Source code for MDAnalysis.selections

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Selection exporters

Functions to write a :class:`MDAnalysis.core.groups.AtomGroup` selection
to a file so that it can be used in another programme.

    VMD_ selections
    PyMol_ selections
    Gromacs_ selections
    CHARMM_ selections

The :class:`MDAnalysis.selections.base.SelectionWriterBase` base class and
helper functions are in :mod:`MDAnalysis.selections.base`, with the
exception of `:func:get_writer`:

.. autofunction:: get_writer
import os.path

from .. import _SELECTION_WRITERS

from . import base
from . import vmd
from . import pymol
from . import gromacs
from . import charmm
from . import jmol

[docs] def get_writer(filename: str, defaultformat: str) -> base.SelectionWriterBase: """Return a SelectionWriter for `filename` or a `defaultformat`. Parameters ---------- filename : str name of the output file; the extension is used to guess the file format defaultformat : str if `filename` does not have an extension, use `defaultformat` instead Returns ------- SelectionWriterBase : `type` the writer *class* for the detected format Raises ------ :exc:`NotImplementedError` for any format that is not defined """ format = None if filename: format = os.path.splitext(filename)[1][1:] # strip initial dot! format = format or defaultformat # use default if no fmt from fn format = format.strip().upper() # canonical for lookup try: return _SELECTION_WRITERS[format] except KeyError: errmsg = (f"Writing as {format} is not implemented; only " f"{ _SELECTION_WRITERS.keys()} will work.") raise NotImplementedError(errmsg) from None