiveBondsFromResidueData ()
BondOrderResult	perceiveBondOrders (const BondOrderOptions &options)
void	perceiveBondOrders ()
void	perceiveSubstitutedCations ()
size_t	coordinate3dCount () const
bool	setCoordinate3d (int coord)
int	coordinate3d () const
Array< Vector3 >	coordinate3d (size_t index) const
const Array< Vector3 > &	coordinate3dRef (size_t index) const
bool	setCoordinate3d (const Array< Vector3 > &coords, size_t index)
void	clearCoordinate3d ()
void	estimateVelocities ()
void	estimateVelocities (double timeStep)
Array< Vector3 >	velocities (int index) const
bool	setVelocities (const Array< Vector3 > &velocities, int index)
void	updateVelocityProperties ()
void	clearVelocities ()
bool	setTimeStep (double timestep, int index)
double	timeStep (int index, bool &status) const
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)
const Residue &	residue (Index index) const
Array< Residue > &	residues ()
const Array< Residue > &	residues () const
Index	residueCount () const
std::string	residueLabel (Index residueIndex) const
bool	setResidueLabel (Index residueIndex, const std::string &label)
const Core::Array< std::string >	residueLabels () const
bool	setResidueLabels (const Core::Array< std::string > &label)
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
std::map< std::string, size_t >	formulaComposition () 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)
void	clearCalculatedResults ()
std::list< Index >	getAtomsAtLayer (size_t layer)
Layer &	layer ()
const Layer &	layer () const
void	copyDisplayStateFrom (const Molecule &other)
std::shared_ptr< MoleculeInfo >	layerInfo () const
void	boundingBox (Vector3 &boxMin, Vector3 &boxMax, const double radius=1.0) const

const CustomElementMap &	customElementMap () const
void	setCustomElementMap (const CustomElementMap &map)

virtual BondType	addBond (Index atom1, Index atom2, unsigned char order=1)
virtual BondType	addBond (const AtomType &atom1, const AtomType &atom2, unsigned char order=1)

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

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

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)

Array< double >	vibrationFrequencies (size_t conformerIndex) const
void	setVibrationFrequencies (const Array< double > &freq, size_t conformerIndex)
Array< double >	vibrationIRIntensities (size_t conformerIndex) const
void	setVibrationIRIntensities (const Array< double > &intensities, size_t conformerIndex)
Array< double >	vibrationRamanIntensities (size_t conformerIndex) const
void	setVibrationRamanIntensities (const Array< double > &intensities, size_t conformerIndex)
Array< Vector3 >	vibrationLx (int mode, size_t conformerIndex) const
void	setVibrationLx (const Array< Array< Vector3 > > &lx, size_t conformerIndex)
Constraints
Methods for distance, angle, torsion, etc. constraints
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
bool	frozenAtomAxis (Index atomId, int axis) const
void	setFrozenAtomAxis (Index atomId, int axis, bool frozen)
Eigen::VectorXd	frozenAtomMask () const
Scan coordinates
Distances, angles and torsions worth following across the coordinate sets, such as the coordinate a relaxed scan stepped through. Unlike constraints these are only ever measured, never enforced, so an optimizer ignores them. They live in the property map, which already travels through CJSON, rather than in a member of their own.
std::vector< Constraint >	scanCoordinates () const
void	setScanCoordinates (const std::vector< Constraint > &coordinates)
void	addScanCoordinate (const Constraint &coordinate)

Static Public Member Functions
static std::pair< Vector3, Vector3 >	bestFitPlane (const Array< Vector3 > &pos)
static std::pair< Index, Index >	makeBondPair (const Index &a, const Index &b)

Protected Attributes
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.
PropertyMap	m_atomProperties
	Custom per-atom properties.
PropertyMap	m_bondProperties
	Custom per-bond properties.
PropertyMap	m_residueProperties
	Custom per-residue properties.
PropertyMap	m_conformerProperties
	Custom per-conformer properties.
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< std::string >	m_residueLabels
Array< Array< Vector3 > >	m_coordinates3d
	Store conformers/trajectories.
int	m_coordinate3dIndex = 0
	Active coordinate set index.
Array< Array< Vector3 > >	m_velocities
	Store velocities.
Array< double >	m_timesteps
Array< AtomHybridization >	m_hybridizations
Array< signed char >	m_formalCharges
Array< unsigned short >	m_isotopes
	Store isotopes of the atoms.
Array< Vector3 >	m_forceVectors
Array< Vector3ub >	m_colors
std::map< size_t, VibrationData >	m_vibrations
std::vector< bool >	m_selectedAtoms
std::vector< Mesh * >	m_meshes
std::vector< Cube * >	m_cubes
Index	m_activeCubeIndex = 0
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

using AtomType = Atom

Typedef for Atom class.

◆ BondType

using BondType = Bond

Typedef for Bond class.

◆ CustomElementMap

using CustomElementMap = std::map<unsigned char, std::string>

Type for custom element map.

◆ ElementMask

using ElementMask = std::bitset<element_count>

Type for element masks (e.g., does this molecule contain certain elements)

Constructor & Destructor Documentation

◆ Molecule() [1/3]

Molecule ( )

Creates a new, empty molecule.

◆ Molecule() [2/3]

Molecule ( const Molecule & other )

Copy constructor

◆ Molecule() [3/3]

Molecule ( Molecule && other )

noexcept

Move constructor.

Takes every member from other and leaves it equivalent to a default-constructed Molecule. The layer state is a shared_ptr whose handle is transferred, not rebuilt. noexcept, but not allocation-free: leaving the source empty allocates small empty containers, and the graph's edge list may be copied. An allocation failure here terminates the program.

