prodock 0.0.4

ProDock — automation utilities for Molecular Docking workflows.

ProDock

Automatic pipeline for molecular modeling

Toolkit for molecular modeling For more details on each utility within the repository, please refer to the documentation provided in the respective folders.

Step-by-Step Installation Guide

1. Python Installation: Ensure that Python 3.11 or later is installed on your system. You can download it from python.org.

2. Creating a Virtual Environment (Optional but Recommended): It's recommended to use a virtual environment to avoid conflicts with other projects or system-wide packages. Use the following commands to create and activate a virtual environment:

python -m venv prodock-env
source prodock-env/bin/activate  

Or Conda

conda create --name prodock-env python=3.11
conda activate prodock-env

3. Cloning and Installing SynTemp: Clone the SynTemp repository from GitHub and install it:

git clone https://github.com/Medicine-Artificial-Intelligence/ProDock.git
cd ProDock
pip install -r requirements.txt
pip install black flake8 pytest # black for formating, flake8 for checking format, pytest for testing

Setting Up Your Development Environment

Before you start, ensure your local development environment is set up correctly. Pull the latest version of the main branch to start with the most recent stable code.

git checkout main
git pull

Working on New Features

1. Create a New Branch:
   For every new feature or bug fix, create a new branch from the main branch. Name your branch meaningfully, related to the feature or fix you are working on.

   git checkout -b feature/your-feature-name
   

2. Develop and Commit Changes:
   Make your changes locally, commit them to your branch. Keep your commits small and focused; each should represent a logical unit of work.

   git commit -m "Describe the change"
   

3. Run Quality Checks:
   Before finalizing your feature, run the following commands to ensure your code meets our formatting standards and passes all tests:

   ./lint.sh # Check code format
   pytest Test # Run tests
   

   Fix any issues or errors highlighted by these checks.

Integrating Changes

1. Rebase onto Staging:
   Once your feature is complete and tests pass, rebase your changes onto the staging branch to prepare for integration.

   git fetch origin
   git rebase origin/staging
   

   Carefully resolve any conflicts that arise during the rebase.

2. Push to Your Feature Branch: After successfully rebasing, push your branch to the remote repository.

   git push origin feature/your-feature-name
   

3. Create a Pull Request: Open a pull request from your feature branch to the staging branch. Ensure the pull request description clearly describes the changes and any additional context necessary for review.

Important Notes

• Direct Commits Prohibited: Do not push changes directly to the main or staging branches. All changes must come through pull requests reviewed by at least one other team member.
• Merge Restrictions: The main branch can only be updated from the staging branch, not directly from feature branches.

Publication

ProDock

License

This project is licensed under MIT License - see the License file for details.

Acknowledgments

This work has received support from the Korea International Cooperation Agency (KOICA) under the project entitled “Education and Research Capacity Building Project at University of Medicine and Pharmacy at Ho Chi Minh City”, conducted from 2024 to 2025 (Project No. 2021-00020-3).