Tutorials
=========

The following tutorials are available to help you get started with ASAP.
These are designed as an introduction to the library layer of `drugforge`.

.. note::
   Many of these functionalities are available in easy to use CLI tools.
   See the Guide section and  CLI documentation for more information.


Start here
----------

:any:`Start Here <../_collections/notebooks/start_here>` will introduce you to the `drugforge` library and some of our key concepts.


Docking and scoring
-------------------

:any:`Docking and Scoring <../_collections/notebooks/docking_and_scoring>` will guide you through the process of docking a small molecule to an ASAP target and scoring its interactions with physics based scorers and E3 equivariant ML models .


Running alchemical free energy calculations
-------------------------------------------

:any:`Running alchemical free energy calculations <../_collections/notebooks/running_alchemical_free_energy_calculations>` will guide you through the process of running alchemical free energy calculations for an ASAP target and analyzing the results.


Training ML models on ASAP data
--------------------------------

:any:`Training ML models on ASAP data <../_collections/notebooks/training_ml_models_on_asap_data>` will guide you through the process of training 2D graph models and equivariant E3 models  on ASAP data.


Running ML inference
--------------------

:any:`Running ML inference <../_collections/notebooks/running_ml_inference>`  will guide you through the process of running ML inference on ASAP targets.

Exploring related sequences and structures
-------------------------------------------

:any:`Exploring related sequences and structures <../_collections/notebooks/exploring_related_sequences_and_structures>` will show you how to structurally enable sequence space around a given target.

Visualizing ASAP targets
-------------------------

:any:`Visualizing ASAP targets <../_collections/notebooks/visualizing_asap_targets>` will guide you through the process of visualizing ASAP targets and their interactions with ligands.

Working with fitness data
-------------------------

:any:`Working with fitness data <../_collections/notebooks/working_with_fitness_data>` this tutorial is still under development.


Running MD simulations
-------------------------

:any:`Running MD simulations <../_collections/notebooks/running_md_simulations>` will show you how to run MD simulations on ASAP targets.


Interfacing with databases and systems
--------------------------------------

:any:`Interfacing with databases and systems <../_collections/notebooks/interfacing_with_databases_and_systems>` will introduce you to the tools available in ASAP for interfacing with databases and systems.



Tutorial Index
---------------

.. toctree::
    :maxdepth:1
    :caption: Contents:

    ../_collections/notebooks/start_here
    ../_collections/notebooks/docking_and_scoring.ipynb
    ../_collections/notebooks/running_alchemical_free_energy_calculations.ipynb
    ../_collections/notebooks/training_ml_models_on_asap_data.ipynb
    ../_collections/notebooks/running_ml_inference.ipynb
    ../_collections/notebooks/exploring_related_sequences_and_structures.ipynb
    ../_collections/notebooks/visualizing_asap_targets.ipynb
    ../_collections/notebooks/working_with_fitness_data.ipynb
    ../_collections/notebooks/running_md_simulations.ipynb
    ../_collections/notebooks/interfacing_with_databases_and_systems.ipynb