shnitsel.geo.geomatch_exact
===========================

.. py:module:: shnitsel.geo.geomatch_exact


Functions
---------

.. autoapisummary::

   shnitsel.geo.geomatch_exact.flag_exact
   shnitsel.geo.geomatch_exact.get_bats_matching


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

.. py:function:: flag_exact(mol, l_smarts)

   Compute and flag bonds, angles, and dihedrals in a single call,
   for multiple structural features

   :param mol: Molecule under study.
   :type mol: rdkit.Chem.rdchem.Mol
   :param l_smarts: SMARTS patterns for filtering interactions.
   :type l_smarts: list[str], optional

   :returns: * *dict* --

               {
                   'bonds':      [...],
                   'angles':     [...],
                   'dihedrals':  [...]
               }
             * *Note that even if no BATs of a certain type (e.g. no bonds) are*
             * *requested, the returned dictionary will still contain the corresponding*
             * *key, associated with an empty list.*


.. py:function:: get_bats_matching(atXYZ, l_smarts, signed = None, ang = False)

   Get bond lengths, angles and torsions according to a list of SMARTS searches.

   :param atXYZ: The coordinates to use.
   :param l_smarts: SMARTS patterns to search for.
   :type l_smarts: list[str], optional
   :param signed: Whether to distinguish between clockwise and anticlockwise rotation,
                  when returning angles as opposed to cosine & sine values;
                  by default, do not distinguish.
                  NB. This applies only to the dihedrals, not to the three-center angles.
                  The latter are always unsigned.
   :param optional: Whether to distinguish between clockwise and anticlockwise rotation,
                    when returning angles as opposed to cosine & sine values;
                    by default, do not distinguish.
                    NB. This applies only to the dihedrals, not to the three-center angles.
                    The latter are always unsigned.
   :param ang: If False (the default), returns sines and cosines;
               if set to 'deg', returns angles in degrees
               if set to 'rad', returns angles in radians
   :param optional: If False (the default), returns sines and cosines;
                    if set to 'deg', returns angles in degrees
                    if set to 'rad', returns angles in radians

   :rtype: An :py:class:`xarray.DataArray` containing bond lengths, angles and tensions as specified.

   .. rubric:: Examples

   >>> geom.get_bats_matching(frames['atXYZ'], ['C~C=C~C', '[#7]~[#6]'])
   # Finds and calculates all-carbon torsions with a central double bond
   # and bond-lengths between carbon and nitrogen.