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Graph based Reaction Template Extraction

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# SynTemp
Graph-based Reaction Templates/Rules Extraction

## Overview

This repository is dedicated to the systematic extraction of reaction rules from reaction databases. Our primary focus is the computational analysis and transformation of molecular reactions into a structured set of rules. This work facilitates a deeper understanding of reaction mechanisms and pathways. The `SynTemp` framework is organized into four main phases:

1. **AAMs Inference**: Based on ensemble AAMs for accurate atom mapping.
2. **Imaginary Transition State (ITS) Completion**: Enhances ITS by incorporating hydrogen inference to fully capture the reaction mechanism.
3. **Reaction Center Detection and Extension**: Focuses on identifying and extending the core active sites of reactions.
4. **Hierarchical Clustering**: Groups extended reaction centers or partial ITS to analyze reaction patterns.

The general framework and its components are depicted in Figures A, B, and C below. Please visit [full user guide & API reference](https://syntemp.readthedocs.io/en/latest/) for detailed examples, configuration options, and best practices.

![screenshot](https://github.com/TieuLongPhan/SynTemp/raw/main/Docs/Image/TOC.png)

### Downstream Applications

- **Templates Analysis**: We have developed topological descriptors for ITS graphs to encapsulate the essential information of templates.
- **Rules Application**: Observes the trade-off between radii and coverage/novelty metrics. Increased coverage tends to reduce the number of output solutions due to the complexities of subgraph matching within the DPO framework. However, it also decreases novelty. This trade-off serves as a precursor to our forthcoming research, which will focus on developing a constrained framework for synthesis planning.

## Table of Contents
- [Installation](#installation)
- [Usage](#usage)
- [Contributing](#contributing)
- [Publication](#publication)
- [License](#license)
- [Acknowledgments](#acknowledgments)

## Installation

To install and set up the SynTemp framework, follow these steps.

### Prerequisites

- Python 3.11
- rdkit>=2024.3.5
- networkx>=3.3
- synrbl>=1.0.0
- synkit>=0.0.4

If you want to run ensemble AAMs

- dgl==2.1.0
- dgllife==0.3.2
- localmapper>=0.1.5
- rxn-chem-utils>=1.6.0
- rxn-utils>=2.0.0
- rxnmapper>=0.4.1
- chython==1.78
- chytorch>=1.65
- chytorch-rxnmap>=1.4
- torch==2.2.0
- torchdata==0.7.1

### 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](https://www.python.org/downloads/).

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:

```bash
  python -m venv syntemp-env
  source syntemp-env/bin/activate  # On Windows use `syntemp-env\Scripts\activate`
  ```
  Or Conda

```bash
  conda create --name syntemp-env python=3.11
  conda activate syntemp-env
  ```

3. **Install from PyPi:**
  The easiest way to use SynTemp is by installing the PyPI package 
  [syntemp](https://pypi.org/project/syntemp/).

```
  pip install syntemp
  ```
  Optional if you want to install full version including three types of atom map
  ```
  pip install syntemp[all]
  ```

4. **Verify Installation:**
  After installation, you can verify that Syn Temp is correctly installed by running a simple test

```bash
  echo -e "R-id,reaction\n0,COC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)Nc1cc(OC)cc(C(C)(C)C)c1O>>COC(=O)[C@H](CCCCN)NC(=O)Nc1cc(OC)cc(C(C)(C)C)c1O" > test.csv
  python -m syntemp --data_path test.csv --rebalancing --id 'R-id' --rsmi 'reaction' --rerun_aam --fix_hydrogen --log_file ./log.txt --save_dir ./
  ```

