Bio.PDB.Atom module¶
Atom class, used in Structure objects.
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class
Bio.PDB.Atom.
Atom
(name, coord, bfactor, occupancy, altloc, fullname, serial_number, element=None, pqr_charge=None, radius=None)¶ Bases:
object
Define Atom class.
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.
In the case of PQR files, B factor and occupancy are replaced by atomic charge and radius.
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__init__
(self, name, coord, bfactor, occupancy, altloc, fullname, serial_number, element=None, pqr_charge=None, radius=None)¶ Initialize Atom object.
- Parameters
name (string) – atom name (eg. “CA”). Note that spaces are normally stripped.
coord (Numeric array (Float0, size 3)) – atomic coordinates (x,y,z)
bfactor (number) – isotropic B factor
occupancy (number) – occupancy (0.0-1.0)
altloc (string) – alternative location specifier for disordered atoms
fullname (string) – full atom name, including spaces, e.g. ” CA “. Normally these spaces are stripped from the atom name.
element (uppercase string (or None if unknown)) – atom element, e.g. “C” for Carbon, “HG” for mercury,
pqr_charge (number) – atom charge
radius (number) – atom radius
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__eq__
(self, other)¶ Test equality.
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__ne__
(self, other)¶ Test inequality.
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__gt__
(self, other)¶ Test greater than.
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__ge__
(self, other)¶ Test greater or equal.
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__lt__
(self, other)¶ Test less than.
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__le__
(self, other)¶ Test less or equal.
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__hash__
(self)¶ Return atom full identifier.
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__repr__
(self)¶ Print Atom object as <Atom atom_name>.
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__sub__
(self, other)¶ Calculate distance between two atoms.
- Parameters
other (L{Atom}) – the other atom
Examples
This is an incomplete but illustrative example:
distance = atom1 - atom2
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set_serial_number
(self, n)¶ Set serial number.
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set_bfactor
(self, bfactor)¶ Set isotroptic B factor.
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set_coord
(self, coord)¶ Set coordinates.
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set_altloc
(self, altloc)¶ Set alternative location specifier.
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set_occupancy
(self, occupancy)¶ Set occupancy.
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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.
- Parameters
sigatm_array (Numeric array (length 5)) – standard deviations of atomic parameters.
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set_siguij
(self, siguij_array)¶ Set standard deviations of anisotropic temperature factors.
- Parameters
siguij_array (Numeric array (length 6)) – standard deviations of anisotropic temperature factors.
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set_anisou
(self, anisou_array)¶ Set anisotropic B factor.
- Parameters
anisou_array (Numeric array (length 6)) – anisotropic B factor.
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set_charge
(self, pqr_charge)¶ Set charge.
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set_radius
(self, radius)¶ Set radius.
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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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is_disordered
(self)¶ Return the disordered flag (1 if disordered, 0 otherwise).
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set_parent
(self, parent)¶ Set the parent residue.
- Arguments:
parent - Residue object
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detach_parent
(self)¶ Remove reference to parent.
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get_sigatm
(self)¶ Return standard deviation of atomic parameters.
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get_siguij
(self)¶ Return standard deviations of anisotropic temperature factors.
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get_anisou
(self)¶ Return anisotropic B factor.
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get_parent
(self)¶ Return parent residue.
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get_serial_number
(self)¶ Return the serial number.
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get_name
(self)¶ Return atom name.
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get_id
(self)¶ Return the id of the atom (which is its atom name).
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get_full_id
(self)¶ Return the full id of the atom.
The full id of an atom is a tuple used to uniquely identify the atom and consists of the following elements: (structure id, model id, chain id, residue id, atom name, altloc)
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get_coord
(self)¶ Return atomic coordinates.
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get_bfactor
(self)¶ Return B factor.
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get_occupancy
(self)¶ Return occupancy.
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get_fullname
(self)¶ Return the atom name, including leading and trailing spaces.
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get_altloc
(self)¶ Return alternative location specifier.
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get_level
(self)¶ Return level.
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get_charge
(self)¶ Return charge.
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get_radius
(self)¶ Return radius.
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transform
(self, rot, tran)¶ Apply rotation and translation to the atomic coordinates.
- Parameters
rot (3x3 Numeric array) – A right multiplying rotation matrix
tran (size 3 Numeric array) – the translation vector
Examples
This is an incomplete but illustrative example:
from numpy import pi, array from Bio.PDB.vectors import Vector, rotmat rotation = rotmat(pi, Vector(1, 0, 0)) translation = array((0, 0, 1), 'f') atom.transform(rotation, translation)
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get_vector
(self)¶ Return coordinates as Vector.
- Returns
coordinates as 3D vector
- Return type
Bio.PDB.Vector class
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copy
(self)¶ Create a copy of the Atom.
Parent information is lost.
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class
Bio.PDB.Atom.
DisorderedAtom
(id)¶ Bases:
Bio.PDB.Entity.DisorderedEntityWrapper
Contains all Atom objects that represent the same disordered atom.
One of these atoms is “selected” and all method calls not caught by DisorderedAtom are forwarded to the selected Atom object. In that way, a DisorderedAtom behaves exactly like a normal Atom. By default, the selected Atom object represents the Atom object with the highest occupancy, but a different Atom object can be selected by using the disordered_select(altloc) method.
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__init__
(self, id)¶ Create DisorderedAtom.
- Arguments:
id - string, atom name
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__iter__
(self)¶ Iterate through disordered atoms.
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__repr__
(self)¶ Return disordered atom identifier.
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disordered_get_list
(self)¶ Return list of atom instances.
Sorts children by altloc (empty, then alphabetical).
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disordered_add
(self, atom)¶ Add a disordered atom.
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transform
(self, rot, tran)¶ Apply rotation and translation to all children.
See the documentation of Atom.transform for details.
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