biopython v1.71.0 Bio.PDB.Atom.Atom
Create 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 element: uppercase string (or None if unknown)
Link to this section Summary
Functions
Print Atom object as
Calculate distance between two atoms
Tries to guess element from atom name if not recognised
Create a copy of the Atom
Remove reference to parent
Set the disordered flag to 1
Return alternative location specifier
Return anisotropic B factor
Return B factor
Return atomic coordinates
Return the full id of the atom
Return the atom name, including leading and trailing spaces
Return the id of the atom (which is its atom name)
Return atom name
Return occupancy
Return parent residue
Return standard deviation of atomic parameters
Return standard deviations of anisotropic temperature factors
Return coordinates as Vector
Return the disordered flag (1 if disordered, 0 otherwise)
Set anisotropic B factor
Set the parent residue
Set standard deviation of atomic parameters
Set standard deviations of anisotropic temperature factors
Apply rotation and translation to the atomic coordinates
Link to this section Functions
Print Atom object as
Calculate distance between two atoms.
Example:
>>> distance=atom1-atom2:param other: the other atom :type other: L{Atom}
Tries to guess element from atom name if not recognised.
Create a copy of the Atom.
Parent information is lost.
Remove reference to parent.
Set the disordered flag to 1.
The disordered flag indicates whether the atom is disordered or not.
Return alternative location specifier.
Return anisotropic B factor.
Return B factor.
Return atomic coordinates.
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).
Return the atom name, including leading and trailing spaces.
Return the id of the atom (which is its atom name).
Return atom name.
Return occupancy.
Return parent residue.
Return standard deviation of atomic parameters.
Return standard deviations of anisotropic temperature factors.
Return coordinates as Vector.
:return: coordinates as 3D vector :rtype: Vector
Return the disordered flag (1 if disordered, 0 otherwise).
Set anisotropic B factor.
:param anisou_array: anisotropic B factor. :type anisou_array: Numeric array (length 6)
Set the parent residue.
Arguments:
- parent - Residue object
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)
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