.. _commandlineinterface: CLI Reference ============= We refer to the command-line-tools collectively as the command-line-interface, or CLI. Their options go well beyond those shown in the :ref:`Basic-Usage`, as we saw in the :ref:`Highlights`. Use these pages (menu to the left) or the ``mdc_command.py -h`` syntax to get help. For an inline overview of all options and ready-to-use examples, use:: >>> mdc_examples.py usage: mdc_examples.py [-h] [-x] [--short_options] clt Wrapper script to showcase and optionally run examples of the command-line-tools that ship with mdciao. Available command line tools are: * mdc_GPCR_overview.py * mdc_CGN_overview.py * mdc_KLIFS_overview.py * mdc_compare.py * mdc_fragments.py * mdc_interface.py * mdc_neighborhoods.py * mdc_notebooks.py * mdc_pdb.py * mdc_residues.py * mdc_sites.py You can type for example: > mdc_interface.py -h to view the command's documentation or > mdc_examples.py interf to show and/or run an example of that command .. toctree:: :maxdepth: 2 :hidden: mdc_neighborhoods mdc_interface mdc_sites mdc_fragments mdc_compare mdc_GPCR_overview mdc_CGN_overview mdc_KLIFS_overview mdc_residues mdc_pdb mdc_notebooks