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# Copyright (C) 2002, Thomas Hamelryck ([email protected])
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Atom class, used in Structure objects."""
import copy
import sys
import warnings
import numpy as np
from Bio.PDB.Entity import DisorderedEntityWrapper
from Bio.PDB.PDBExceptions import PDBConstructionWarning
from Bio.PDB.vectors import Vector
from Bio.Data import IUPACData
class Atom:
"""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.
"""
def __init__(
self,
name,
coord,
bfactor,
occupancy,
altloc,
fullname,
serial_number,
element=None,
pqr_charge=None,
radius=None,
):
"""Initialize Atom object.
: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)
:param pqr_charge: atom charge
:type pqr_charge: number
:param radius: atom radius
:type radius: number
"""
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()
self.pqr_charge = pqr_charge
self.radius = radius
# For atom sorting (protein backbone atoms first)
self._sorting_keys = {"N": 0, "CA": 1, "C": 2, "O": 3}
# Sorting Methods
# standard across different objects and allows direct comparison
def __eq__(self, other):
"""Test equality."""
if isinstance(other, Atom):
return self.full_id[1:] == other.full_id[1:]
else:
return NotImplemented
def __ne__(self, other):
"""Test inequality."""
if isinstance(other, Atom):
return self.full_id[1:] != other.full_id[1:]
else:
return NotImplemented
def __gt__(self, other):
"""Test greater than."""
if isinstance(other, Atom):
if self.parent != other.parent:
return self.parent > other.parent
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s > order_o
elif self.name != other.name:
return self.name > other.name
else:
return self.altloc > other.altloc
else:
return NotImplemented
def __ge__(self, other):
"""Test greater or equal."""
if isinstance(other, Atom):
if self.parent != other.parent:
return self.parent >= other.parent
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s >= order_o
elif self.name != other.name:
return self.name >= other.name
else:
return self.altloc >= other.altloc
else:
return NotImplemented
def __lt__(self, other):
"""Test less than."""
if isinstance(other, Atom):
if self.parent != other.parent:
return self.parent < other.parent
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s < order_o
elif self.name != other.name:
return self.name < other.name
else:
return self.altloc < other.altloc
else:
return NotImplemented
def __le__(self, other):
"""Test less or equal."""
if isinstance(other, Atom):
if self.parent != other.parent:
return self.parent <= other.parent
order_s = self._sorting_keys.get(self.name, 4)
order_o = self._sorting_keys.get(other.name, 4)
if order_s != order_o:
return order_s <= order_o
elif self.name != other.name:
return self.name <= other.name
else:
return self.altloc <= other.altloc
else:
return NotImplemented
# Hash method to allow uniqueness (set)
def __hash__(self):
"""Return atom full identifier."""
return hash(self.get_full_id())
def _assign_element(self, element):
"""Guess element from atom name if not recognised (PRIVATE).
There is little documentation about extracting/encoding element
information in atom names, but some conventions seem to prevail:
- C, N, O, S, H, P, F atom names start with a blank space (e.g. " CA ")
unless the name is 4 characters long (e.g. HE21 in glutamine). In both
these cases, the element is the first character.
- Inorganic elements do not have a blank space (e.g. "CA " for calcium)
but one must check the full name to differentiate between e.g. helium
("HE ") and long-name hydrogens (e.g. "HE21").
- Atoms with unknown or ambiguous elements are marked with 'X', e.g.
PDB 4cpa. If we fail to identify an element, we should mark it as
such.
"""
if not element or element.capitalize() not in IUPACData.atom_weights:
if self.fullname[0].isalpha() 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 = "X" # mark as unknown/ambiguous
warnings.warn(msg, PDBConstructionWarning)
return element
def _assign_atom_mass(self):
"""Return atom weight (PRIVATE)."""
try:
return IUPACData.atom_weights[self.element.capitalize()]
except (AttributeError, KeyError):
return float("NaN")
# Special methods
def __repr__(self):
"""Print Atom object as <Atom atom_name>."""
return f"<Atom {self.get_id()}>"
def __sub__(self, other):
"""Calculate distance between two atoms.
