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
55
56
57
58
59
60
61
62
63
64
65
66
|
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause 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
from Bio.PDB.internal_coords import IC_Chain
class Structure(Entity):
"""The Structure class contains a collection of Model instances."""
def __init__(self, id):
"""Initialize the class."""
self.level = "S"
Entity.__init__(self, id)
def __repr__(self):
"""Return the structure identifier."""
return "<Structure id=%s>" % self.get_id()
def get_models(self):
"""Return models."""
yield from self
def get_chains(self):
"""Return chains from models."""
for m in self.get_models():
yield from m
def get_residues(self):
"""Return residues from chains."""
for c in self.get_chains():
yield from c
def get_atoms(self):
"""Return atoms from residue."""
for r in self.get_residues():
yield from r
def atom_to_internal_coordinates(self, verbose: bool = False) -> None:
"""Create/update internal coordinates from Atom X,Y,Z coordinates.
Internal coordinates are bond length, angle and dihedral angles.
:param verbose bool: default False
describe runtime problems
"""
for chn in self.get_chains():
chn.atom_to_internal_coordinates(verbose)
def internal_to_atom_coordinates(self, verbose: bool = False) -> None:
"""Create/update atom coordinates from internal coordinates.
:param verbose bool: default False
describe runtime problems
:raises Exception: if any chain does not have .pic attribute
"""
for chn in self.get_chains():
chn.internal_to_atom_coordinates(verbose)
|
