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# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Classes that deal with macromolecular crystal structures.
Includes: 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
from .MMCIFParser import MMCIFParser
from .MMCIFParser import FastMMCIFParser
# 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.Data.SCOPData import protein_letters_3to1
# 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.
from . import Selection
# Superimpose atom sets
from .Superimposer import Superimposer
# 3D vector class
from .Vector import Vector, calc_angle, calc_dihedral, refmat, rotmat, rotaxis
from .Vector import 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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