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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.
"""The structure class, representing a macromolecular structure."""
from Bio.PDB.Entity import Entity
class Structure(Entity):
"""
The Structure class contains a collection of Model instances.
"""
def __init__(self, id):
self.level = "S"
Entity.__init__(self, id)
# Special methods
def __repr__(self):
return "<Structure id=%s>" % self.get_id()
# Private methods
def _sort(self, m1, m2):
"""Sort models.
This sorting function sorts the Model instances in the Structure instance.
The sorting is done based on the model id, which is a simple int that
reflects the order of the models in the PDB file.
Arguments:
o m1, m2 - Model instances
"""
return cmp(m1.get_id(), m2.get_id())
# Public
def get_models(self):
for m in self:
yield m
def get_chains(self):
for m in self.get_models():
for c in m:
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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