Installation
============

Requirements:

    * `Python 3.8+ <https://docs.python.org/3/>`_.
    * `RDKit <https://www.rdkit.org/docs/>`_ (2022.3.5+).
    * `Pandas <https://pandas.pydata.org/>`_.
    * `NumPy <https://numpy.org/>`_.
    * `tqdm <https://tqdm.github.io/>`_.
    * `CReM <https://github.com/DrrDom/crem>`_ (0.2.9+).
    * `Meeko <https://pypi.org/project/meeko/>`_.
    * `AutoDock-Vina <https://vina.scripps.edu/>`_.

Via pip (standard)
------------------
pip install
~~~~~~~~~~~

.. code-block:: bash

    # To get the last "stable" version (strongly recommended). This project is still in beta state.
    pip install moldrug

or:

.. code-block:: bash

    # To get the version on development (not recommended)
    pip install -U git+https://github.com/ale94mleon/moldrug.git@main

There are multiple methods to obtain `AutoDock-Vina <https://vina.scripps.edu/>`_. You can use `conda <https://anaconda.org/conda-forge/vina>`_ or download the latest release from the `Vina Repository <https://github.com/ccsb-scripps/AutoDock-Vina/releases>`_.
We highly recommend using the last release posted on `Vina Repository <https://github.com/ccsb-scripps/AutoDock-Vina/releases>`_.

Via conda
---------

moldrug is also available through conda. However, the pip installation is the recommended one.

.. code-block:: bash

    conda create -n moldrug
    conda activate moldrug
    conda install -c ale94mleon -c conda-forge moldrug

.. note::
    MacOS users may face some problems trying to install because of the AutoDock-Vina dependency. If that is the case, just download the executable as it is explained next.

If some dependencies are missing, please install them through pip. Some of them could be:

.. code-block:: bash

    pip install meeko crem pyyaml scipy tqdm


AutoDock-Vina dependency and related software
---------------------------------------------

.. note::
    `AutoDock-Vina <https://vina.scripps.edu/>`_ is the only non-pip dependency required for ``moldrug``. This section is useful in case you would like to use the build-in cost functions of moldrug from :mod:`moldrug.fitness`

AutoDock-Vina is an ongoing project, and it is advisable to stay up-to-date by regularly checking for the latest `release <https://github.com/ccsb-scripps/AutoDock-Vina/releases/>`_.
As of the creation of this documentation, the most recent version is `v1.2.5 <https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.5>`_.
We will be using this version as a demonstration, but we strongly recommend using the most recent release for optimal performance and features. For detailed information, please visit:
`AutoDock-Vina installation Instruction <https://autodock-vina.readthedocs.io/en/latest/installation.html>`_.

Unix- and Linux-based OS
~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

    wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.5/vina_1.2.5_linux_x86_64
    chmod a+x vina_1.2.5_linux_x86_64
    ./vina_1.2.5_linux_x86_64 --help

MacOS
~~~~~

.. code-block:: bash

    wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.5/vina_1.2.5_mac_x86_64
    chmod a+x vina_1.2.5_mac_x86_64
    ./vina_1.2.5_mac_x86_64 --help


.. note::
    MacOs users might need to allow the execution of the application on ``Privacy & Security`` depending on the MacOS version.

Windows
~~~~~~~

Please, download from `release <https://github.com/ccsb-scripps/AutoDock-Vina/releases/>`_. Conda installation may not work.

Converting pdb to pdbqt
~~~~~~~~~~~~~~~~~~~~~~~

This step can be achieved through `OpenBabel <https://github.com/openbabel/openbabel>`__ or `ADFR <https://ccsb.scripps.edu/adfr/downloads/>`_. We recommend ADFR. Depending on the platform, you should be able to access the program ``prepare_receptor`` in different ways. In my case, it lies on ``/Users/klimt/ADFRsuite-1.0/bin/prepare_receptor``. Then you can convert your ``pdb`` with:

.. code-block:: bash

    /Users/klimt/ADFRsuite-1.0/bin/prepare_receptor -r your_protein.pdb -o your_protein.pdbqt

Check `here <https://ccsb.scripps.edu/adfr/how-to-create-a-pdbqt-for-my-receptor/>`_ for more information.

Getting box information
~~~~~~~~~~~~~~~~~~~~~~~

To perform the docking you must provide ``boxcenter`` (``center`` for AutoDock-Vina) and ``boxsize`` (``size`` for AutoDock-Vina) to the cost functions defined in :mod:`moldrug.fitness`. For that, two PyMol plugins are useful: `GetBox <https://github.com/MengwuXiao/GetBox-PyMOL-Plugin/blob/master/GetBox%20Plugin.py>`_ and/or `autodock <https://github.com/ADplugin/ADplugin/blob/master/autodock.py>`_. Details of their installation and use are not discussed here, please visit their corresponding repositories for more information.

Work with a docker container
----------------------------

#. Use the `Docker configuration file on GitHub <https://github.com/ale94mleon/moldrug/blob/main/Dockerfile>`__.
#. Visit the `moldrug <https://hub.docker.com/r/ale94mleon/4moldrug>`__ docker container.

Finally ``pip install moldrug`` inside it.