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Atom.py
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Atom.py
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# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Atom class, used in Structure objects."""
import numpy
import warnings
import copy
from Bio.PDB.Entity import DisorderedEntityWrapper
from Bio.PDB.PDBExceptions import PDBConstructionWarning
from Bio.PDB.Vector import Vector
from Bio.Data import IUPACData
class Atom(object):
def __init__(self, name, coord, bfactor, occupancy, altloc, fullname, serial_number,
element=None):
"""
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)
"""
self.level="A"
# Reference to the residue
self.parent=None
# the atomic data
self.name=name # eg. CA, spaces are removed from atom name
self.fullname=fullname # e.g. " CA ", spaces included
self.coord=coord
self.bfactor=bfactor
self.occupancy=occupancy
self.altloc=altloc
self.full_id=None # (structure id, model id, chain id, residue id, atom id)
self.id=name # id of atom is the atom name (e.g. "CA")
self.disordered_flag=0
self.anisou_array=None
self.siguij_array=None
self.sigatm_array=None
self.serial_number=serial_number
# Dictionary that keeps additional properties
self.xtra={}
assert not element or element == element.upper(), element
self.element = self._assign_element(element)
self.mass = self._assign_atom_mass()
def _assign_element(self, element):
"""Tries to guess element from atom name if not recognised."""
if not element or element.capitalize() not in IUPACData.atom_weights:
# Inorganic elements have their name shifted left by one position
# (is a convention in PDB, but not part of the standard).
# isdigit() check on last two characters to avoid mis-assignment of
# hydrogens atoms (GLN HE21 for example)
if self.fullname[0] != " " and not self.fullname[2:].isdigit():
putative_element = self.name.strip()
else:
# Hs may have digit in [0]
if self.name[0].isdigit():
putative_element = self.name[1]
else:
putative_element = self.name[0]
if putative_element.capitalize() in IUPACData.atom_weights:
msg = "Used element %r for Atom (name=%s) with given element %r" \
% (putative_element, self.name, element)
element = putative_element
else:
msg = "Could not assign element %r for Atom (name=%s) with given element %r" \
% (putative_element, self.name, element)
element = ""
warnings.warn(msg, PDBConstructionWarning)
return element
def _assign_atom_mass(self):
# Needed for Bio/Struct/Geometry.py C.O.M. function
if self.element:
return IUPACData.atom_weights[self.element.capitalize()]
else:
return float('NaN')
# Special methods
def __repr__(self):
"Print Atom object as <Atom atom_name>."
return "<Atom %s>" % self.get_id()
def __sub__(self, other):
"""
Calculate distance between two atoms.
Example:
>>> distance=atom1-atom2
@param other: the other atom
@type other: L{Atom}
"""
diff=self.coord-other.coord
return numpy.sqrt(numpy.dot(diff,diff))
# set methods
def set_serial_number(self, n):
self.serial_number=n
def set_bfactor(self, bfactor):
self.bfactor=bfactor
def set_coord(self, coord):
self.coord=coord
def set_altloc(self, altloc):
self.altloc=altloc
def set_occupancy(self, occupancy):
self.occupancy=occupancy
def 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.
@param sigatm_array: standard deviations of atomic parameters.
@type sigatm_array: Numeric array (length 5)
"""
self.sigatm_array=sigatm_array
def set_siguij(self, siguij_array):
"""
Set standard deviations of anisotropic temperature factors.
@param siguij_array: standard deviations of anisotropic temperature factors.
@type siguij_array: Numeric array (length 6)
"""
self.siguij_array=siguij_array
def set_anisou(self, anisou_array):
"""
Set anisotropic B factor.
@param anisou_array: anisotropic B factor.
@type anisou_array: Numeric array (length 6)
"""
self.anisou_array=anisou_array
# Public methods
def flag_disorder(self):
"""Set the disordered flag to 1.
The disordered flag indicates whether the atom is disordered or not.
"""
self.disordered_flag=1
def is_disordered(self):
"Return the disordered flag (1 if disordered, 0 otherwise)."
return self.disordered_flag
def set_parent(self, parent):
"""Set the parent residue.
Arguments:
o parent - Residue object
"""
self.parent=parent
def detach_parent(self):
"Remove reference to parent."
self.parent=None
def get_sigatm(self):
"Return standard deviation of atomic parameters."
return self.sigatm_array
def get_siguij(self):
"Return standard deviations of anisotropic temperature factors."
return self.siguij_array
def get_anisou(self):
"Return anisotropic B factor."
return self.anisou_array
def get_parent(self):
"Return parent residue."
return self.parent
def get_serial_number(self):
return self.serial_number
def get_name(self):
"Return atom name."
return self.name
def get_id(self):
"Return the id of the atom (which is its atom name)."
return self.id
def 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).
"""
return self.parent.get_full_id()+((self.name, self.altloc),)
def get_coord(self):
"Return atomic coordinates."
return self.coord
def get_bfactor(self):
"Return B factor."
return self.bfactor
def get_occupancy(self):
"Return occupancy."
return self.occupancy
def get_fullname(self):
"Return the atom name, including leading and trailing spaces."
return self.fullname
def get_altloc(self):
"Return alternative location specifier."
return self.altloc
def get_level(self):
return self.level
def transform(self, rot, tran):
"""
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
"""
self.coord=numpy.dot(self.coord, rot)+tran
def get_vector(self):
"""
Return coordinates as Vector.
@return: coordinates as 3D vector
@rtype: Vector
"""
x,y,z=self.coord
return Vector(x,y,z)
def copy(self):
"""
Create a copy of the Atom.
Parent information is lost.
"""
# Do a shallow copy then explicitly copy what needs to be deeper.
shallow = copy.copy(self)
shallow.detach_parent()
shallow.set_coord(copy.copy(self.get_coord()))
shallow.xtra = self.xtra.copy()
return shallow
class DisorderedAtom(DisorderedEntityWrapper):
"""
This class 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.
"""
def __init__(self, id):
"""
Arguments:
o id - string, atom name
"""
self.last_occupancy=-1
DisorderedEntityWrapper.__init__(self, id)
# Special methods
def __repr__(self):
return "<Disordered Atom %s>" % self.get_id()
def disordered_add(self, atom):
"Add a disordered atom."
# Add atom to dict, use altloc as key
atom.flag_disorder()
# set the residue parent of the added atom
residue=self.get_parent()
atom.set_parent(residue)
altloc=atom.get_altloc()
occupancy=atom.get_occupancy()
self[altloc]=atom
if occupancy>self.last_occupancy:
self.last_occupancy=occupancy
self.disordered_select(altloc)