#include <nuri/core/molecule.h>

Public Member Functions
	AtomData ()
	Creates a dummy atom with unknown hybridization.
	AtomData (const Element &element, int implicit_hydrogens=0, int formal_charge=0, constants::Hybridization hyb=constants::kOtherHyb, double partial_charge=0.0, int mass_number=-1, bool is_aromatic=false, bool is_in_ring=false, bool is_chiral=false, bool is_clockwise=false)
int	atomic_number () const
	Get the atomic number of the atom.
double	atomic_weight () const
	Get the atomic weight of the atom.
std::string_view	element_symbol () const
	Get the element symbol of the atom.
std::string_view	element_name () const
	Get the element name of the atom.
AtomData &	set_element (const Element &element)
	Change the element of the atom.
AtomData &	set_element (int atomic_number)
	Set the element of the atom by atomic number.
const Element &	element () const noexcept
	Get the element data of the atom.
const Isotope &	isotope () const
	Get the isotope of the atom.
AtomData &	set_isotope (const Isotope &isotope)
	Set explicit isotope of the atom.
AtomData &	set_isotope (int mass_number)
	Set explicit isotope of the atom by mass number.
internal::Nullable< const Isotope * >	explicit_isotope () const
	Get the explicitly set isotope of the atom.
AtomData &	set_hybridization (constants::Hybridization hyb)
constants::Hybridization	hybridization () const
AtomData &	set_implicit_hydrogens (int implicit_hydrogens)
	Set the number of implicit hydrogen atoms.
int	implicit_hydrogens () const
	Get the number of implicit hydrogen atoms.
AtomData &	set_aromatic (bool is_aromatic)
bool	is_aromatic () const
AtomData &	set_conjugated (bool is_conjugated)
bool	is_conjugated () const
AtomData &	set_ring_atom (bool is_ring_atom)
bool	is_ring_atom () const
AtomData &	set_chiral (bool is_chiral)
bool	is_chiral () const
AtomData &	set_clockwise (bool is_clockwise)
bool	is_clockwise () const
	Get handedness of a chiral atom.
AtomFlags	flags () const
AtomData &	add_flags (AtomFlags flags)
AtomData &	del_flags (AtomFlags flags)
AtomData &	reset_flags ()
AtomData &	set_partial_charge (double charge)
double	partial_charge () const
AtomData &	set_formal_charge (int charge)
int	formal_charge () const
std::string_view	get_name () const
template<class ST>
AtomData &	set_name (ST &&name)
template<class KT, class VT>
AtomData &	add_prop (KT &&key, VT &&val)
internal::PropertyMap &	props ()
const internal::PropertyMap &	props () const

Friends
bool	operator== (const AtomData &lhs, const AtomData &rhs)

Constructor & Destructor Documentation

◆ AtomData() [1/2]

nuri::AtomData::AtomData ( )

inline

Creates a dummy atom with unknown hybridization.

◆ AtomData() [2/2]

nuri::AtomData::AtomData	(	const Element &	element,
		int	implicit_hydrogens = 0,
		int	formal_charge = 0,
		constants::Hybridization	hyb = constants::kOtherHyb,
		double	partial_charge = 0.0,
		int	mass_number = -1,
		bool	is_aromatic = false,
		bool	is_in_ring = false,
		bool	is_chiral = false,
		bool	is_clockwise = false )

Member Function Documentation

◆ add_flags()

AtomData & nuri::AtomData::add_flags ( AtomFlags flags )

inline

◆ add_prop()

template<class KT, class VT>

AtomData & nuri::AtomData::add_prop	(	KT &&	key,
		VT &&	val )

inline

◆ atomic_number()

int nuri::AtomData::atomic_number ( ) const

inline

Get the atomic number of the atom.

Note: This is equivalent to element().Element::atomic_number(), provided for convenience.

Returns: The atomic number of the element.

◆ atomic_weight()

double nuri::AtomData::atomic_weight ( ) const

inline

Get the atomic weight of the atom.

Note: This is equivalent to element().Element::atomic_weight(), provided for convenience.

Returns: The atomic weight of the element.

◆ del_flags()

AtomData & nuri::AtomData::del_flags ( AtomFlags flags )

inline

◆ element()

const Element & nuri::AtomData::element ( ) const

inlinenoexcept

Get the element data of the atom.

Returns: Immutable reference to the element object.

◆ element_name()

std::string_view nuri::AtomData::element_name ( ) const

inline

Get the element name of the atom.

Note: This is equivalent to element().Element::name(), provided for convenience.

Returns: The name of the element.

◆ element_symbol()

std::string_view nuri::AtomData::element_symbol ( ) const

inline

Get the element symbol of the atom.

Note: This is equivalent to element().Element::symbol(), provided for convenience.

Returns: The symbol of the element.

◆ explicit_isotope()

internal::Nullable< const Isotope * > nuri::AtomData::explicit_isotope ( ) const

inline

Get the explicitly set isotope of the atom.

Returns: A pointer to the explicitly set isotope object. If none was explicitly given, returns nullptr. Normally isotope() would be the preferred method to get the isotope, which returns the representative isotope of the element if none was explicitly given.

See also: isotope()

◆ flags()

AtomFlags nuri::AtomData::flags ( ) const

inline

◆ formal_charge()

int nuri::AtomData::formal_charge ( ) const

inline

◆ get_name()

std::string_view nuri::AtomData::get_name ( ) const

inline

◆ hybridization()

constants::Hybridization nuri::AtomData::hybridization ( ) const

inline

◆ implicit_hydrogens()

int nuri::AtomData::implicit_hydrogens ( ) const

inline

Get the number of implicit hydrogen atoms.

