Chemistry::MoleculeInterface Interface Reference

The Molecule interface provides a collection of atoms. More...

Inheritance diagram for Chemistry::MoleculeInterface:

[legend]List of all members.

Public Member Functions
void	initialize (in long natom, in string unitname)
	Initialize a molecule.
Physics.UnitsInterface	get_units ()
	Returns a units object that corresponds to the units that are used by get_cart_coor or set_cart_coor.
long	get_n_atom ()
	Returns the number of atoms.
int	get_atomic_number (in long atomnum)
	Returns the atomic number of an atom.
void	set_atomic_number (in long atomnum, in int atomic_number)
	Sets atomic number of an atom.
double	get_net_charge ()
	Returns net charge of the molecule.
void	set_net_charge (in double charge)
	Sets the net charge of the molecule.
double	get_charge (in long atomnum)
	Returns charge at an atom.
void	set_charge (in long atomnum, in double charge)
	Sets charge of an atom.
array< double, 1 >	get_coor ()
	Returns the Cartesian coordinate array.
void	set_coor (in array< double, 1 > x)
	Sets the Cartesian coordinates.
double	get_cart_coor (in long atomnum, in int xyz)
	Gets individual Cartesian coordinate.
void	set_cart_coor (in long atomnum, in int xyz, in double val)
	Sets individual Cartesian coordinate.
string	get_atomic_label (in long atomnum)
	Returns label for atom.
void	set_atomic_label (in long atomnum, in string label)
	Sets label for atom.

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Detailed Description

The Molecule interface provides a collection of atoms.

Each atom is associated with a charge, an atomic number, a Cartesian coordinate, and an optional label.

Ghost atoms (atoms do not contribute a charge) have the appropriate atomic number but a zero charge. Point charges have an atomic number of zero, but have a nonzero charge.

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Member Function Documentation

string Chemistry::MoleculeInterface::get_atomic_label (  in long  atomnum  )

Returns label for atom. Parameters: atomnum

int Chemistry::MoleculeInterface::get_atomic_number (  in long  atomnum  )

Returns the atomic number of an atom. Parameters: atomnum  The number of the atom. Returns: The atomic number.

double Chemistry::MoleculeInterface::get_cart_coor (  in long  atomnum, in int  xyz )

Gets individual Cartesian coordinate. Parameters: atomnum  The atom number. xyz  Give 0 for x, 1 for y, and 2 for z. Returns: The Cartesian coordinate.

double Chemistry::MoleculeInterface::get_charge (  in long  atomnum  )

Returns charge at an atom. Parameters: atomnum  The number of the atom. Returns: The charge on the atom.

array< double , 1 > Chemistry::MoleculeInterface::get_coor (   )

Returns the Cartesian coordinate array. Returns: An array with all Cartesian coordinates.

long Chemistry::MoleculeInterface::get_n_atom (   )

Returns the number of atoms. Returns: The number of atoms.

double Chemistry::MoleculeInterface::get_net_charge (   )

Returns net charge of the molecule. Returns: The net charge.

Physics.UnitsInterface Chemistry::MoleculeInterface::get_units (   )

Returns a units object that corresponds to the units that are used by get_cart_coor or set_cart_coor. Returns: The units of the coordinates.

void Chemistry::MoleculeInterface::initialize (  in long  natom, in string  unitname )

Initialize a molecule. Parameters: natom  The number of atoms. unitname  The name of the units ("angstroms" or "bohr").

void Chemistry::MoleculeInterface::set_atomic_label (  in long  atomnum, in string  label )

Sets label for atom. Parameters: atomnum.

void Chemistry::MoleculeInterface::set_atomic_number (  in long  atomnum, in int  atomic_number )

Sets atomic number of an atom. Parameters: atomnum  The number of the atom. atomic_number  The atom's new atomic number.

void Chemistry::MoleculeInterface::set_cart_coor (  in long  atomnum, in int  xyz, in double  val )

Sets individual Cartesian coordinate. Parameters: atomnum  The atom number. xyz  Give 0 for x, 1 for y, and 2 for z. val  The new Cartesian coordinate.

void Chemistry::MoleculeInterface::set_charge (  in long  atomnum, in double  charge )

Sets charge of an atom. set_net_charge must called as well to ensure internal consistency. Parameters: atomnum  The number of the atom.

void Chemistry::MoleculeInterface::set_coor (  in array< double, 1 >  x  )

Sets the Cartesian coordinates. Parameters: x  The new coordinates.

void Chemistry::MoleculeInterface::set_net_charge (  in double  charge  )

Sets the net charge of the molecule. charge The new net charge.

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

• chem-interface.java

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