Source code for MDAnalysis.core._get_readers

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# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see AUTHORS for the full list)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""Functions for fetching Readers

These functions officially live in in topology/core (parsers) and
coordinates/core (all others).  They are declared here to avoid
circular imports.

"""
import copy
import inspect

from .. import (_READERS, _READER_HINTS,
                _PARSERS, _PARSER_HINTS,
                _MULTIFRAME_WRITERS, _SINGLEFRAME_WRITERS, _CONVERTERS)
from ..lib import util


[docs]def get_reader_for(filename, format=None): """Return the appropriate trajectory reader class for `filename`. Parameters ---------- filename filename of the input trajectory or coordinate file. Also can handle a few special cases, see notes below. format : str or :class:`Reader` (optional) Define the desired format. Can be a string to request a given Reader. If a class is passed, it will be assumed that this is a Reader and will be returned. Returns ------- :class:`Reader` A Reader object Raises ------ ValueError If no appropriate Reader is found Notes ----- There are a number of special cases that can be handled: - If `filename` is a numpy array, :class:`~MDAnalysis.coordinates.memory.MemoryReader` is returned. - If `filename` is an MMTF object, :class:`~MDAnalysis.coordinates.MMTF.MMTFReader` is returned. - If `filename` is a ParmEd Structure, :class:`~MDAnalysis.coordinates.ParmEd.ParmEdReader` is returned. - If `filename` is an iterable of filenames, :class:`~MDAnalysis.coordinates.chain.ChainReader` is returned. Automatic detection is disabled when an explicit `format` is provided, unless a list of filenames is given, in which case :class:`~MDAnalysis.coordinates.chain.ChainReader` is returned and `format` passed to the :class:`~MDAnalysis.coordinates.chain.ChainReader`. .. versionchanged:: 1.0.0 Added format_hint functionalityx """ # check if format is actually a Reader if inspect.isclass(format): return format # ChainReader gets returned even if format is specified if _READER_HINTS['CHAIN'](filename): format = 'CHAIN' # Only guess if format is not specified if format is None: for fmt_name, test in _READER_HINTS.items(): if test(filename): format = fmt_name break else: # hits else if for loop completes # else let the guessing begin! format = util.guess_format(filename) format = format.upper() try: return _READERS[format] except KeyError: errmsg = ( "Unknown coordinate trajectory format '{0}' for '{1}'. The FORMATs \n" " {2}\n" " are implemented in MDAnalysis.\n" " See https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1\n" " Use the format keyword to explicitly set the format: 'Universe(...,format=FORMAT)'\n" " For missing formats, raise an issue at " "https://github.com/MDAnalysis/mdanalysis/issues".format( format, filename, _READERS.keys())) raise ValueError(errmsg) from None
[docs]def get_writer_for(filename, format=None, multiframe=None): """Return an appropriate trajectory or frame writer class for `filename`. The format is determined by the `format` argument or the extension of `filename`. If `format` is provided, it takes precedence over the extension of `filename`. Parameters ---------- filename : str or ``None`` If no *format* is supplied, then the filename for the trajectory is examined for its extension and the Writer is chosen accordingly. If ``None`` is provided, then :class:`~MDAnalysis.coordinates.null.NullWriter` is selected (and all output is discarded silently). format : str (optional) Explicitly set a format. multiframe : bool (optional) ``True``: write multiple frames to the trajectory; ``False``: only write a single coordinate frame; ``None``: first try trajectory (multi frame writers), then the single frame ones. Default is ``None``. Returns ------- :class:`Writer` A Writer object Raises ------ ValueError: The format could not be deduced from `filename` or an unexpected value was provided for the `multiframe` argument. TypeError: No writer was found for the required format or the required `filename` argument was omitted. .. versionchanged:: 0.7.6 Added `multiframe` keyword; the default ``None`` reflects the previous behaviour. .. versionchanged:: 0.14.0 Removed the default value for the `format` argument. Now, the value provided with the `format` parameter takes precedence over the extension of `filename`. A :exc:`ValueError` is raised if the format cannot be deduced from `filename`. .. versionchanged:: 0.16.0 The `filename` argument has been made mandatory. """ if filename is None: format = 'NULL' elif format is None: try: root, ext = util.get_ext(filename) except (TypeError, AttributeError): # An AttributeError is raised if filename cannot # be manipulated as a string. # A TypeError is raised in py3.6 # "TypeError: expected str, bytes or os.PathLike object" errmsg = f'File format could not be guessed from "{filename}"' raise ValueError(errmsg) from None else: format = util.check_compressed_format(root, ext) if format == '': raise ValueError(( 'File format could not be guessed from {}, ' 'resulting in empty string - ' 'only None or valid formats are supported.' ).format(filename)) format = format.upper() if multiframe is None: # Multiframe takes priority, else use singleframe options = copy.copy(_SINGLEFRAME_WRITERS) # do copy to avoid changing in place options.update(_MULTIFRAME_WRITERS) # update overwrites existing entries errmsg = "No trajectory or frame writer for format '{0}'" elif multiframe is True: options = _MULTIFRAME_WRITERS errmsg = "No trajectory writer for format '{0}'" elif multiframe is False: options = _SINGLEFRAME_WRITERS errmsg = "No single frame writer for format '{0}'" else: raise ValueError("Unknown value '{0}' for multiframe," " only True, False, None allowed" "".format(multiframe)) try: return options[format] except KeyError: raise TypeError(errmsg.format(format)) from None
def get_parser_for(filename, format=None): """Return the appropriate topology parser for `filename`. Automatic detection is disabled when an explicit `format` is provided. Parameters ---------- filename : str or mmtf.MMTFDecoder name of the topology file; if this is an instance of :class:`mmtf.MMTFDecoder` then directly use the MMTF format. format : str description of the file format Raises ------ ValueError If no appropriate parser could be found. .. versionchanged:: 1.0.0 Added format_hint functionality """ if inspect.isclass(format): return format # Only guess if format is not provided if format is None: for fmt_name, test in _PARSER_HINTS.items(): if test(filename): format = fmt_name break else: format = util.guess_format(filename) format = format.upper() try: return _PARSERS[format] except KeyError: try: rdr = get_reader_for(filename) except ValueError: errmsg = ( "'{0}' isn't a valid topology format, nor a coordinate format\n" " from which a topology can be minimally inferred.\n" " You can use 'Universe(topology, ..., topology_format=FORMAT)'\n" " to explicitly specify the format and\n" " override automatic detection. Known FORMATs are:\n" " {1}\n" " See https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats\n" " For missing formats, raise an issue at \n" " https://github.com/MDAnalysis/mdanalysis/issues".format( format, _PARSERS.keys())) raise ValueError(errmsg) from None else: return _PARSERS['MINIMAL'] def get_converter_for(format): """Return the appropriate topology converter for ``format``. Parameters ---------- format : str description of the file format Raises ------ TypeError If no appropriate parser could be found. .. versionadded:: 1.0.0 """ try: writer = _CONVERTERS[format] except KeyError: errmsg = f'No converter found for {format} format' raise TypeError(errmsg) from None return writer