Getting Started

Welcome to the synkit documentation! This guide walks you through installing and verifying synkit, a modular toolkit for chemical informatics and graph-based workflows.

Introduction

synkit provides a suite of tools to simplify reaction canonicalization, atom-map validation, graph transformation, and more. Whether you’re automating chemical data pipelines or building custom rule-based systems, synkit helps you get started quickly and scale confidently.

Requirements

Before installing synkit, ensure that:

• Python ≥ 3.11 is available on your system.

• You have a working C/C++ compiler for any native extensions.

• (Recommended) You use an isolated virtual environment to avoid dependency conflicts.

Virtual Environment (Recommended)

Creating an isolated environment prevents conflicts between synkit and other Python projects.

1. Using venv (cross-platform)

   python3 -m venv synkit-env
   source synkit-env/bin/activate    # Linux/macOS
   synkit-env\Scripts\activate       # Windows PowerShell
   

2. Using Conda (if you prefer Conda environments)

   conda create -n synkit-env python=3.11
   conda activate synkit-env
   

Installing Dependencies

Some synkit features require the external package mod.

Note

On Linux you can install mod via Conda:

conda install -c jakobandersen -c conda-forge "mod>=0.17" -y

For other platforms, see the upstream instructions: <https://jakobandersen.github.io/mod/installation.html>_

Installing synkit

With your environment activated and dependencies in place, install synkit from PyPI:

pip install synkit

This will pull in synkit and all required dependencies.

Quick Verification

After installation, verify that synkit is available and check its version:

python -c "import importlib.metadata as m; print(m.version('synkit'))"
# Should print the installed synkit version

Docker Installation

Install SynKit using Docker.

Pull the image:

docker pull tieulongphan/synkit:latest

Run a quick version check:

docker run --rm tieulongphan/synkit:latest \
  python -c "import importlib.metadata as m; print(m.version('synkit'))"

Use as a base image in your own Dockerfile:

FROM tieulongphan/synkit:latest
WORKDIR /app
COPY . .
CMD ["python", "your_script.py"]

Further Resources

• Official documentation: SynKit Docs

• Tutorials and examples: Tutorials and Examples

Support

If you encounter issues or have questions:

• Report bugs and feature requests on GitHub: SynKit Issues

Enjoy using synkit!