Atom represents an atom in a Molecule. More...

#include <chemistry/molecule/atom.h>

Inheritance diagram for sc::Atom:

Public Member Functions
	Atom (int Z, double x, double y, double z, const std::string &label, double mass=0, int have_charge=0, double charge=0, int have_fragment=0, int fragment=0)
	Creates an atom for use in the sc::Molecule class. More...

	Atom (int Z, double x, double y, double z, const char *label=0, double mass=0, int have_charge=0, double charge=0, int have_fragment=0, int fragment=0)
	Constructs an atom object that takes a c style char * array.

	Atom ()
	Default constructor supplied so that Atom will work with sc::SavableState. More...

	Atom (const Atom &other)

double &	r (int xyz)
	Returns a reference to the x,y, or z coordinate.

const double &	r (int xyz) const

double *	r ()
	Returns a pointer to the coordinate array.

const double *	r () const

int	Z () const
	Returns atomic number.

double	mass () const

bool	have_charge () const

double	charge () const

bool	have_fragment () const

int	fragment () const

const std::string &	label () const

Friends
void	FromStateIn (Atom &a, StateIn &so, int &count)
	reads Atom from sc::StateIn

Detailed Description

Atom represents an atom in a Molecule.

Its position is defined relative to the coordinate system of the Molecule. It also has an atomic number. Optionally, it can has a charge, mass, and it can belong to a fragment.

Constructor & Destructor Documentation

◆ Atom() [1/2]

sc::Atom::Atom	(	int	Z,
		double	x,
		double	y,
		double	z,
		const std::string &	label,
		double	mass = `0`,
		int	have_charge = `0`,
		double	charge = `0`,
		int	have_fragment = `0`,
		int	fragment = `0`
	)

inline

Creates an atom for use in the sc::Molecule class.

Parameters

Z	Atomic charge of the nucleous.
x	x Coordinate of position vector.
y	y Coordinate of position vector.
z	z Coordinate of position vector.
label	A string which gives the atom a user defined label.
mass	The mass of the nuclous.
have_charge	A boolean which signals a charge different than Z has been specified by the user.
charge	A user specified charge which is different than Z.
have_fragment_	A boolean which specifies that the atom belongs to a specific fragment.
fragment	Specifies to which fragment the atom belongs if 0 then the atom does not belong to a fragment.

◆ Atom() [2/2]

sc::Atom::Atom ( )

inline

Default constructor supplied so that Atom will work with sc::SavableState.

The user should not use this.

@Warning Do not use, meant for sc::SavableState

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

src/lib/chemistry/molecule/atom.h

Public Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Atom() [1/2]

◆ Atom() [2/2]