shnitsel.vis.vmd
================

.. py:module:: shnitsel.vis.vmd


Attributes
----------

.. autoapisummary::

   shnitsel.vis.vmd._tcl_script_path


Functions
---------

.. autoapisummary::

   shnitsel.vis.vmd.traj_to_xyz
   shnitsel.vis.vmd.traj_vmd


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

.. py:function:: traj_to_xyz(traj_atXYZ, units='angstrom')

   Convert an entire trajectory's worth of geometries to an XYZ string

   :param traj_atXYZ: Molecular geometries -- should have dimensions 'atom' and 'direction'; should
                      also be groupable by 'time' (i.e. either have a 'time' dimension or
                      a 'time' coordinate)
   :param units: The units to which to convert before creating the XYZ string

   :rtype: The XYZ data as a string, with time indicated in the comment line of each frame

   .. rubric:: Notes

   The units of the outputs will be the same as the array;
   consider converting to angstrom first, as most tools will expect this.


.. py:data:: _tcl_script_path

.. py:function:: traj_vmd(atXYZ, groupby='trajid')

   Open geometries in the VMD viewer, if installed

   :param atXYZ: The geometries to transmit
   :param groupby: A set of frames will be grouped into a VMD molecule if
                   they have the same value in this coordinate, by default this is 'trajid'
                   so that each trajectory
   :param optional: A set of frames will be grouped into a VMD molecule if
                    they have the same value in this coordinate, by default this is 'trajid'
                    so that each trajectory