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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.
"""Chain class, used in Structure objects."""
from Bio.PDB.Entity import Entity
class Chain(Entity):
"""Define Chain class.
Chain is an object of type Entity, stores residues and includes a method to
access atoms from residues.
"""
def __init__(self, id):
"""Initialize the class."""
self.level = "C"
Entity.__init__(self, id)
# Sorting methods: empty chain IDs come last.
def __gt__(self, other):
"""Validate if id is greater than other.id."""
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id > other.id
else:
return NotImplemented
def __ge__(self, other):
"""Validate if id is greater or equal than other.id."""
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id >= other.id
else:
return NotImplemented
def __lt__(self, other):
"""Validate if id is less than other.id."""
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id < other.id
else:
return NotImplemented
def __le__(self, other):
"""Validate if id is less or equal than other id."""
if isinstance(other, Chain):
if self.id == ' ' and other.id != ' ':
return 0
elif self.id != ' ' and other.id == ' ':
return 1
else:
return self.id <= other.id
else:
return NotImplemented
def _translate_id(self, id):
"""Translate sequence identifier to tuple form (PRIVATE).
A residue id is normally a tuple (hetero flag, sequence identifier,
insertion code). Since for most residues the hetero flag and the
insertion code are blank (i.e. " "), you can just use the sequence
identifier to index a residue in a chain. The _translate_id method
translates the sequence identifier to the (" ", sequence identifier,
" ") tuple.
Arguments:
- id - int, residue resseq
"""
if isinstance(id, int):
id = (' ', id, ' ')
return id
def __getitem__(self, id):
"""Return the residue with given id.
The id of a residue is (hetero flag, sequence identifier, insertion code).
If id is an int, it is translated to (" ", id, " ") by the _translate_id
method.
Arguments:
- id - (string, int, string) or int
"""
id = self._translate_id(id)
return Entity.__getitem__(self, id)
def __contains__(self, id):
"""Check if a residue with given id is present in this chain.
Arguments:
- id - (string, int, string) or int
"""
id = self._translate_id(id)
return Entity.__contains__(self, id)
def __delitem__(self, id):
"""Delete item.
Arguments:
- id - (string, int, string) or int
"""
id = self._translate_id(id)
return Entity.__delitem__(self, id)
def __repr__(self):
"""Return the chain identifier."""
return "<Chain id=%s>" % self.get_id()
# Public methods
def get_unpacked_list(self):
"""Return a list of undisordered residues.
Some Residue objects hide several disordered residues
(DisorderedResidue objects). This method unpacks them,
ie. it returns a list of simple Residue objects.
"""
unpacked_list = []
for residue in self.get_list():
if residue.is_disordered() == 2:
for dresidue in residue.disordered_get_list():
unpacked_list.append(dresidue)
else:
unpacked_list.append(residue)
return unpacked_list
def has_id(self, id):
"""Return 1 if a residue with given id is present.
The id of a residue is (hetero flag, sequence identifier, insertion code).
If id is an int, it is translated to (" ", id, " ") by the _translate_id
method.
Arguments:
- id - (string, int, string) or int
"""
id = self._translate_id(id)
return Entity.has_id(self, id)
# Public
def get_residues(self):
"""Return residues."""
for r in self:
yield r
def get_atoms(self):
"""Return atoms from residues."""
for r in self.get_residues():
for a in r:
yield a
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