1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
|
# 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):
"""Initialize.
Arguments:
- id - int
- 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)
def __repr__(self):
"""Return model identifier."""
return "<Model id=%s>" % self.get_id()
def get_chains(self):
"""Return chains."""
for c in self:
yield c
def get_residues(self):
"""Return residues."""
for c in self.get_chains():
for r in c:
yield r
def get_atoms(self):
"""Return atoms."""
for r in self.get_residues():
for a in r:
yield a
|
