.. DeepProtein documentation master file, created by
   sphinx-quickstart on Fri Oct 18 10:58:00 2024.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.


DeepProtein documentation
================================================================
DeepProtein is a comprehensive deep learning library and benchmark designed to fill these gaps:

* Comprehensive Benchmarking: Evaluating CNNs, RNNs, transformers, and GNNs on 7 essential protein learning tasks, such as function prediction and antibody developability.
* User-friendly Interface: Simplifying execution with one command for all tasks.
* Enhanced Accessibility: Extensive documentation and tutorials for reproducible research.
The Github repository is located `here <https://github.com/jiaqingxie/DeepProtein>`_.


.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Background 

   notes/introduction
   notes/task



.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Install DeepProtein

   notes/download 


.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Get Started

   notes/examples
   notes/casestudy


.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Tutorials

   notes/notebooks

.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Package Reference

   notes/models
   notes/dataset
   notes/chemutils
   notes/oneliner
   notes/model_helper
   notes/utils


.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Importance Function

   notes/model
   notes/encoder
   notes/process_data
   notes/configuration
   notes/utility_function