# -*- coding: utf-8 -*-
"""
====================================================
PDB format (:mod:`sknano.io.pdb`)
====================================================
.. currentmodule:: sknano.io.pdb
"""
from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
__docformat__ = 'restructuredtext en'
from collections import OrderedDict
from monty.io import zopen
from pyparsing import ParseException
from sknano.core import get_fpath
from sknano.core.atoms import Atom
from .tokenizers import PDBTokenizer
from .base import StructureData, StructureDataError, StructureDataFormatter, \
default_comment_line
__all__ = ['PDB', 'PDBData', 'PDBReader', 'PDBWriter', 'PDBFormatter',
'PDBError', 'PDBIO', 'PDBIOReader', 'PDBIOWriter', 'PDBIOFormatter',
'PDBIOError', 'PDBFormatSpec']
[docs]class PDBReader(StructureData):
"""Class for reading pdb chemical file format.
Parameters
----------
fpath : str
pdb structure file
"""
def __init__(self, fpath, formatter=None, **kwargs):
if formatter is None or not isinstance(formatter, PDBFormatter):
formatter = PDBFormatter()
super().__init__(fpath=fpath, formatter=formatter)
self.records = OrderedDict()
self.tokenizer = PDBTokenizer()
if self.fpath is not None:
self.read()
[docs] def read(self):
"""Read PDB file."""
tokenizer = self.tokenizer
# formatter = self.formatter
self.structure.clear()
with zopen(self.fpath) as f:
while True:
line = f.readline().strip()
record = line[:6].strip()
if record == 'END':
break
parse_method = '_parse_{}'.format(record.lower())
if not hasattr(tokenizer, parse_method):
print('No parser for {} records'.format(record))
continue
try:
record = getattr(tokenizer, parse_method)(line)
except ParseException as e:
print('Error in PDB file format')
raise StructureDataError(e)
else:
if isinstance(record, Atom):
self.structure.append(record)
PDBIOReader = PDBReader
[docs]class PDBWriter:
"""Class for writing pdb chemical file format."""
@classmethod
[docs] def write(cls, fname=None, outpath=None, fpath=None, structure=None,
atoms=None, **kwargs):
"""Write structure data to file.
Parameters
----------
fname : str, optional
Output file name.
outpath : str, optional
Output file path.
fpath : str, optional
Full path (directory path + file name) to output data file.
atoms : :py:class:`~sknano.io.atoms.Atoms`
An :py:class:`~sknano.io.atoms.Atoms` instance.
"""
if structure is None and atoms is None:
raise ValueError('Expected either `structure` or `atoms` object.')
if structure is not None and atoms is None:
atoms = structure.atoms
if fpath is None:
fpath = get_fpath(fname=fname, ext='pdb', outpath=outpath,
overwrite=True, add_fnum=False)
pdb = PDBData()
pdb.write(pdbfile=fpath, atoms=atoms, **kwargs)
PDBIOWriter = PDBWriter
[docs]class PDBData(PDBReader):
"""Class for reading and writing structure data in PDB data format.
Parameters
----------
fpath : str, optional
"""
def __init__(self, fpath=None):
try:
# super(PDBData, self).__init__(fpath=fpath)
super().__init__(fpath=fpath)
except StructureDataError:
pass
[docs] def write(self, pdbfile=None, atoms=None, mode='w',
comment_line=None, **kwargs):
"""Write pdb file.
Parameters
----------
pdbfile : {None, str}, optional
atoms : :class:`~sknano.core.atoms.Atoms`, optional
mode : {'w', 'a'}, optional
"""
try:
kwargs.update(self.kwargs)
if not pdbfile:
if self.fpath is None:
error_msg = 'Invalid `pdbfile` {}'.format(pdbfile)
raise ValueError(error_msg)
else:
pdbfile = self.fpath
if comment_line is None:
comment_line = default_comment_line
if atoms is not None:
self._atoms = atoms
super()._update_atoms(**kwargs)
mode += 't'
try:
with zopen(pdbfile, mode) as stream:
self._write_header(stream, comment_line)
self._write_atoms(stream)
except OSError as e:
print(e)
self._atoms = self._atoms_copy
except (TypeError, ValueError) as e:
print(e)
def _write_header(self, stream, comment_line):
pass
def _write_atoms(self, stream):
formatter = self.formatter
for atom in self.atoms:
stream.write(formatter.format(atom))
stream.write('\n')
PDB = PDBIO = PDBData
PDBFormatSpec = PDBFormatter
mandatory_records = ['HEADER', 'TITLE', 'COMPND', 'SOURCE', 'KEYWDS',
'EXPDTA', 'AUTHOR', 'REVDAT', 'REMARK 2',
'REMARK 3', 'SEQRES', 'CRYST1', 'ORIGX1',
'ORIGX2', 'ORIGX3', 'SCALE1', 'SCALE2', 'SCALE3',
'MASTER', 'END']
optional_records = ['OBSLTE', 'SPLIT', 'CAVEAT', 'NUMMDL', 'MDLTYP',
'SPRSDE', 'JRNL', 'REMARK 0', 'REMARK 1',
'REMARK N', 'DBREF', 'DBREF1', 'DBREF2',
'SEQADV', 'MODRES', 'HET', 'HETNAM', 'HETSYN',
'FORMUL', 'HELIX', 'SHEET', 'SSBOND', 'LINK',
'CISPEP', 'SITE', 'MTRIX1', 'MTRIX2', 'MTRIX3',
'MODEL', 'ATOM', 'ANISOU', 'TER', 'HETATM',
'ENDMDL', 'CONECT']
PDBIOFormatter = PDBFormatter
[docs]class PDBError(StructureDataError):
"""Exception class for :class:`PDBData` I/O errors."""
pass
PDBIOError = PDBError
