shnitsel.core.parse
===================

.. py:module:: shnitsel.core.parse


Submodules
----------

.. toctree::
   :maxdepth: 1

   /api/shnitsel/core/parse/common/index
   /api/shnitsel/core/parse/nx/index
   /api/shnitsel/core/parse/pyrai2md/index
   /api/shnitsel/core/parse/sharc_icond/index
   /api/shnitsel/core/parse/sharc_traj/index
   /api/shnitsel/core/parse/xyz/index


Attributes
----------

.. autoapisummary::

   shnitsel.core.parse.Trajid
   shnitsel.core.parse._exnum
   shnitsel.core.parse._idfn
   shnitsel.core.parse._read_traj
   shnitsel.core.parse.READERS


Classes
-------

.. autoapisummary::

   shnitsel.core.parse.Trajres


Functions
---------

.. autoapisummary::

   shnitsel.core.parse._default_idfn
   shnitsel.core.parse.read_trajs_list
   shnitsel.core.parse._per_traj
   shnitsel.core.parse.read_trajs_parallel
   shnitsel.core.parse.gather_traj_metadata
   shnitsel.core.parse.concat_trajs
   shnitsel.core.parse.layer_trajs
   shnitsel.core.parse.read_trajs


Package Contents
----------------

.. py:type:: Trajid
   :canonical: int


.. py:data:: _exnum

.. py:class:: Trajres

   .. py:attribute:: trajid
      :type:  int


   .. py:attribute:: missing_file
      :type:  str | None


   .. py:attribute:: misc_error
      :type:  Exception | None


   .. py:attribute:: data
      :type:  xarray.Dataset | None


.. py:function:: _default_idfn(path)

.. py:data:: _idfn

.. py:data:: _read_traj
   :type:  Callable

.. py:data:: READERS

.. py:function:: read_trajs_list(paths, kind, idfn=None, sort=True, errors='log')

.. py:function:: _per_traj(trajdir)

.. py:function:: read_trajs_parallel(paths, kind, idfn=None, sort=True)

.. py:function:: gather_traj_metadata(datasets, time_dim='ts')

.. py:function:: concat_trajs(datasets)

.. py:function:: layer_trajs(datasets)

.. py:function:: read_trajs(path, kind, pattern = 'TRAJ*', format = 'frames', parallel = True, errors = 'log')

   Read all trajectories from a folder of trajectory folders

   :param path: The path to the folder of folders
   :param kind: The kind of trajectory, i.e. whether it was produced by SHARC, Newton-X or PyRAI2MD
   :param pattern: The search pattern to append to the path (the whole thing will be read by :external:py:func:`glob.glob`),
                   by default 'TRAJ*'
   :param format: Whether to return the trajectories concatenated along the time axis ('frames') using a
                  :external:py:class:`xarray.indexes.PandasMultiIndex`
                  or along a new axis ('layers'), by default 'frames'
   :param parallel: Whether to read multiple trajectories at the same time (which, in the current implementation,
                    is only faster on storage that allows non-sequential reads), by default False

   :rtype: An :external:py:class:`xarray.Dataset` containing the data of the trajectories

   :raises FileNotFoundError: If the search (``= path + pattern``) doesn't match any paths according to :external:py:func:`glob.glob`
   :raises ValueError: If an invalid value for ``format`` is passed.