◆ ~Molecule()

virtual ~Molecule ( )

virtual

Destroys the molecule object.

Reimplemented in Molecule.

Member Function Documentation

◆ operator=() [1/2]

Molecule & operator= ( const Molecule & other )

Assignment operator

◆ operator=() [2/2]

Molecule & operator= ( Molecule && other )

noexcept

Move assignment operator. noexcept but may allocate, as the move constructor does; an allocation failure terminates the program.

◆ readProperties()

void readProperties ( const Molecule & other )

Adds the properties from the supplied molecule to this molecule. Does not otherwise modify atoms / bonds / residues, etc.

◆ setData()

void setData	(	const std::string &	name,
		const Variant &	value )

Sets the data value with name to value.

◆ data()

Variant data ( const std::string & name ) const

Returns: the data value for name.

◆ hasData()

bool hasData ( const std::string & name ) const

Returns: true if the molecule has data with the given key, false otherwise.

◆ setDataMap()

void setDataMap ( const VariantMap & map )

Set the molecule's variant data to the entries in map.

◆ dataMap() [1/2]

const VariantMap & dataMap ( ) const

Returns: the molecule's variant data.

◆ dataMap() [2/2]

VariantMap & dataMap ( )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ spectra()

MatrixX spectra ( const std::string & name ) const

Returns: a specific spectra entry

◆ setSpectra()

void setSpectra	(	const std::string &	name,
		const MatrixX &	value )

Sets the spectra value with name to value.

◆ spectraTypes()

std::set< std::string > spectraTypes ( ) const

Returns: the list of available spectra

◆ setPartialCharges()

void setPartialCharges	(	const std::string &	type,
		const MatrixX &	value )

Sets atomic partial charges with type to value.

◆ removePartialCharges()

void removePartialCharges ( const std::string & type )

Discards the stored partial charges of type type, if any. Other charge types are left alone.

◆ partialCharges()

MatrixX partialCharges ( const std::string & type ) const

Returns: the atomic partial charges of type type

◆ partialChargeTypes()

std::set< std::string > partialChargeTypes ( ) const

Returns: the types of partial charges available stored with this molecule.

◆ atomProperties() [1/2]

PropertyMap & atomProperties ( )

Returns: the per-atom custom property map.

◆ atomProperties() [2/2]

const PropertyMap & atomProperties ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ bondProperties() [1/2]

PropertyMap & bondProperties ( )

Returns: the per-bond custom property map.

◆ bondProperties() [2/2]

const PropertyMap & bondProperties ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ residueProperties() [1/2]

PropertyMap & residueProperties ( )

Returns: the per-residue custom property map.

◆ residueProperties() [2/2]

const PropertyMap & residueProperties ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ conformerProperties() [1/2]

PropertyMap & conformerProperties ( )

Returns: the per-conformer custom property map.

◆ conformerProperties() [2/2]

const PropertyMap & conformerProperties ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ hybridizations() [1/2]

Array< AtomHybridization > & hybridizations ( )

Returns: a vector of hybridizations for the atoms in the molecule.

◆ hybridizations() [2/2]

const Array< AtomHybridization > & hybridizations ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ hybridization()

AtomHybridization hybridization ( Index atomId ) const

Get the hybridization for the requested atom.

Parameters

atomId The index of the atom.

Returns: The hybridization of the atom indexed at atomId, or 0 if atomId is invalid.

◆ setHybridizations()

bool setHybridizations ( const Core::Array< AtomHybridization > & hybs )

Replace the current array of hybridizations.

Parameters

hybs	The new hybridization array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setHybridization()

bool setHybridization	(	Index	atomId,
		AtomHybridization	hybridization )

Set the hybridization of a single atom.

Parameters

atomId	The index of the atom to modify.
hybridization	The new hybridization.

Returns: True on success, false otherwise.

◆ formalCharges() [1/2]

Array< signed char > & formalCharges ( )

Returns: a vector of formal charges for the atoms in the molecule.

◆ formalCharges() [2/2]

const Array< signed char > & formalCharges ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ formalCharge()

signed char formalCharge ( Index atomId ) const

Get the formal charge for the requested atom.

Parameters

atomId The index of the atom.

Returns: The formal charge of the atom indexed at atomId, or 0 if atomId is invalid.

◆ setFormalCharges()

bool setFormalCharges ( const Core::Array< signed char > & charges )

Replace the current array of formal charges.

Parameters

charges The new formal charge array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setFormalCharge()

bool setFormalCharge	(	Index	atomId,
		signed char	charge )

Set the formal charge of a single atom.

Parameters

atomId	The index of the atom to modify.
charge	The new formal charge.

Returns: True on success, false otherwise.

◆ totalCharge()

signed char totalCharge ( ) const

Get the total charge on the molecule. The method will first check to see if a total charge has been set. If not, it will calculate the total charge from the formal charges (if set). If neither has been set, it will assume the total charge is zero.

Returns: The total charge of the molecule.

◆ totalSpinMultiplicity()

char totalSpinMultiplicity ( ) const

Get the total spin multiplicity of the molecule. The method will first check to see if a total spin has been set. If not, it will either suggest a singlet if an even number of electrons are present, or a doublet if an odd number of electrons are present.

Returns: The total spin multiplicity of the molecule.

◆ isotopes() [1/2]

Array< unsigned short > & isotopes ( )

Returns: an array of the isotopes for the atoms in the molecule.

◆ isotopes() [2/2]

const Array< unsigned short > & isotopes ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ isotope()

unsigned short isotope ( Index atomId ) const

Get the isotope for the requested atom.

Parameters

atomId The index of the atom.

Returns: The isotope of the atom indexed at atomId, or 0 if atomId is invalid.

