Table of Contents

Class: Atom Bio/PDB/Atom.py
Methods   
__init__
__repr__
destroy
detach_parent
flag_disorder
get_altloc
get_anisou
get_bfactor
get_coord
get_full_id
get_fullname
get_id
get_name
get_occupancy
get_parent
get_sigatm
get_siguij
is_disordered
set_anisou
set_parent
set_sigatm
set_siguij
  __init__ 
__init__ (
        self,
        name,
        coord,
        bfactor,
        occupancy,
        altloc,
        fullname,
        )

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.

Arguments: o name - string, atom name e.g. "CA", note that spaces are normally stripped o coord - Numpy array (Float0, size 3), atomic coordinates o bfactor - float o occupancy - float o altloc - string, alternative location specifier for disordered atoms o fullname - string, full atom name, including spaces, e.g. " CA ". Normally these spaces are stripped from the atom name.

  __repr__ 
__repr__ ( self )

  destroy 
destroy ( self )

  detach_parent 
detach_parent ( self )

Remove reference to parent.

  flag_disorder 
flag_disorder ( self )

Set the disordered flag to 1.

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

  get_altloc 
get_altloc ( self )

Return alternative location specifier.

  get_anisou 
get_anisou ( self )

Return anisotropic B factor.

  get_bfactor 
get_bfactor ( self )

Return B factor.

  get_coord 
get_coord ( self )

Return atomic coordinates.

  get_full_id 
get_full_id ( self )

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).

  get_fullname 
get_fullname ( self )

Return the atom name, including leading and trailing spaces.

  get_id 
get_id ( self )

Return the id of the atom (which is its atom name).

  get_name 
get_name ( self )

Return atom name.

  get_occupancy 
get_occupancy ( self )

Return occupancy.

  get_parent 
get_parent ( self )

Return parent residue.

  get_sigatm 
get_sigatm ( self )

Return standard deviation of atomic parameters.

  get_siguij 
get_siguij ( self )

Return standard deviations of anisotropic temperature factors.

  is_disordered 
is_disordered ( self )

Return the disordered flag (1 if disordered, 0 otherwise).

  set_anisou 
set_anisou ( self,  anisou_array )

Set anisotropic B factor.

Arguments: o anisou_array - Numpy array (length 6), anisotropic B factor.

  set_parent 
set_parent ( self,  parent )

Set the parent residue.

Arguments: o parent - Residue object

  set_sigatm 
set_sigatm ( self,  sigatm_array )

Set standard deviation of atomic parameters.

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

Arguments: o sigatm_array - Numpy array (length 5), standard deviations of atomic parameters.

  set_siguij 
set_siguij ( self,  siguij_array )

Set standard deviations of anisotropic temperature factors.

Arguments: o siguij_array - Numpy array (length 6), standard deviations of anisotropic temperature factors.


Table of Contents

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