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# Copyright (C) 2002, Thomas Hamelryck ([email protected])
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause 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.
Original Author: Thomas Hamelryck.
Contributions by:
- Peter Cock
- Joe Greener
- Rob Miller
- Lenna X. Peterson
- Joao Rodrigues
- Kristian Rother
- Eric Talevich
- and many others.
"""
# 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
from .Polypeptide import is_aa, standard_aa_names, is_nucleic
# IO of PDB files (including flexible selective output)
from .PDBIO import PDBIO, Select
from .mmcifio import MMCIFIO
# Some methods to eg. get a list of Residues
# from a list of Atoms.
from . import Selection
# Superimpose atom sets
from .Superimposer import Superimposer
# CEAlign structural alignment
from .cealign import CEAligner
# 3D vector class
from .vectors import Vector, calc_angle, calc_dihedral, refmat, rotmat, rotaxis
from .vectors 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 kdtrees C module
try:
from .NeighborSearch import NeighborSearch
except ImportError:
pass
# Native Shrake-Rupley algorithm for SASA calculations.
# Depends on kdtrees C module
try:
from .SASA import ShrakeRupley
except ImportError:
pass
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