◆ setIsotopes()

bool setIsotopes ( const Core::Array< unsigned short > & isotopes )

Replace the current array of isotopes.

Parameters

charges The new isotope array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setIsotope()

bool setIsotope	(	Index	atomId,
		unsigned short	isotope )

Set the isotope of a single atom.

Parameters

atomId	The index of the atom to modify.
isotope	The new isotope (or zero for most common)

Returns: True on success, false otherwise.

◆ colors() [1/2]

Array< Vector3ub > & colors ( )

Returns: a vector of colors for the atoms in the moleucle.

◆ colors() [2/2]

const Array< Vector3ub > & colors ( ) const

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ color()

Vector3ub color ( Index atomId ) const

Get the color for the requested atom.

Parameters

atomId The index of the atom.

Returns: The color of the atom indexed at atomId, or (0,0,0) if atomId is invalid. If no color is set for the given atomId, the default color for the atomic number of the atomId is returned.

◆ setColors()

bool setColors ( const Core::Array< Vector3ub > & colors )

Replace the current array of colors.

Parameters

colors The new color array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setColor()

bool setColor	(	Index	atomId,
		Vector3ub	color )

Set the color of a single atom.

Parameters

atomId	The index of the atom to modify.
color	The new color.

Returns: True on success, false otherwise.

◆ atomPositions2d() [1/2]

const Array< Vector2 > & atomPositions2d ( ) const

Returns: a vector of 2d atom positions for the atoms in the molecule.

◆ atomPositions2d() [2/2]

Array< Vector2 > & atomPositions2d ( )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ atomPosition2d()

Vector2 atomPosition2d ( Index atomId ) const

Get the 2D position of a single atom.

Parameters

atomId The index of the atom.

Returns: The position of the atom, or Vector3::Zero() if no position information has been set.

◆ setAtomPositions2d()

bool setAtomPositions2d ( const Core::Array< Vector2 > & pos )

Replace the current array of 2D atomic coordinates.

Parameters

pos	The new coordinate array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setAtomPosition2d()

bool setAtomPosition2d	(	Index	atomId,
		const Vector2 &	pos )

Set the 2D position of a single atom.

Parameters

atomId	The index of the atom to modify.
pos	The new position of the atom.

Returns: True on success, false otherwise.

◆ atomPositions3d() [1/2]

const Array< Vector3 > & atomPositions3d ( ) const

Returns: a vector of 3d atom positions for the atoms in the molecule.

◆ atomPositions3d() [2/2]

Array< Vector3 > & atomPositions3d ( )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ atomPosition3d()

Vector3 atomPosition3d ( Index atomId ) const

Get the 3D position of a single atom.

Parameters

atomId The index of the atom.

Returns: The position of the atom, or Vector3::Zero() if no position information has been set.

◆ setAtomPositions3d()

bool setAtomPositions3d ( const Core::Array< Vector3 > & pos )

Replace the current array of 3D atomic coordinates.

Parameters

pos	The new coordinate array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setAtomPosition3d()

bool setAtomPosition3d	(	Index	atomId,
		const Vector3 &	pos )

Set the 3D position of a single atom.

Parameters

atomId	The index of the atom to modify.
pos	The new position of the atom.

Returns: True on success, false otherwise.

◆ atomLabel()

std::string atomLabel ( Index atomId ) const

Returns: Any custom label for the requested atom.

Parameters

atomId The index of the atom.

◆ setAtomLabel()

bool setAtomLabel	(	Index	atomId,
		const std::string &	label )

Set the custom label of a single atom.

Parameters

atomId	The index of the atom to modify.
label	The new label of the atom.

Returns: True on success, false otherwise.

◆ setAtomLabels()

bool setAtomLabels ( const Core::Array< std::string > & label )

Set all the atom labels in the molecule.

Parameters

label The new label array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setAtomSelected()

void setAtomSelected	(	Index	atomId,
		bool	selected )

Set whether the specified atom is selected or not.

◆ atomSelected()

bool atomSelected ( Index atomId ) const

Query whether the supplied atom index has been selected.

◆ isSelectionEmpty()

bool isSelectionEmpty ( ) const

Returns: whether the selection is empty or not

◆ customElementMap()

const CustomElementMap & customElementMap ( ) const

A map of custom element atomic numbers to string identifiers. These ids can be used to override the generic custom element names returned by the Elements class, and should be somewhat meaningful to the user.

Note: Custom element atomic numbers lie between CustomElementMin and CustomElementMax.

See also: Avogadro::QtGui::CustomElementDialog; hasCustomElements

◆ setCustomElementMap()

void setCustomElementMap ( const CustomElementMap & map )

A map of custom element atomic numbers to string identifiers. These ids can be used to override the generic custom element names returned by the Elements class, and should be somewhat meaningful to the user.

Note: Custom element atomic numbers lie between CustomElementMin and CustomElementMax.

See also: Avogadro::QtGui::CustomElementDialog; hasCustomElements

◆ elements()

const Molecule::ElementMask elements ( ) const

Returns: the elements currently in this molecule

◆ addAtom()

virtual AtomType addAtom ( unsigned char atomicNumber )

virtual

Adds an atom to the molecule.

Reimplemented in Molecule.

◆ removeAtom() [1/2]

virtual bool removeAtom ( Index index )

virtual

Parameters

index The index of the atom to be removed.

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

Reimplemented in Molecule.

◆ removeAtom() [2/2]

virtual bool removeAtom ( const AtomType & atom )

virtual

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 in Molecule.

◆ clearAtoms()

virtual void clearAtoms ( )

virtual

Remove all atoms from the molecule.

◆ atom()

AtomType atom ( Index index ) const

Returns: the atom at index in the molecule.

