Getting Started with SynTemp

Welcome to the SynTemp documentation! This guide helps you install, configure, and verify SynTemp, a modular toolkit for high‑quality reaction template extraction using ensemble atom mapping.

Contents

Introduction

SynTemp systematically extracts reaction rules from chemical databases by transforming molecular reactions into structured templates. Our workflow comprises four core phases:

AAM Inference: Leverages ensemble atom‑atom mapping (AAM) for precise atom correspondence.
Imaginary Transition State (ITS) Completion: Infers implicit hydrogens to complete the ITS representation.
Reaction Center Detection & Extension: Identifies core reactive sites and propagates neighboring atoms to capture context.
Hierarchical Clustering: Aggregates extended centers or partial ITS into clusters to reveal common reaction motifs.

Prerequisites

Before proceeding, ensure you have:

Python 3.11 or later installed.
(Optional) [conda](https://docs.conda.io/en/latest/) for environment management.

We strongly recommend using an isolated environment to prevent dependency conflicts.

Virtual Environment Setup

Choose one of the following methods:

1. Using Python venv (cross-platform)

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

2. Using Conda

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

Installation

Install core dependencies and SynTemp:

pip install -r requirements.txt
pip install "syntemp[all]"

This will install SynTemp along with all optional components.

Verification

Confirm that SynTemp is correctly installed and check its version:

python -c "import importlib.metadata as m; print(m.version('syntemp'))"

You should see the installed version number printed.

Further Resources

Full documentation: https://syntemp.readthedocs.io/en/latest/
Tutorials and examples: Tutorials and Examples
GitHub repository: https://github.com/TieuLongPhan/SynTemp
Issue tracker: https://github.com/TieuLongPhan/SynTemp/issues

Support

If you encounter problems or have questions, feel free to:

Open an issue on GitHub.
Join the discussion via the project’s mailing list.

Happy templating with SynTemp!