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.

:mod:`MDAnalysis.selections.vmd`
    VMD_ selections
:mod:`MDAnalysis.selections.pymol`
    PyMol_ selections
:mod:`MDAnalysis.selections.gromacs`
    Gromacs_ selections
:mod:`MDAnalysis.selections.charmm`
    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