:param other: the other atom
:type other: L{Atom}
Examples
--------
This is an incomplete but illustrative example::
distance = atom1 - atom2
"""
diff = self.coord - other.coord
return np.sqrt(np.dot(diff, diff))
# set methods
def set_serial_number(self, n):
"""Set serial number."""
self.serial_number = n
def set_bfactor(self, bfactor):
"""Set isotroptic B factor."""
self.bfactor = bfactor
def set_coord(self, coord):
"""Set coordinates."""
self.coord = coord
def set_altloc(self, altloc):
"""Set alternative location specifier."""
self.altloc = altloc
def set_occupancy(self, occupancy):
"""Set 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
def set_charge(self, pqr_charge):
"""Set charge."""
self.pqr_charge = pqr_charge
def set_radius(self, radius):
"""Set radius."""
self.radius = radius
# 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:
- parent - Residue object
"""
self.parent = parent
self.full_id = self.get_full_id()
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 the serial number."""
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 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)
"""
try:
return self.parent.get_full_id() + ((self.name, self.altloc),)
except AttributeError:
return (None, None, None, None, 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 level."""
return self.level
def get_charge(self):
"""Return charge."""
return self.pqr_charge
def get_radius(self):
"""Return radius."""
return self.radius
def transform(self, rot, tran):
"""Apply rotation and translation to the atomic coordinates.
:param rot: A right multiplying rotation matrix
:type rot: 3x3 Numeric array
:param tran: the translation vector
:type tran: size 3 Numeric array
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)
"""
self.coord = np.dot(self.coord, rot) + tran
def get_vector(self):
"""Return coordinates as Vector.
:return: coordinates as 3D vector
:rtype: Bio.PDB.Vector class
"""
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):
"""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):
"""Create DisorderedAtom.
Arguments:
- id - string, atom name
"""
# TODO - make this a private attribute?
self.last_occupancy = -sys.maxsize
DisorderedEntityWrapper.__init__(self, id)
# Special methods
# Override parent class __iter__ method
def __iter__(self):
"""Iterate through disordered atoms."""
yield from self.disordered_get_list()
def __repr__(self):
"""Return disordered atom identifier."""
if self.child_dict:
return f"<DisorderedAtom {self.get_id()}>"
else:
return f"<Empty DisorderedAtom {self.get_id()}>"
# This is a separate method from Entity.center_of_mass since DisorderedAtoms
# will be unpacked by Residue.get_unpacked_list(). Here we allow for a very
# specific use case that is much simpler than the general implementation.
def center_of_mass(self):
"""Return the center of mass of the DisorderedAtom as a numpy array.
Assumes all child atoms have the same mass (same element).
"""
children = self.disordered_get_list()
if not children:
raise ValueError(f"{self} does not have children")
coords = np.asarray([a.coord for a in children], dtype=np.float32)
return np.average(coords, axis=0, weights=None)
def disordered_get_list(self):
"""Return list of atom instances.
Sorts children by altloc (empty, then alphabetical).
"""
return sorted(self.child_dict.values(), key=lambda a: ord(a.altloc))
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)
def disordered_remove(self, altloc):
"""Remove a child atom altloc from the DisorderedAtom.
Arguments:
- altloc - name of the altloc to remove, as a string.
"""
# Get child altloc
atom = self.child_dict[altloc]
is_selected = self.selected_child is atom
# Detach
del self.child_dict[altloc]
atom.detach_parent()
if is_selected and self.child_dict: # pick next highest occupancy
child = sorted(self.child_dict.values(), key=lambda a: a.occupancy)[-1]
self.disordered_select(child.altloc)
elif not self.child_dict:
self.selected_child = None
self.last_occupancy = -sys.maxsize
def transform(self, rot, tran):
"""Apply rotation and translation to all children.
See the documentation of Atom.transform for details.
"""
for child in self:
child.coord = np.dot(child.coord, rot) + tran
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