# 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

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