Class Atom

Atom object.

The Atom object stores atom name (both with and without spaces),
coordinates, B factor, occupancy, alternative location specifier
and (optionally) anisotropic B factor and standard deviations of
B factor and positions.

@param name: atom name (eg. "CA"). Note that spaces are normally stripped.
@type name: string

@param coord: atomic coordinates (x,y,z)
@type coord: Numeric array (Float0, size 3)

@param bfactor: isotropic B factor
@type bfactor: number

@param occupancy: occupancy (0.0-1.0)
@type occupancy: number

@param altloc: alternative location specifier for disordered atoms
@type altloc: string

@param fullname: full atom name, including spaces, e.g. " CA ". Normally
these spaces are stripped from the atom name.
@type fullname: string

@param element: atom element, e.g. "C" for Carbon, "HG" for mercury,
@type fullname: uppercase string (or None if unknown)

Overrides: object.__init__

Print Atom object as <Atom atom_name>.

Overrides: object.__repr__

Calculate distance between two atoms.

Example:
    >>> distance=atom1-atom2

@param other: the other atom
@type other: L{Atom}

Set standard deviation of atomic parameters.

The standard deviation of atomic parameters consists
of 3 positional, 1 B factor and 1 occupancy standard
deviation.

@param sigatm_array: standard deviations of atomic parameters.
@type sigatm_array: Numeric array (length 5)

Set standard deviations of anisotropic temperature factors.

@param siguij_array: standard deviations of anisotropic temperature factors.
@type siguij_array: Numeric array (length 6)

Set anisotropic B factor.

@param anisou_array: anisotropic B factor.
@type anisou_array: Numeric array (length 6)

Set the disordered flag to 1.

The disordered flag indicates whether the atom is disordered or not.

Set the parent residue.

Arguments:
o parent - Residue object

Return the full id of the atom.

The full id of an atom is the tuple
(structure id, model id, chain id, residue id, atom name, altloc).

Apply rotation and translation to the atomic coordinates.

Example:
        >>> rotation=rotmat(pi, Vector(1,0,0))
        >>> translation=array((0,0,1), 'f')
        >>> atom.transform(rotation, translation)

@param rot: A right multiplying rotation matrix
@type rot: 3x3 Numeric array

@param tran: the translation vector
@type tran: size 3 Numeric array

Return coordinates as Vector.

@return: coordinates as 3D vector
@rtype: Vector

Create a copy of the Atom.
Parent information is lost.