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__doc__="""
Classes that deal with macromolecular crystal structures. (eg.
PDB and mmCIF parsers, a Structure class, a module to keep
a local copy of the PDB up-to-date, selective IO of PDB files,
etc.). Author: Thomas Hamelryck. Additional code by Kristian
Rother.
"""
# Get a Structure object from a PDB file
from PDBParser import PDBParser
try:
# Get a Structure object from an mmCIF file
from MMCIFParser import MMCIFParser
except:
# Not compiled I guess
pass
# Download from the PDB
from PDBList import PDBList
# Parse PDB header directly
from parse_pdb_header import parse_pdb_header
# Find connected polypeptides in a Structure
from Polypeptide import PPBuilder, CaPPBuilder, is_aa, standard_aa_names
# This is also useful :-)
from Bio.SCOP.Raf import to_one_letter_code
# IO of PDB files (including flexible selective output)
from PDBIO import PDBIO, Select
# Some methods to eg. get a list of Residues
# from a list of Atoms.
import Selection
# Superimpose atom sets
from Superimposer import Superimposer
# 3D vector class
from Vector import Vector, calc_angle, calc_dihedral, refmat, rotmat, rotaxis,\
vector_to_axis, m2rotaxis, rotaxis2m
# Alignment module
from StructureAlignment import StructureAlignment
# DSSP handle
# (secondary structure and solvent accessible area calculation)
from DSSP import DSSP, make_dssp_dict
# Residue depth:
# distance of residue atoms from solvent accessible surface
from ResidueDepth import ResidueDepth, get_surface
# Calculation of Half Sphere Solvent Exposure
from HSExposure import HSExposureCA, HSExposureCB, ExposureCN
# Kolodny et al.'s backbone libraries
from FragmentMapper import FragmentMapper
# Write out chain(start-end) to PDB file
from Dice import extract
# Fast atom neighbor search
# Depends on KDTree C++ module
try:
from NeighborSearch import NeighborSearch
except ImportError:
pass
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