shnitsel.geo.analogs
====================

.. py:module:: shnitsel.geo.analogs


Functions
---------

.. autoapisummary::

   shnitsel.geo.analogs._find_atom_pairs
   shnitsel.geo.analogs._substruct_match_to_submol
   shnitsel.geo.analogs.list_analogs
   shnitsel.geo.analogs._combine_compounds_unstacked
   shnitsel.geo.analogs._combine_compounds_stacked
   shnitsel.geo.analogs.combine_analogs


Module Contents
---------------

.. py:function:: _find_atom_pairs(mol, atoms)

.. py:function:: _substruct_match_to_submol(mol, substruct_match)

.. py:function:: list_analogs(ensembles, smarts = '', vis = False)

   Extract a common moiety from a selection of ensembles

   :param ensembles: An ``Iterable`` of ``xr.DataArray``s, each containing the geometries of an ensemble of
                     trajectories for a different compound; they
   :param smarts: A SMARTS-string indicating the moiety to cut out of each compound;
                  in each case, the match returned by :py:func:`rdkit.Chem.Mol.GetSubstrucMatch`
                  (not necessarily the only possible match) will be used;
                  if no SMARTS is provided, a minimal common submol will be extracted using
                  ``rdFMCS.FindMCS``
   :param optional: A SMARTS-string indicating the moiety to cut out of each compound;
                    in each case, the match returned by :py:func:`rdkit.Chem.Mol.GetSubstrucMatch`
                    (not necessarily the only possible match) will be used;
                    if no SMARTS is provided, a minimal common submol will be extracted using
                    ``rdFMCS.FindMCS``
   :param vis: Whether to display a visual indication of the match
   :param optional: Whether to display a visual indication of the match

   :rtype: An ``Iterable`` of ``xr.DataArray``s


.. py:function:: _combine_compounds_unstacked(compounds, names=None, concat_kws=None)

.. py:function:: _combine_compounds_stacked(compounds, names=None, concat_kws=None)

.. py:function:: combine_analogs(ensembles, smarts = '', names = None, vis = False, *, concat_kws = None)

   Combine ensembles for different compounds by finding the
   moieties they have in common

   :param ensembles: An ``Iterable`` of ``xr.DataArray``s, each containing the geometries of an ensemble of
                     trajectories for a different compound; these trajectories should all
                     be in the same format, i.e.:

                         - all stacked (with 'frames' dimension indexed by'trajid' and 'time' MultiIndex levels)
                         - all unstacked (with independent 'trajid' and 'time' dimensions)
   :param smarts: A SMARTS-string indicating the moiety to cut out of each compound;
                  in each case, the match returned by :py:func:`rdkit.Chem.Mol.GetSubstrucMatch`
                  (not necessarily the only possible match) will be used;
                  if no SMARTS is provided, a minimal common submol will be extracted using
                  ``rdFMCS.FindMCS``
   :param names: An ``Iterable`` of ``Hashable`` to identify the compounds;
                 these values will end up in the ``compound`` coordinate, by default None
   :param vis: Whether to display a visual indication of the match, by default False
   :param concat_kws: Keyword arguments for internal calls to ``xr.concat``

   :returns: * *An xr.Dataset of trajectories, with a MultiIndex level identifying each*
             * *trajectory by its compound name (or index, if no names were provided)*
             * *and trajid*

   :raises ValueError: If the ensembles provided are in a mixture of formats (i.e. some have trajectories
       stacked, others unstacked)