Package Bio :: Package PDB
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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  from .MMCIFParser import MMCIFParser 
18  from .MMCIFParser import FastMMCIFParser 
19   
20  # Download from the PDB 
21  from .PDBList import PDBList 
22   
23  # Parse PDB header directly 
24  from .parse_pdb_header import parse_pdb_header 
25   
26  # Find connected polypeptides in a Structure 
27  from .Polypeptide import PPBuilder, CaPPBuilder, is_aa, standard_aa_names 
28  # This is also useful :-) 
29  from Bio.Data.SCOPData import protein_letters_3to1 
30   
31  # IO of PDB files (including flexible selective output) 
32  from .PDBIO import PDBIO, Select 
33   
34  # Some methods to eg. get a list of Residues 
35  # from a list of Atoms. 
36  from . import Selection 
37   
38  # Superimpose atom sets 
39  from .Superimposer import Superimposer 
40   
41  # 3D vector class 
42  from .Vector import Vector, calc_angle, calc_dihedral, refmat, rotmat, rotaxis 
43  from .Vector import vector_to_axis, m2rotaxis, rotaxis2m 
44   
45  # Alignment module 
46  from .StructureAlignment import StructureAlignment 
47   
48  # DSSP handle 
49  # (secondary structure and solvent accessible area calculation) 
50  from .DSSP import DSSP, make_dssp_dict 
51   
52  # Residue depth: 
53  # distance of residue atoms from solvent accessible surface 
54  from .ResidueDepth import ResidueDepth, get_surface 
55   
56  # Calculation of Half Sphere Solvent Exposure 
57  from .HSExposure import HSExposureCA, HSExposureCB, ExposureCN 
58   
59  # Kolodny et al.'s backbone libraries 
60  from .FragmentMapper import FragmentMapper 
61   
62  # Write out chain(start-end) to PDB file 
63  from .Dice import extract 
64   
65  # Fast atom neighbor search 
66  # Depends on KDTree C++ module 
67  try: 
68      from .NeighborSearch import NeighborSearch 
69  except ImportError: 
70      pass 
71