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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.
"""Model class, used in Structure objects."""
from Bio.PDB.Entity import Entity
class Model(Entity):
"""
The object representing a model in a structure. In a structure
derived from an X-ray crystallography experiment, only a single
model will be present (with some exceptions). NMR structures
normally contain many different models.
"""
def __init__(self, id, serial_num=None):
"""
Arguments:
o id - int
o serial_num - int
"""
self.level = "M"
if serial_num is None:
self.serial_num = id
else:
self.serial_num = serial_num
Entity.__init__(self, id)
# Private methods
def _sort(self, c1, c2):
"""Sort the Chains instances in the Model instance.
Chain instances are sorted alphabetically according to
their chain id. Blank chains come last, as they often consist
of waters.
Arguments:
o c1, c2 - Chain objects
"""
id1 = c1.get_id()
id2 = c2.get_id()
# make sure blank chains come last (often waters)
if id1 == " " and not id2 == " ":
return 1
elif id2 == " " and not id1 == " ":
return -1
return cmp(id1, id2)
# Special methods
def __repr__(self):
return "<Model id=%s>" % self.get_id()
# Public
def get_chains(self):
for c in self:
yield c
def get_residues(self):
for c in self.get_chains():
for r in c:
yield r
def get_atoms(self):
for r in self.get_residues():
for a in r:
yield a
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