Methods
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__init__
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__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.
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__repr__
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__repr__ ( self )
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destroy
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destroy ( self )
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detach_parent
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detach_parent ( self )
Remove reference to parent.
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flag_disorder
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flag_disorder ( self )
Set the disordered flag to 1.
The disordered flag indicates whether the atom is disordered or not.
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get_altloc
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get_altloc ( self )
Return alternative location specifier.
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get_anisou
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get_anisou ( self )
Return anisotropic B factor.
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get_bfactor
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get_bfactor ( self )
Return B factor.
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get_coord
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get_coord ( self )
Return atomic coordinates.
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get_full_id
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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).
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get_fullname
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get_fullname ( self )
Return the atom name, including leading and trailing spaces.
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get_id
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get_id ( self )
Return the id of the atom (which is its atom name).
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get_name
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get_name ( self )
Return atom name.
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get_occupancy
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get_occupancy ( self )
Return occupancy.
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get_parent
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get_parent ( self )
Return parent residue.
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get_sigatm
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get_sigatm ( self )
Return standard deviation of atomic parameters.
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get_siguij
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get_siguij ( self )
Return standard deviations of anisotropic temperature factors.
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is_disordered
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is_disordered ( self )
Return the disordered flag (1 if disordered, 0 otherwise).
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set_anisou
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set_anisou ( self, anisou_array )
Set anisotropic B factor.
Arguments:
o anisou_array - Numpy array (length 6), anisotropic B factor.
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set_parent
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set_parent ( self, parent )
Set the parent residue.
Arguments:
o parent - Residue object
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set_sigatm
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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.
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set_siguij
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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.
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