Installation Guide
=========================================================

Quick installation for the release
----------------------------------
Please download the lastest version of ChemFAST at `Github Release <https://github.com/DoMD-toolkit/DoMD/releases>`_. Release includes the large database files ``opls.db``, which are required for the force field assignment. After downloading and unzipping the release zip file, you can set up the environment and test the installation with the following commands:


.. code-block:: bash

   # Download and unzip the release zip file
   $ cd <path-to-domd>
   $ conda env create -f environment.yml
   $ conda activate domd-toolkit
   $ python -c 'from domd_tools import *; print("Success install domd.")'

Step-by-step installation from repo
-----------------------------------
This is the installation process if you want to install from the git repository, which is recommended for developers or users who want to use the latest features. For users who just want to use the stable version, we recommend downloading the release version as described above. This process needs to be done in the root directory of DoMD, where `setup.py` is located.

.. code-block:: bash

   # Setup Environment
   $ conda create -n domd-toolkit -c conda-forge numpy nomkl rdkit=2025.03.6 openbabel numba networkx pandas scipy jupyter scikit-learn matplotlib python==3.12
   $ conda activate domd-toolkit
   $ pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cpu
   $ pip3 install torch_geometric pdbreader
   # Download DoMD
   $ git clone https://github.com/DoMD-toolkit/DoMD.git
   # Download and move `opls.db` to `DoMD/domd_forcefield/oplsaa/resources/opls.db`
   # Or you can download the release .zip file, it contains the `opls.db` file
   # cd to the root directory of DoMD, for example `DoMD` if cloned from github
   # where `setup.py` is under the root directory
   $ pip install -e .

Database Setup (Large Files)
----------------------------

**Important:** DoMD requires specific large database files for force field parameterization. These are not included in the git repository due to size limits.

**Download Link:** `Google Drive <https://drive.google.com/file/d/1Q9FBS0TziJf5vbszmCIH9dgCWFTmniXs/view>`_

* ``domd_database/forcefield/oplsaa/data/ligpargen/AllData.pkl``: **This file is the OPLS-AA force field database, for training the force field model, this file is NOT NEEDED for the program.**
* ``domd_forcefield/oplsaa/resources/opls.db``: **This file is required for force field assignment.**

.. code-block:: text

   DoMD/
   └── domd_forcefield/
       └── oplsaa/
           └── resources/
               └──opls.db  <-- Required for parameterization


.. note::
    If you download the release version, the ``opls.db`` file is already included in the release package, so you don't need to download it separately.