AtomTemplate< Molecule_T > Class Template Reference

Public Types
using	MoleculeType = Molecule_T

Public Member Functions
	AtomTemplate ()
	AtomTemplate (MoleculeType *m, Index i)
bool	operator== (const AtomTemplate< MoleculeType > &other) const
bool	operator!= (const AtomTemplate< MoleculeType > &other) const
AtomTemplate< MoleculeType > &	operator++ ()
AtomTemplate< MoleculeType >	operator++ (int)
AtomTemplate< MoleculeType > &	operator-- ()
AtomTemplate< MoleculeType >	operator-- (int)
bool	isValid () const
MoleculeType *	molecule () const
Index	index () const
Real	mass () const
void	setSelected (bool selected)
bool	selected () const
void	setForceVector (const Vector3 &force)
Vector3	forceVector () const
void	setLabel (const std::string &label)
std::string	label () const
void	setAtomicNumber (unsigned char num)
unsigned char	atomicNumber () const
void	setPosition2d (const Vector2 &pos)
Vector2	position2d () const
void	setPosition3d (const Vector3 &pos)
Vector3	position3d () const
void	setHybridization (AtomHybridization hyb)
AtomHybridization	hybridization () const
void	setFormalCharge (signed char charge)
signed char	formalCharge () const
void	setIsotope (unsigned short isotope)
unsigned short	isotope () const
void	setColor (Vector3ub color)
Vector3ub	color () const
void	setLayer (size_t layer)
size_t	layer () const
void	setProperty (const std::string &name, double value)
void	setProperty (const std::string &name, int value)
void	setProperty (const std::string &name, const std::string &value)
void	setProperty (const std::string &name, const MatrixX &value)
template<typename T>
std::optional< T >	property (const std::string &name) const

Constructor & Destructor Documentation

AtomTemplate() [1/2]

template<class Molecule_T>

AtomTemplate

(

)

Creates a new, invalid atom object.

AtomTemplate() [2/2]

template<class Molecule_T>

AtomTemplate	(	MoleculeType *	m,
		Index	i )

Creates a new atom object representing the atom at index i in molecule m.

Member Function Documentation

operator==()

template<class Molecule_T>

bool operator==

(

const AtomTemplate< MoleculeType > &

other

)

const

Returns

True if this and other share the same index and molecule.

operator!=()

template<class Molecule_T>

bool operator!=

(

const AtomTemplate< MoleculeType > &

other

)

const

Returns

True if this and other do not share the same index or molecule.

operator++() [1/2]

template<class Molecule_T>

AtomTemplate< Molecule_T > & operator++

(

)

Prefix increment operator. Increment this Atom's index by 1 and return a self-reference. Check isValid() before calling any other methods.

operator++() [2/2]

template<class Molecule_T>

AtomTemplate< Molecule_T > operator++

(

int

)

Postfix increment operator. Increment this Atom's index by 1 and return a copy of the current Atom. Check isValid() before calling any other methods.

operator--() [1/2]

template<class Molecule_T>

AtomTemplate< Molecule_T > & operator--

(

)

Prefix decrement operator. Decrement this Atom's index by 1 and return a self-reference. Check isValid() before calling any other methods.

operator--() [2/2]

template<class Molecule_T>

AtomTemplate< Molecule_T > operator--

(

int

)

Postfix decrement operator. Decrement this Atom's index by 1 and return a copy of the current Atom. Check isValid() before calling any other methods.

isValid()

template<class Molecule_T>

bool isValid

(

)

const

Returns

True if the molecule is set and the index is less than the number of atoms.

molecule()

template<class Molecule_T>

AtomTemplate< Molecule_T >::MoleculeType * molecule

(

)

const

Returns

The molecule that contains this Atom.

index()

template<class Molecule_T>

Index index

(

)

const

Returns

The index of this atom in molecule().

setAtomicNumber()

template<class Molecule_T>

void setAtomicNumber

(

unsigned char

num

)

The proton count of the atom.

atomicNumber()

template<class Molecule_T>

unsigned char atomicNumber

(

)

const

The proton count of the atom.

mass()

template<class Molecule_T>

Real mass

(

)

const

Returns

The mass of this atom

setPosition2d()

template<class Molecule_T>

void setPosition2d

(

const Vector2 &

pos

)

The 2D position of this atom.

Note

Not all molecule types support 2D positions. If the current MoleculeType class does not, calling this method will result in a compilation error.

position2d()

template<class Molecule_T>

Vector2 position2d

(

)

const

The 2D position of this atom.

Note

Not all molecule types support 2D positions. If the current MoleculeType class does not, calling this method will result in a compilation error.

setPosition3d()

template<class Molecule_T>

void setPosition3d

(

const Vector3 &

pos

)

The 3D position of this atom.

position3d()

template<class Molecule_T>

Vector3 position3d

(

)

const

The 3D position of this atom.

setHybridization()

template<class Molecule_T>

void setHybridization

(

AtomHybridization

hyb

)

The hybridization / coordination of this atom

hybridization()

template<class Molecule_T>

AtomHybridization hybridization

(

)

const

The hybridization / coordination of this atom

setFormalCharge()

template<class Molecule_T>

void setFormalCharge

(

signed char

charge

)

The formal charge of this atom

formalCharge()

template<class Molecule_T>

signed char formalCharge

(

)

const

The formal charge of this atom

setIsotope()

template<class Molecule_T>

void setIsotope

(

unsigned short

isotope

)

The isotope of this atom

isotope()

template<class Molecule_T>

unsigned short isotope

(

)

const

The isotope of this atom

setColor()

template<class Molecule_T>

void setColor

(

Vector3ub

color

)

The color of this atom

color()

template<class Molecule_T>

Vector3ub color

(

)

const

The color of this atom

setLayer()

template<class Molecule_T>

void setLayer

(

size_t

layer

)

The layer of this atom

layer()

template<class Molecule_T>

size_t layer

(

)

const

The layer of this atom

setSelected()

template<class Molecule_T>

void setSelected

(

bool

selected

)

Is the atom selected. {@

setForceVector()

template<class Molecule_T>

void setForceVector

(

const Vector3 &

force

)

The force on this atom. {@

setProperty() [1/4]

template<class Molecule_T>

void setProperty	(	const std::string &	name,
		double	value )

Custom property access. Setters are overloaded by value type. The template getter returns std::nullopt if the property is missing or if the requested type does not match the stored type. int and double values convert to string automatically.

setProperty() [2/4]

template<class Molecule_T>

void setProperty	(	const std::string &	name,
		int	value )

Custom property access. Setters are overloaded by value type. The template getter returns std::nullopt if the property is missing or if the requested type does not match the stored type. int and double values convert to string automatically.

setProperty() [3/4]

template<class Molecule_T>

void setProperty	(	const std::string &	name,
		const std::string &	value )

Custom property access. Setters are overloaded by value type. The template getter returns std::nullopt if the property is missing or if the requested type does not match the stored type. int and double values convert to string automatically.

setProperty() [4/4]

template<class Molecule_T>

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

Custom property access. Setters are overloaded by value type. The template getter returns std::nullopt if the property is missing or if the requested type does not match the stored type. int and double values convert to string automatically.

property()

template<class Molecule_T>

template<typename T>

std::optional< T > property

(

const std::string &

name

)

const

Custom property access. Setters are overloaded by value type. The template getter returns std::nullopt if the property is missing or if the requested type does not match the stored type. int and double values convert to string automatically.

---

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

• atom.h