◆ addBond() [1/2]

virtual BondType addBond	(	Index	atom1,
		Index	atom2,
		unsigned char	order = 1 )

virtual

Create a new bond in the molecule.

Parameters

atom1	The first atom in the bond.
atom2	The second atom in the bond.
order	The bond order.

Returns: The new bond object. Will be invalid if atom1 or atom2 does not exist.

Reimplemented in Molecule.

◆ addBond() [2/2]

virtual BondType addBond	(	const AtomType &	atom1,
		const AtomType &	atom2,
		unsigned char	order = 1 )

virtual

Create a new bond in the molecule.

Parameters

atom1	The first atom in the bond.
atom2	The second atom in the bond.
order	The bond order.

Returns: The new bond object. Will be invalid if atom1 or atom2 does not exist.

Reimplemented in Molecule.

◆ removeBond() [1/4]

virtual bool removeBond ( Index index )

virtual

Parameters

index The index of the bond to be removed.

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

Reimplemented in Molecule.

◆ removeBond() [2/4]

virtual bool removeBond ( const BondType & bond )

virtual

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 in Molecule.

◆ removeBond() [3/4]

virtual bool removeBond	(	Index	atom1,
		Index	atom2 )

virtual

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 in Molecule.

◆ removeBond() [4/4]

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

virtual

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 in Molecule.

◆ clearBonds()

virtual void clearBonds ( )

virtual

Remove all bonds from the molecule.

◆ bond() [1/3]

BondType bond ( Index index ) const

Returns: the bond at index in the molecule.

◆ bond() [2/3]

BondType bond	(	const AtomType &	a,
		const AtomType &	b ) const

Returns: the bond between atoms a and b.

◆ bond() [3/3]

BondType bond	(	Index	atomId1,
		Index	atomId2 ) const

Returns: the bond between atomId1 and atomId2.

◆ bondLabel()

std::string bondLabel ( Index bondIndex ) const

Returns: Any custom label for the requested bond.

Parameters

bondIndex The index of the bond.

◆ setBondLabel()

bool setBondLabel	(	Index	bondIndex,
		const std::string &	label )

Set the custom label of a single bond.

Parameters

bondIndex	The index of the bond to modify.
label	The new label of the bond.

Returns: True on success, false otherwise.

◆ setBondLabels()

bool setBondLabels ( const Core::Array< std::string > & label )

Set all the bond labels in the molecule.

Parameters

label The new label array. Must be of length bondCount().

Returns: True on success, false otherwise.

◆ bonds() [1/3]

Array< BondType > bonds ( const AtomType & a )

Returns: A vector of bonds to the supplied atom a.

◆ bonds() [2/3]

Array< BondType > bonds ( Index a )

Returns: A vector of bonds to the supplied atom a.

◆ bonds() [3/3]

Array< const BondType * > bonds ( Index a ) const

Returns: A vector of bonds to the supplied atom a.

◆ addMesh()

Mesh * addMesh ( )

Returns: The mesh object added to the molecule.

◆ addCube()

Cube * addCube ( )

Returns: The cube object added to the molecule.

◆ setActiveCubeIndex()

bool setActiveCubeIndex ( Index index )

Parameters

index The index of the cube to make active.

Returns: True if the index is valid and was set, false otherwise.

◆ activeCubeIndex()

Index activeCubeIndex ( ) const

Returns: The active cube index, or 0 if no cubes exist.

◆ activeCube()

Cube * activeCube ( )

Returns: A pointer to the active cube, or nullptr if no cubes exist.

◆ cubes()

std::vector< Cube * > cubes ( )

Returns: The cube vector for the molecule

◆ formula()

std::string formula	(	const std::string &	delimiter = "",
		int	showCountsOver = 1 ) const

Returns: the chemical formula of the molecule.

Parameters

delimiter	Delimiter to insert between tokens, defaults to none.
showCountsOver	Show atom counts above this (defaults to 1).

◆ mass()

double mass ( ) const

Returns: The mass of the molecule obtained by summing constituent atomic masses.

◆ monoisotopicMass()

double monoisotopicMass ( ) const

Returns: the monoisotopic mass of the molecule obtained by summing the isotopic masses of the atoms (including the most common isotope if not specified).

◆ centerOfGeometry()

Vector3 centerOfGeometry ( ) const

Returns: The center of geometry of the molecule obtained by summing the coordinates of the atoms.

◆ centerOfMass()

Vector3 centerOfMass ( ) const

Returns: The center of mass of the molecule obtained by summing the coordinates of the atoms weighted by mass.

◆ radius()

double radius ( ) const

Returns: The minimum radius of a sphere centered on centerOfGeometry containing all the centers of the atoms.

◆ bestFitPlane() [1/2]

std::pair< Vector3, Vector3 > bestFitPlane ( ) const

Returns: The (centroid, normal vector) pair of the best-fit plane of the atoms of the molecule.

◆ bestFitPlane() [2/2]

std::pair< Vector3, Vector3 > bestFitPlane ( const Array< Vector3 > & pos )

static

Returns: The normal vector of the best-fit plane of some specific atoms.

◆ setBasisSet()

void setBasisSet ( BasisSet * basis )

Set the basis set for the molecule. The molecule takes ownership of basis and deletes the basis set it replaces. Passing the current basis set is a no-op. Passing nullptr removes (and deletes) the current one.

◆ basisSet()

BasisSet * basisSet ( )

Returns: the basis set (if present) for the molecule.

◆ setUnitCell()

void setUnitCell ( UnitCell * uc )

The unit cell for this molecule. May be nullptr for non-periodic structures.

◆ unitCell() [1/2]

UnitCell * unitCell ( )

The unit cell for this molecule. May be nullptr for non-periodic structures.

