Welcome to DOCKTOPUS's documentation!
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.. toctree::
   :maxdepth: 1
   :caption: Contents:

   installation
   api

.. .. automodule:: DOCKTOPUS
..    :members:
..    :undoc-members:
..    :show-inheritance:

Overview
--------

The DOCKTOPUS package provides a simplified interface for running molecular docking
simulations using various docking engines. It handles input preparation, docking execution,
and results processing in a streamlined workflow.

The package supports multiple docking engines:

* **GNINA**: Deep learning-based docking with CNN scoring
* **Vina**: Traditional molecular docking with empirical scoring
* **GalaxyDock2 HEME**: Specialized docking for heme-containing proteins
* **RFAA**: AlphaFold2-based protein-ligand structure prediction

Key Features
------------

* Automated input preparation and format conversion
* Support for SMILES-based ligand generation
* Comprehensive logging and error handling
* Post-docking validation and quality assessment
* Batch processing capabilities for virtual screening

Dependencies
------------

* Open Babel (for molecular format conversion)
* RDKit (for molecular manipulation)
* Autodock VINA python interface (installed automatically)
* GNINA, GalaxyDock2 HEME and RFAA if you intend to use them
* scikit-learn and mdtraj for the included analysis module

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`