jlaw9 / doranet

DORAnet (Designing Optimal Reaction Avenues Network Enumeration Tool)

This is a repo containing the DORAnet network generation framework.
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Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. License
5. Contact
6. Acknowledgments

About The Project

This project is a rework of both minedatabase and NetGen. It is intended to streamline and extend the implementation of chemical reaction network generation for research purposes. The aforementioned programs possess some weaknesses in terms of a lack of transferability, customizability, and ease of use. DORAnet is intended to solve these problems using the industry-standard molecule manipulation framework RDKit (though others can be implemented), an object-oriented approach to network generation, and a flexible dependency injection scheme which can handle low-level performance tradeoffs such as speed-memory and parallelization.

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Built With

• Git
• GitHub
• Numpy
• Pandas
• PyPI
• Python
• RDKit
• Visual Studio Code

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Getting Started

To get a local copy up and running follow these simple example steps.

Prerequisites

You will need to the pip package manager to install DORAnet, either in a virtual environment (recommended) or in your system installation. Virtual environments can be generated using venv, Anaconda, or a package manager of your choice.

Installation

1. Activate a virtual environment in a terminal (CMD/bash/etc.) using the methods provided in their documentation. Make sure that python and pip are installed.
2. Install DORAnet using pip.

pip install doranet

3. The program is now installed! If this is your first time, please proceed to the Tutorial.

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Usage

There are tutorials available for the core code here.

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Contact

William Sprague - [email protected]

Project Link: https://github.com/wsprague-nu/doranet

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Acknowledgments

• Dr. Quan Zhang
• Dr. Manali Dhawan
• Geoffrey Bonnanzio
• Dr. Kevin Shebek
• Dr. Lauren Lopez
• Dr. Joseph Ni
• Dr. Jon Strutz
• Dr. Stefan Pate
• Prof. Linda Broadbelt
• Prof. Keith Tyo
• Prof. Brent Shanks

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