◆ unitCell() [2/2]

const UnitCell * unitCell ( ) const

The unit cell for this molecule. May be nullptr for non-periodic structures.

◆ setHallNumber()

void setHallNumber ( unsigned short hallNumber )

The space group for this molecule. It is updated after every space group operation.

Setting a Hall number other than 0 removes the entry that file readers keep in the data map when they only know the international table number of the space group (SpaceGroups::internationalNumberKey()): it is superseded. Setting 0 leaves the data map alone.

◆ hallNumber()

unsigned short hallNumber ( ) const

The space group for this molecule. It is updated after every space group operation.

Setting a Hall number other than 0 removes the entry that file readers keep in the data map when they only know the international table number of the space group (SpaceGroups::internationalNumberKey()): it is superseded. Setting 0 leaves the data map alone.

◆ vibrationFrequencies() [1/2]

Array< double > vibrationFrequencies ( ) const

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ setVibrationFrequencies() [1/2]

void setVibrationFrequencies ( const Array< double > & freq )

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ vibrationIRIntensities() [1/2]

Array< double > vibrationIRIntensities ( ) const

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ setVibrationIRIntensities() [1/2]

void setVibrationIRIntensities ( const Array< double > & intensities )

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ vibrationRamanIntensities() [1/2]

Array< double > vibrationRamanIntensities ( ) const

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ setVibrationRamanIntensities() [1/2]

void setVibrationRamanIntensities ( const Array< double > & intensities )

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ vibrationLx() [1/2]

Array< Vector3 > vibrationLx ( int mode ) const

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ setVibrationLx() [1/2]

void setVibrationLx ( const Array< Array< Vector3 > > & lx )

Vibrational data for the active conformer (see coordinate3d()). Molecules with no coordinate sets store their single set of vibrations under the default active index, so these behave exactly as before for the common one-geometry-one-Hessian case.

Each getter returns an empty Array when the active conformer has no vibrational data, or when mode is out of range.

◆ vibrationFrequencies() [2/2]

Array< double > vibrationFrequencies ( size_t conformerIndex ) const

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ setVibrationFrequencies() [2/2]

void setVibrationFrequencies	(	const Array< double > &	freq,
		size_t	conformerIndex )

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ vibrationIRIntensities() [2/2]

Array< double > vibrationIRIntensities ( size_t conformerIndex ) const

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ setVibrationIRIntensities() [2/2]

void setVibrationIRIntensities	(	const Array< double > &	intensities,
		size_t	conformerIndex )

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ vibrationRamanIntensities() [2/2]

Array< double > vibrationRamanIntensities ( size_t conformerIndex ) const

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ setVibrationRamanIntensities() [2/2]

void setVibrationRamanIntensities	(	const Array< double > &	intensities,
		size_t	conformerIndex )

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ vibrationLx() [2/2]

Array< Vector3 > vibrationLx	(	int	mode,
		size_t	conformerIndex ) const

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ setVibrationLx() [2/2]

void setVibrationLx	(	const Array< Array< Vector3 > > &	lx,
		size_t	conformerIndex )

Vibrational data for a specific conformer, for files that carry a Hessian at more than one geometry.

◆ hasVibrations() [1/2]

bool hasVibrations ( size_t conformerIndex ) const

Returns: True if conformerIndex has vibrational data.

◆ hasVibrations() [2/2]

bool hasVibrations ( ) const

Returns: True if the active conformer has vibrational data.

◆ vibrationConformerCount()

size_t vibrationConformerCount ( ) const

Returns: The number of conformers carrying vibrational data. This is not the number of conformers: most trajectories have a Hessian at only one geometry, if any.

◆ vibrationConformers()

Array< size_t > vibrationConformers ( ) const

Returns: The indices of the conformers carrying vibrational data, in increasing order.

◆ clearVibrations()

void clearVibrations ( )

Remove all vibrational data from every conformer.

◆ vibrationData()

const VibrationData * vibrationData ( size_t conformerIndex ) const

Returns: The vibrational data for conformerIndex, or nullptr when that conformer has none. The per-field accessors above are thin wrappers over this; new code that wants several fields at once should prefer it.

◆ setVibrationData()

void setVibrationData	(	const VibrationData &	data,
		size_t	conformerIndex )

Store a whole set of vibrational data against conformerIndex, replacing anything already there. Parsers that assemble a complete Hessian should prefer this to the per-field setters: it is one lookup, and a new field added to VibrationData needs no new call.

◆ perceiveBondsSimple()

void perceiveBondsSimple	(	const double	tolerance = 0.45,
		const double	minDistance = 0.32 )

Perceives bonds in the molecule based on the 3D coordinates of the atoms. atoms are considered bonded if within the sum of radii plus a small tolerance.

Parameters

tolerance	The calculation tolerance.
minDistance	= atoms closer than the square of this are ignored

◆ perceiveBondsFromResidueData()

void perceiveBondsFromResidueData ( )

Perceives bonds in the molecule based on preset residue data.

Use this if you have residue data available (e.g., reading PDB or MMTF files) Otherwise consider

See also: perceiveBondsSimple and; perceiveBondOrders

◆ perceiveBondOrders() [1/2]

BondOrderResult perceiveBondOrders ( const BondOrderOptions & options )

Perceives bond orders from the connectivity (and, optionally, the geometry) of the molecule. Bonds are assumed to be present already; only bonds currently of order 1 are ever raised.

