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Chemistry::MoleculeInterface Interface Reference

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

Inheritance diagram for Chemistry::MoleculeInterface:

Inheritance graph
[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.

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.


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.


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