CLI Examples
============

These examples demonstrate how to use OCDocker from the command line.

Basic Docking
-------------

Example of basic docking operations with Vina:

.. literalinclude:: ../../../examples/01_cli_basic_docking.sh
   :language: bash
   :caption: Basic Vina docking example

Multi-Engine Pipeline
---------------------

Example of running a multi-engine docking pipeline:

.. literalinclude:: ../../../examples/02_cli_multi_engine_pipeline.sh
   :language: bash
   :caption: Multi-engine docking pipeline

Diagnostics
-----------

Example of running diagnostics to check your installation:

.. literalinclude:: ../../../examples/03_cli_diagnostics.sh
   :language: bash
   :caption: Diagnostics script

Interactive Console
-------------------

Example of using the interactive console:

.. literalinclude:: ../../../examples/04_cli_console.py
   :language: python
   :caption: Interactive console example