Every non-metal atom has one target valence, from atomValence() for its element, formal charge and current bond order sum. The atom's unsaturation is that target minus the bond order sum it already has. The task is then to give each candidate bond (a single bond between two unsaturated atoms) an extra order of 0, 1 or 2 so that the extras at every atom add up to exactly its unsaturation. This is a degree-constrained subgraph problem; it is solved exactly by constraint propagation with bounded backtracking, separately for each connected group of candidate bonds. A group that can be solved is written back; a group that cannot is left exactly as it was, and its unsaturated atoms are reported.

Rules, all of them chemistry judgements for a reviewer to check:

No bond ends up above order 3, and a bond to hydrogen or a halogen stays single.
Bonds that already have an order above 1 are kept as they are, and count toward their atoms' valence.
Metal atoms (see Elements::isMetal()) are never given bond orders, and their bonds do not count toward their ligands' valence: a pyridine nitrogen bound to zinc is still a pyridine nitrogen.
If the molecule has 3D coordinates and options asks for it, bond lengths decide which of several valid assignments is tried first. For a bond of length d the order k nearest to d, among the AtomUtilities::idealBondLength() values for k = 1, 2, 3, is the one preferred, and bonds that look most strongly multiple are branched on first. This only steers the search: the first valid assignment found is taken, with no attempt to find the best one overall.

Limits: there is one fixed valence per atom, chosen by the sum of its existing bond orders. Atoms whose valence depends on the answer (hypervalent S and P, nitro groups, N-oxides), charged or radical atoms, and heavy-atom-only structures with missing hydrogens will be reported as failures instead of being assigned charges or implicit hydrogens.

Returns: which atoms, if any, could not be satisfied.

◆ perceiveBondOrders() [2/2]

void perceiveBondOrders ( )

Perceives bond orders with default options, ignoring the result.

See also: perceiveBondOrders(const BondOrderOptions&)

◆ perceiveSubstitutedCations()

void perceiveSubstitutedCations ( )

Perceives all-carbon-substituted onium ions of nitrogen, oxygen, phosphorus, sulfur, arsenic and selenium.

◆ coordinate3d()

int coordinate3d ( ) const

Returns: the index of the currently active coordinate set.

◆ coordinate3dRef()

const Array< Vector3 > & coordinate3dRef ( size_t index ) const

Returns: the coordinate set at index without copying it, or an empty array if there is no such set.

coordinate3d() hands back a copy of every atom position in the set, which is what reading a whole trajectory one set at a time should not pay for.

◆ clearCoordinate3d()

void clearCoordinate3d ( )

Clear coordinate sets (except the default set)

◆ estimateVelocities() [1/2]

void estimateVelocities ( )

Estimate velocities from the coordinate sets and timesteps.

Does nothing unless there is one timestep per coordinate set. The timesteps are taken as they are stored, so a conventional dynamics trajectory – coordinates in Angstrom, timesteps in picoseconds – gives velocities in Angstrom per picosecond, which is what the derived properties below assume.

Alongside the per-atom velocities this fills three per-coordinate-set properties, next to "energies" and "forces" in the data map:

"velocities": the mean atomic speed, in Angstrom / picosecond
"velocityDeviations": the standard deviation of those speeds
"temperatures": the instantaneous temperature, in Kelvin

◆ estimateVelocities() [2/2]

void estimateVelocities ( double timeStep )

Estimate velocities taking the coordinate sets to be timeStep apart, rather than reading the stored timesteps.

Most trajectory files do not record when each frame was written, so the spacing has to come from the caller instead. The stored timesteps are left untouched; everything else behaves as the overload above.

Parameters

timeStep the interval between consecutive coordinate sets, in picoseconds.

◆ velocities()

Array< Vector3 > velocities ( int index ) const

Get the velocities for the specified index.

◆ setVelocities()

bool setVelocities	(	const Array< Vector3 > &	velocities,
		int	index )

Set the velocities for the specified index.

Call updateVelocityProperties() once the last set is in to bring the derived per-coordinate-set properties up to date with them.

◆ updateVelocityProperties()

void updateVelocityProperties ( )

Fill the per-coordinate-set properties derived from the velocities – "velocities", "velocityDeviations" and "temperatures", described under estimateVelocities() above.

estimateVelocities() does this for the velocities it works out itself. Anything that supplies velocities of its own, through setVelocities(), should call this afterwards.

◆ clearVelocities()

void clearVelocities ( )

Clear all velocity sets.

◆ setTimeStep()

bool setTimeStep	(	double	timestep,
		int	index )

Timestep property is used when molecular dynamics trajectories are read

◆ forceVectors() [1/2]

const Array< Vector3 > & forceVectors ( ) const

Returns: a vector of forces for the atoms in the molecule.

◆ forceVectors() [2/2]

Array< Vector3 > & forceVectors ( )

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ forceVector()

Vector3 forceVector ( Index atomId ) const

Get the force of a single atom.

Parameters

atomId The index of the atom.

Returns: The force vector of the atom, or Vector3::Zero() if no force information has been set.

◆ setForceVectors()

bool setForceVectors ( const Core::Array< Vector3 > & forces )

Replace the current array of force vectors.

Parameters

forces The new coordinate array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setForceVector()

bool setForceVector	(	Index	atomId,
		const Vector3 &	force )

Set the 3D position of a single atom.

Parameters

atomId	The index of the atom to modify.
force	The new position of the atom.

Returns: True on success, false otherwise.

◆ residueCount()

Index residueCount ( ) const

Returns: The number of residues in the molecule.

◆ residueLabel()

std::string residueLabel ( Index residueIndex ) const

Returns: Any custom label for the requested residue.

Parameters

residueIndex The index of the residue.

◆ setResidueLabel()

bool setResidueLabel	(	Index	residueIndex,
		const std::string &	label )

Set the custom label of a single residue.

Parameters

residueIndex	The index of the residue to modify.
label	The new label of the residue.

