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:

md-davis --help

which provides the following output:

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:

md-davis <command> -h

For example, md-davis xvg -h shows the help for xvg command:

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.