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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.
"""Residue class, used by Structure objects."""
# My Stuff
import warnings
from Bio import BiopythonDeprecationWarning
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.Entity import Entity, DisorderedEntityWrapper
_atom_name_dict = {}
_atom_name_dict["N"] = 1
_atom_name_dict["CA"] = 2
_atom_name_dict["C"] = 3
_atom_name_dict["O"] = 4
class Residue(Entity):
"""Represents a residue. A Residue object stores atoms."""
def __init__(self, id, resname, segid):
"""Initialize the class."""
self.level = "R"
self.disordered = 0
self.resname = resname
self.segid = segid
Entity.__init__(self, id)
def __repr__(self):
"""Return the residue full id."""
resname = self.get_resname()
hetflag, resseq, icode = self.get_id()
full_id = (resname, hetflag, resseq, icode)
return "<Residue %s het=%s resseq=%s icode=%s>" % full_id
def add(self, atom):
"""Add an Atom object.
Checks for adding duplicate atoms, and raises a
PDBConstructionException if so.
"""
atom_id = atom.get_id()
if self.has_id(atom_id):
raise PDBConstructionException(
"Atom %s defined twice in residue %s" % (atom_id, self))
Entity.add(self, atom)
def sort(self):
"""Sort child atoms.
Atoms N, CA, C, O always come first, thereafter alphabetically
by name, with any alternative location specifier for disordered
atoms (altloc) as a tie-breaker.
"""
warnings.warn("The custom sort() method will be removed in the "
"future in favour of rich comparison methods. Use the "
"built-in sorted() function instead.",
BiopythonDeprecationWarning)
self.child_list.sort()
def flag_disordered(self):
"""Set the disordered flag."""
self.disordered = 1
def is_disordered(self):
"""Return 1 if the residue contains disordered atoms."""
return self.disordered
def get_resname(self):
"""Return the residue name."""
return self.resname
def get_unpacked_list(self):
"""Return the list of all atoms, unpack DisorderedAtoms."""
atom_list = self.get_list()
undisordered_atom_list = []
for atom in atom_list:
if atom.is_disordered():
undisordered_atom_list = (undisordered_atom_list + atom.disordered_get_list())
else:
undisordered_atom_list.append(atom)
return undisordered_atom_list
def get_segid(self):
"""Return the segment identifier."""
return self.segid
def get_atoms(self):
"""Return atoms."""
for a in self:
yield a
def get_atom(self):
"""Return atom."""
warnings.warn("`get_atom` has been deprecated and we intend to remove it"
" in a future release of Biopython. Please use `get_atoms` instead.",
BiopythonDeprecationWarning)
for a in self:
yield a
class DisorderedResidue(DisorderedEntityWrapper):
"""DisorderedResidue is a wrapper around two or more Residue objects.
It is used to represent point mutations (e.g. there is a Ser 60 and a Cys 60
residue, each with 50 % occupancy).
"""
def __init__(self, id):
"""Initialize the class."""
DisorderedEntityWrapper.__init__(self, id)
def __repr__(self):
"""Return disordered residue full identifier."""
resname = self.get_resname()
hetflag, resseq, icode = self.get_id()
full_id = (resname, hetflag, resseq, icode)
return "<DisorderedResidue %s het=%s resseq=%i icode=%s>" % full_id
def add(self, atom):
"""Add atom to residue."""
residue = self.disordered_get()
if not atom.is_disordered() == 2:
# Atoms in disordered residues should have non-blank
# altlocs, and are thus represented by DisorderedAtom objects.
resname = residue.get_resname()
het, resseq, icode = residue.get_id()
# add atom anyway, if PDBParser ignores exception the atom will be part of the residue
residue.add(atom)
raise PDBConstructionException(
"Blank altlocs in duplicate residue %s (%s, %i, %s)"
% (resname, het, resseq, icode))
residue.add(atom)
def sort(self):
"""Sort the atoms in the child Residue objects."""
for residue in self.disordered_get_list():
residue.sort()
def disordered_add(self, residue):
"""Add a residue object and use its resname as key.
Arguments:
- residue - Residue object
"""
resname = residue.get_resname()
# add chain parent to residue
chain = self.get_parent()
residue.set_parent(chain)
assert(not self.disordered_has_id(resname))
self[resname] = residue
self.disordered_select(resname)
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