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python-biopython  1.60
__init__.py
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00001 # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
00002 # This code is part of the Biopython distribution and governed by its
00003 # license.  Please see the LICENSE file that should have been included
00004 # as part of this package.
00005 
00006 """Classes that deal with macromolecular crystal structures.
00007 
00008 Includes: PDB and mmCIF parsers, a Structure class, a module to keep a local
00009 copy of the PDB up-to-date, selective IO of PDB files, etc.
00010 
00011 Author: Thomas Hamelryck.  Additional code by Kristian Rother.
00012 """
00013 
00014 # Get a Structure object from a PDB file
00015 from PDBParser import PDBParser
00016 
00017 try:
00018     # Get a Structure object from an mmCIF file
00019     from MMCIFParser import MMCIFParser
00020 except:
00021     # Not compiled I guess 
00022     pass
00023 
00024 # Download from the PDB
00025 from PDBList import PDBList 
00026 
00027 # Parse PDB header directly
00028 from parse_pdb_header import parse_pdb_header
00029 
00030 # Find connected polypeptides in a Structure
00031 from Polypeptide import PPBuilder, CaPPBuilder, is_aa, standard_aa_names
00032 # This is also useful :-)
00033 from Bio.SCOP.Raf import to_one_letter_code
00034 
00035 # IO of PDB files (including flexible selective output)
00036 from PDBIO import PDBIO, Select
00037 
00038 # Some methods to eg. get a list of Residues
00039 # from a list of Atoms.
00040 import Selection
00041 
00042 # Superimpose atom sets
00043 from Superimposer import Superimposer
00044 
00045 # 3D vector class
00046 from Vector import Vector, calc_angle, calc_dihedral, refmat, rotmat, rotaxis,\
00047         vector_to_axis, m2rotaxis, rotaxis2m
00048 
00049 # Alignment module
00050 from StructureAlignment import StructureAlignment
00051 
00052 # DSSP handle 
00053 # (secondary structure and solvent accessible area calculation)
00054 from DSSP import DSSP, make_dssp_dict
00055 
00056 # Residue depth: 
00057 # distance of residue atoms from solvent accessible surface
00058 from ResidueDepth import ResidueDepth, get_surface
00059 
00060 # Calculation of Half Sphere Solvent Exposure
00061 from HSExposure import HSExposureCA, HSExposureCB, ExposureCN
00062 
00063 # Kolodny et al.'s backbone libraries
00064 from FragmentMapper import FragmentMapper
00065 
00066 # Write out chain(start-end) to PDB file
00067 from Dice import extract
00068 
00069 # Fast atom neighbor search
00070 # Depends on KDTree C++ module
00071 try:
00072     from NeighborSearch import NeighborSearch
00073 except ImportError:
00074     pass