Returns: True on success, false otherwise.

◆ setResidueLabels()

bool setResidueLabels ( const Core::Array< std::string > & label )

Set all the residue labels in the molecule.

Parameters

label The new label array. Must be of length residueCount().

Returns: True on success, false otherwise.

◆ atomCount() [1/2]

Index atomCount ( ) const

Returns: The number of atoms in the molecule.

◆ atomCount() [2/2]

Index atomCount ( unsigned char atomicNumber ) const

Parameters

atomicNumber The atomic number to match on.

Returns: The number of atoms with the supplied atomic number.

◆ bondCount()

Index bondCount ( ) const

Returns: the number of bonds in the molecule.

◆ bondPair()

std::pair< Index, Index > bondPair ( Index bondId ) const

Get the set of bonded atoms corresponding to bondId.

Parameters

bondId The index of the requested bond.

Returns: The bonded atom pair, represented as a pair of atom indices.

◆ setBondPairs()

bool setBondPairs ( const Array< std::pair< Index, Index > > & pairs )

Replace the current array of bonded atoms.

Parameters

pairs The array.

Returns: True on success, false on failure.

Note: The bonded atoms are represented as a pair of bond indices.; If needed, the elements in pairs will be modified to ensure that the first atom index is less than the second.

◆ bondPairs()

const Array< std::pair< Index, Index > > & bondPairs ( ) const

Returns: a vector of pairs of atom indices of the bonds in the molecule.

◆ bondOrders()

const Array< unsigned char > & bondOrders ( ) const

Returns: a vector of the bond orders for the bonds in the molecule.

◆ graph()

const Graph & graph ( ) const

Returns: the graph for the molecule.

◆ atomicNumbers()

const Array< unsigned char > & atomicNumbers ( ) const

Returns: a vector of atomic numbers for the atoms in the molecule.

◆ atomicNumber()

unsigned char atomicNumber ( Index atomId ) const

Get the atomic number for the requested atom.

Parameters

atomId The index of the atom.

Returns: The atomic number of the atom indexed at atomId, or Avogadro::InvalidElement if atomId is invalid.

◆ setBondOrders()

bool setBondOrders ( const Array< unsigned char > & orders )

Replace the current array of bond orders.

Parameters

orders The new array.

Returns: True on success, false on failure.

◆ setBondOrder()

bool setBondOrder	(	Index	bondId,
		unsigned char	order )

Set the order of a bond in the molecule.

Parameters

bondId	The bond's index.
order	The new order of the bond.

Returns: True on success, false on failure.

◆ hasCustomElements()

bool hasCustomElements ( ) const

Returns: True if custom elements exist in the molecule.

Note: Custom element atomic numbers lie between CustomElementMin and CustomElementMax.

◆ setBondPair()

bool setBondPair	(	Index	bondId,
		const std::pair< Index, Index > &	pair )

Set the bonded atoms for a bond.

Parameters

bondId	The bond to modify.
pair	The new bond pair.

Returns: True on success, false otherwise.

Note: If needed, pair will be modified to ensure that the first atom index is less than the second.

◆ bondOrder()

unsigned char bondOrder ( Index bondId ) const

Get the order of a bond.

Parameters

bondId The id of the bond.

Returns: The bond order.

◆ setAtomicNumbers()

bool setAtomicNumbers ( const Core::Array< unsigned char > & nums )

Replace the current array of atomic numbers.

Parameters

nums	The new atomic number array. Must be of length atomCount().

Returns: True on success, false otherwise.

◆ setAtomicNumber()

bool setAtomicNumber	(	Index	atomId,
		unsigned char	atomicNumber )

Set the atomic number of a single atom.

Parameters

atomId	The index of the atom to modify.
atomicNumber	The new atomic number.

Returns: True on success, false otherwise.

◆ addConstraint() [1/2]

void addConstraint	(	Real	Value,
		Index	a,
		Index	b,
		Index	c = MaxIndex,
		Index	d = MaxIndex )

Freeze or unfreeze an atom for optimization

◆ addConstraint() [2/2]

void addConstraint ( Constraint & c )

Freeze or unfreeze an atom for optimization

◆ removeConstraint()

void removeConstraint	(	Index	a,
		Index	b,
		Index	c = MaxIndex,
		Index	d = MaxIndex )

Freeze or unfreeze an atom for optimization

◆ clearConstraints()

void clearConstraints ( )

Freeze or unfreeze an atom for optimization

◆ setConstraints()

void setConstraints ( const std::vector< Core::Constraint > & constraints )

Freeze or unfreeze an atom for optimization

◆ constraints() [1/2]

std::vector< Core::Constraint > & constraints ( )

Freeze or unfreeze an atom for optimization

◆ constraints() [2/2]

const std::vector< Core::Constraint > & constraints ( ) const

Freeze or unfreeze an atom for optimization

◆ setFrozenAtom()

void setFrozenAtom	(	Index	atomId,
		bool	frozen )

Freeze or unfreeze an atom for optimization

◆ frozenAtom()

bool frozenAtom ( Index atomId ) const

Returns: whether the specified atom is frozen

◆ frozenAtomAxis()

bool frozenAtomAxis	(	Index	atomId,
		int	axis ) const

Parameters

atomId	The index of the atom to check
axis	The axis to check (0 = x, 1 = y, 2 = z)

Returns: whether the specified axis of the specified atom is frozen

◆ setFrozenAtomAxis()

void setFrozenAtomAxis	(	Index	atomId,
		int	axis,
		bool	frozen )

Freeze or unfreeze X, Y, or Z coordinate of an atom for optimization

Parameters

atomId	The index of the atom to modify.
axis	The axis to freeze (0, 1, or 2 for X, Y, or Z)
frozen	True to freeze, false to unfreeze

◆ frozenAtomMask()

Eigen::VectorXd frozenAtomMask ( ) const

Returns: the frozen status of atoms (i.e., 3*N array of 1.0 or 0.0) 0.0 means the atom is frozen, 1.0 means the atom is not frozen. (i.e., multiply this mask with gradients to freeze atoms)

◆ scanCoordinates()

std::vector< Constraint > scanCoordinates ( ) const

Returns: the scan coordinates, skipping any malformed entry

◆ setScanCoordinates()

void setScanCoordinates ( const std::vector< Constraint > & coordinates )

Replace the scan coordinates.