Returns: The number of implicit hydrogen atoms.

Note: The number of implicit hydrogen atoms is always non-negative.

◆ is_aromatic()

bool nuri::AtomData::is_aromatic ( ) const

inline

◆ is_chiral()

bool nuri::AtomData::is_chiral ( ) const

inline

◆ is_clockwise()

bool nuri::AtomData::is_clockwise ( ) const

inline

Get handedness of a chiral atom.

Precondition: is_chiral() == true, otherwise return value would be meaningless.

Returns: Whether the chiral atom is "clockwise." See stereochemistry definition of SMILES for more information.

Note: Unlike the SMILES convention, implicit hydrogen is placed at the end of the neighbor list. This is to ensure that the chirality of the atom is unchanged when the hydrogen is removed or added.

◆ is_conjugated()

bool nuri::AtomData::is_conjugated ( ) const

inline

◆ is_ring_atom()

bool nuri::AtomData::is_ring_atom ( ) const

inline

◆ isotope()

const Isotope & nuri::AtomData::isotope ( ) const

inline

Get the isotope of the atom.

Returns: A const reference to the isotope object. If any isotope was explicitly given, returns that isotope. Otherwise, returns the representative isotope of the element.

See also: explicit_isotope()

◆ partial_charge()

double nuri::AtomData::partial_charge ( ) const

inline

◆ props() [1/2]

internal::PropertyMap & nuri::AtomData::props ( )

inline

◆ props() [2/2]

const internal::PropertyMap & nuri::AtomData::props ( ) const

inline

◆ reset_flags()

AtomData & nuri::AtomData::reset_flags ( )

inline

◆ set_aromatic()

AtomData & nuri::AtomData::set_aromatic ( bool is_aromatic )

inline

◆ set_chiral()

AtomData & nuri::AtomData::set_chiral ( bool is_chiral )

inline

◆ set_clockwise()

AtomData & nuri::AtomData::set_clockwise ( bool is_clockwise )

inline

◆ set_conjugated()

AtomData & nuri::AtomData::set_conjugated ( bool is_conjugated )

inline

◆ set_element() [1/2]

AtomData & nuri::AtomData::set_element ( const Element & element )

inline

Change the element of the atom.

Parameters

element A reference to the new element object.

Returns: *this.

◆ set_element() [2/2]

AtomData & nuri::AtomData::set_element ( int atomic_number )

inline

Set the element of the atom by atomic number.

Parameters

atomic_number The atomic number of the new element.

Returns: *this.

Note: When the atomic number is out of range, the behavior is undefined.

◆ set_formal_charge()

AtomData & nuri::AtomData::set_formal_charge ( int charge )

inline

◆ set_hybridization()

AtomData & nuri::AtomData::set_hybridization ( constants::Hybridization hyb )

inline

◆ set_implicit_hydrogens()

AtomData & nuri::AtomData::set_implicit_hydrogens ( int implicit_hydrogens )

inline

Set the number of implicit hydrogen atoms.

Parameters

implicit_hydrogens The new number of implicit hydrogen atoms.

Returns: *this.

Note: If the number of implicit hydrogen atoms is negative, the behavior is undefined.

◆ set_isotope() [1/2]

AtomData & nuri::AtomData::set_isotope ( const Isotope & isotope )

inline

Set explicit isotope of the atom.

Parameters

isotope A reference to the new isotope object.

Returns: *this.

Note: If the isotope object references an element different from the element of the atom, the behavior is undefined.

◆ set_isotope() [2/2]

AtomData & nuri::AtomData::set_isotope ( int mass_number )

inline

Set explicit isotope of the atom by mass number.

Parameters

mass_number The mass number of the new isotope.

Returns: *this.

Note: If no isotope with the given mass number is known, explicitly-set isotope of this atom will be cleared.

◆ set_name()

template<class ST>

AtomData & nuri::AtomData::set_name ( ST && name )

inline

◆ set_partial_charge()

AtomData & nuri::AtomData::set_partial_charge ( double charge )

inline

◆ set_ring_atom()

AtomData & nuri::AtomData::set_ring_atom ( bool is_ring_atom )

inline

◆ operator==

bool operator==	(	const AtomData &	lhs,
		const AtomData &	rhs )

friend

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

include/nuri/core/molecule.h

Public Member Functions

Friends

Constructor & Destructor Documentation

◆ AtomData() [1/2]

◆ AtomData() [2/2]

Member Function Documentation

◆ add_flags()

◆ add_prop()

◆ atomic_number()

◆ atomic_weight()

◆ del_flags()

◆ element()

◆ element_name()

◆ element_symbol()

◆ explicit_isotope()

◆ flags()

◆ formal_charge()

◆ get_name()

◆ hybridization()

◆ implicit_hydrogens()

◆ is_aromatic()

◆ is_chiral()

◆ is_clockwise()

◆ is_conjugated()

◆ is_ring_atom()

◆ isotope()

◆ partial_charge()

◆ props() [1/2]

◆ props() [2/2]

◆ reset_flags()

◆ set_aromatic()

◆ set_chiral()

◆ set_clockwise()

◆ set_conjugated()

◆ set_element() [1/2]

◆ set_element() [2/2]

◆ set_formal_charge()

◆ set_hybridization()

◆ set_implicit_hydrogens()

◆ set_isotope() [1/2]

◆ set_isotope() [2/2]

◆ set_name()

◆ set_partial_charge()

◆ set_ring_atom()

Friends And Related Symbol Documentation

◆ operator==