Command Line Interface
======================

MD DaVis provides the command line tool ``md-davis`` for analysis and
visualization of data from MD simulations.

Getting Help
------------

The list of available commands can be seen with ``--help`` or ``-h``:

.. code-block:: bash

   md-davis --help

which provides the following output:

.. code-block::

   Usage: md-davis [OPTIONS] COMMAND [ARGS]...

     MD DaVis: A python package for comparative analysis of molecular dynamics
     trajectories

   Options:
     --version   Show the version and exit.
     -h, --help  Show this message and exit.

   Commands:
     collate            Input TOML files.
     electrodynamics    Click wrapper for get_electrodynamics.
     electrostatics     Get the electrostatic potential on the surface...
     hbond              Parse contacts evaluated by gmx hbonds
     landscape          Plot free energy landscapes from .xvg files...
     landscape_animate
     landscape_xvg      Wrapper function for Click
     plot_hbond         H-bond or contact dataframe obtained from md_davis...
     plot_residue       main function
     residue
     sequence           Get the sequence of amino acid residues from a PDB file
     xvg                Plot xmgrace (.xvg) files generated by GROMACS.


Similarly, the help for each command can also be accessed with ``--help`` or
``-h``:

.. code-block:: bash

   md-davis <command> -h

For example, ``md-davis xvg -h`` shows the help for
:ref:`xvg <guides/xvg:Plotting Xmgrace (.xvg) Files>` command:

.. code-block::

   Usage: md-davis xvg [OPTIONS] XVG_FILES...

     Plot xmgrace (.xvg) files generated by GROMACS.

     Arguments:

         xvg_files (Files): Input xmgrace (.xvg) files'

   Options:
     -o, --output TEXT        Output filename
     --matplotlib / --plotly  Use plotly for plotting
     -h, --help               Show this message and exit.