Parameters

coordinates The coordinates to store. Only the atom indices are kept: a scan coordinate has no target value or force constant.

◆ addScanCoordinate()

void addScanCoordinate ( const Constraint & coordinate )

Add one scan coordinate, ignoring it if an equivalent one is already stored.

Parameters

coordinate The coordinate to add

◆ composition()

std::map< unsigned char, size_t > composition ( ) const

Returns: a map of components and count.

◆ formulaComposition()

std::map< std::string, size_t > formulaComposition ( ) const

Returns: a map of element symbols (including isotopes like D, T, 13C) to their count. Handles unit cell fractional contributions for atoms at corners (1/8), edges (1/4), and faces (1/2).

◆ getAtomBonds()

Array< std::pair< Index, Index > > getAtomBonds ( Index index ) const

Returns: the atom pairs for all bonds to the atom indexed at index.

◆ getAtomOrders()

Array< unsigned char > getAtomOrders ( Index index ) const

Returns: the bond orders for all bonds to the atom indexed at index.

◆ removeBonds()

bool removeBonds ( Index atom )

Remove bonds to atom

◆ clearCalculatedResults()

void clearCalculatedResults ( )

Drop everything that was calculated from the structure – partial charges, forces, velocities, normal modes and spectra. Call this from any edit that changes which atoms or bonds exist: those results describe the molecule as it was, and after such an edit it is not that molecule.

Reindexing them instead would keep the arrays the right length while the numbers went on describing something that no longer exists, which is the worse failure because nothing looks wrong.

◆ copyDisplayStateFrom()

void copyDisplayStateFrom ( const Molecule & other )

Copy which display types are on (and their settings) from other, e.g. to keep Ball and Stick showing when this molecule is replaced by one freshly read from a file or script that has no display state of its own.

Copies the per-plugin enable flags, settings and loaded set, cloning the settings as the copy constructor does. The per-layer vectors are then fitted to this molecule's layer count: extra layers are dropped, and missing ones take the first layer's value so that every layer shows what the user had switched on. Layer assignment, visibility and locks are not touched.

◆ layerInfo()

std::shared_ptr< MoleculeInfo > layerInfo ( ) const

Returns: this molecule's layer state, shared with anything that needs it to outlive a single operation. Never null.

◆ boundingBox()

void boundingBox	(	Vector3 &	boxMin,
		Vector3 &	boxMax,
		const double	radius = 1.0 ) const

Calculate and return bounding box of the whole molecule or selected atoms only.

Parameters

boxMin	[out] the minimum corner (first end of the box diagonal)
boxMax	[out] the maximum corner (second end of the box diagonal)
radius	[in] radius of a single sphere

Member Data Documentation

◆ m_elements

ElementMask m_elements

protected

Which elements this molecule contains (e.g., for force fields)

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

core/molecule.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Member Typedef Documentation

◆ AtomType

◆ BondType

◆ CustomElementMap

◆ ElementMask

Constructor & Destructor Documentation

◆ Molecule() [1/3]

◆ Molecule() [2/3]

◆ Molecule() [3/3]

◆ ~Molecule()

Member Function Documentation

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ readProperties()

◆ setData()

◆ data()

◆ hasData()

◆ setDataMap()

◆ dataMap() [1/2]

◆ dataMap() [2/2]

◆ spectra()

◆ setSpectra()

◆ spectraTypes()

◆ setPartialCharges()

◆ removePartialCharges()

◆ partialCharges()

◆ partialChargeTypes()

◆ atomProperties() [1/2]

◆ atomProperties() [2/2]

◆ bondProperties() [1/2]

◆ bondProperties() [2/2]

◆ residueProperties() [1/2]

◆ residueProperties() [2/2]

◆ conformerProperties() [1/2]

◆ conformerProperties() [2/2]

◆ hybridizations() [1/2]

◆ hybridizations() [2/2]

◆ hybridization()

◆ setHybridizations()

◆ setHybridization()

◆ formalCharges() [1/2]

◆ formalCharges() [2/2]

◆ formalCharge()

◆ setFormalCharges()

◆ setFormalCharge()

◆ totalCharge()

◆ totalSpinMultiplicity()

◆ isotopes() [1/2]

◆ isotopes() [2/2]

◆ isotope()

◆ setIsotopes()

◆ setIsotope()

◆ colors() [1/2]

◆ colors() [2/2]

◆ color()

◆ setColors()

◆ setColor()

◆ atomPositions2d() [1/2]

◆ atomPositions2d() [2/2]

◆ atomPosition2d()

◆ setAtomPositions2d()

◆ setAtomPosition2d()

◆ atomPositions3d() [1/2]

◆ atomPositions3d() [2/2]

◆ atomPosition3d()

◆ setAtomPositions3d()

◆ setAtomPosition3d()

◆ atomLabel()

◆ setAtomLabel()

◆ setAtomLabels()

◆ setAtomSelected()

◆ atomSelected()

◆ isSelectionEmpty()

◆ customElementMap()

◆ setCustomElementMap()