Package Bio :: Package PDB
[hide private]
[frames] | no frames]

Source Code for Package Bio.PDB

 1  # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk) 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """Classes that deal with macromolecular crystal structures. 
 7   
 8  Includes: PDB and mmCIF parsers, a Structure class, a module to keep a local 
 9  copy of the PDB up-to-date, selective IO of PDB files, etc. 
10   
11  Author: Thomas Hamelryck.  Additional code by Kristian Rother. 
12  """ 
13   
14  # Get a Structure object from a PDB file 
15  from .PDBParser import PDBParser 
16   
17  try: 
18      # Get a Structure object from an mmCIF file 
19      from .MMCIFParser import MMCIFParser 
20  except: 
21      # Not compiled I guess 
22      pass 
23   
24  # Download from the PDB 
25  from .PDBList import PDBList 
26   
27  # Parse PDB header directly 
28  from .parse_pdb_header import parse_pdb_header 
29   
30  # Find connected polypeptides in a Structure 
31  from .Polypeptide import PPBuilder, CaPPBuilder, is_aa, standard_aa_names 
32  # This is also useful :-) 
33  from Bio.Data.SCOPData import protein_letters_3to1 
34   
35  # IO of PDB files (including flexible selective output) 
36  from .PDBIO import PDBIO, Select 
37   
38  # Some methods to eg. get a list of Residues 
39  # from a list of Atoms. 
40  from . import Selection 
41   
42  # Superimpose atom sets 
43  from .Superimposer import Superimposer 
44   
45  # 3D vector class 
46  from .Vector import Vector, calc_angle, calc_dihedral, refmat, rotmat, rotaxis 
47  from .Vector import vector_to_axis, m2rotaxis, rotaxis2m 
48   
49  # Alignment module 
50  from .StructureAlignment import StructureAlignment 
51   
52  # DSSP handle 
53  # (secondary structure and solvent accessible area calculation) 
54  from .DSSP import DSSP, make_dssp_dict 
55   
56  # Residue depth: 
57  # distance of residue atoms from solvent accessible surface 
58  from .ResidueDepth import ResidueDepth, get_surface 
59   
60  # Calculation of Half Sphere Solvent Exposure 
61  from .HSExposure import HSExposureCA, HSExposureCB, ExposureCN 
62   
63  # Kolodny et al.'s backbone libraries 
64  from .FragmentMapper import FragmentMapper 
65   
66  # Write out chain(start-end) to PDB file 
67  from .Dice import extract 
68   
69  # Fast atom neighbor search 
70  # Depends on KDTree C++ module 
71  try: 
72      from .NeighborSearch import NeighborSearch 
73  except ImportError: 
74      pass 
75