## Usage

### Use in script
  ```python
  from syntemp.auto_template import AutoTemp

data = [{'R-id': 0,
    'reactions': 'COC(=O)C(CCCCNC(=O)OCc1ccccc1)NC(=O)Nc1cc(OC)cc(C(C)(C)C)c1O.O>>COC(=O)C(CCCCN)NC(=O)Nc1cc(OC)cc(C(C)(C)C)c1O.O=C(O)OCc1ccccc1'},
  {'R-id': 1,
    'reactions': 'Nc1cccc2cnccc12.O=C(O)c1cc([N+](=O)[O-])c(Sc2c(Cl)cncc2Cl)s1>>O.O=C(Nc1cccc2cnccc12)c1cc([N+](=O)[O-])c(Sc2c(Cl)cncc2Cl)s1'},
  {'R-id': 4,
    'reactions': 'CCOc1ccc(Oc2ncnc3c2cnn3C2CCNCC2)c(F)c1.O=C(Cl)OC1CCCC1>>CCOc1ccc(Oc2ncnc3c2cnn3C2CCN(C(=O)OC3CCCC3)CC2)c(F)c1.Cl'},
  {'R-id': 5,
    'reactions': 'Cn1cnc(-c2cc(C#N)ccn2)c1Br.OB(O)c1ccc(-n2cccn2)cc1>>Cn1cnc(-c2cc(C#N)ccn2)c1-c1ccc(-n2cccn2)cc1.OB(O)Br'},
  {'R-id': 6,
    'reactions': 'CC1(C)OB(c2ccc(OCc3ccc4ccccc4n3)cc2)OC1(C)C.N#Cc1ccc(OC2CCCCO2)c(Br)c1>>CC1(C)OB(Br)OC1(C)C.N#Cc1ccc(OC2CCCCO2)c(-c2ccc(OCc3ccc4ccccc4n3)cc2)c1'}]

auto = AutoTemp(
      rebalancing=True,
      mapper_types=["rxn_mapper", "graphormer", "local_mapper"],
      id="R-id",
      rsmi="reactions",
      n_jobs=1,
      verbose=2,
      batch_size=1,
      job_timeout=None,
      safe_mode=False,
      save_dir=None,
      fix_hydrogen=True,
  )

(reaction_dicts, templates, hier_templates,
  its_correct, uncertain_hydrogen,) = auto.temp_extract(data, lib_path=None)

core_temp = templates[0]

# In order to perform forward prediction, you can use the following code:
  from synkit.IO import gml_to_its
  from synkit.Synthesis.Reactor.syn_reactor import SynReactor
  reactor = SynReactor(substrate='COC(=O)C(CCCCNC(=O)OCc1ccccc1)NC(=O)Nc1cc(OC)cc(C(C)(C)C)c1O.O', template=gml_to_its(core_temp[0]['gml']))

print(reactor.smarts)
  ```

### Use in command line
  ```bash
  echo -e "R-id,reaction\n0,COC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)Nc1cc(OC)cc(C(C)(C)C)c1O>>COC(=O)[C@H](CCCCN)NC(=O)Nc1cc(OC)cc(C(C)(C)C)c1O" > test.csv
  python -m syntemp --data_path test.csv --rebalancing --id 'R-id' --rsmi 'reaction' --rerun_aam --fix_hydrogen --log_file ./log.txt --save_dir ./
  ```

### Reproduce templates extraction
  Run these commands from the root of the cloned repository.
  ```bash
  python -m syntemp --data_path Data/USPTO_50K_original.csv --log_file Data/Test/log.txt --save_dir Data/Test/ --rebalancing --fix_hydrogen --rerun_aam --n_jobs 3 --batch_size 1000 --rsmi reactions --id ID
  ```
    
## Publication

[SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases](https://pubs.acs.org/doi/full/10.1021/acs.jcim.4c01795)

### Citation
```
@article{phan2025syntemp,
  title={SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases},
  author={Phan, Tieu-Long and Weinbauer, Klaus and Laffitte, Marcos E Gonz{\'a}lez and Pan, Yingjie and Merkle, Daniel and Andersen, Jakob L and Fagerberg, Rolf and Flamm, Christoph and Stadler, Peter F},
  journal={Journal of Chemical Information and Modeling},
  volume={65},
  number={6},
  pages={2882--2896},
  year={2025},
  publisher={ACS Publications}
}
```

## Contributing
- [Tieu-Long Phan](https://tieulongphan.github.io/)

## License

This project is licensed under MIT License - see the [License](LICENSE) file for details.

## Acknowledgments

This project has received funding from the European Unions Horizon Europe Doctoral Network programme under the Marie-Skłodowska-Curie grant agreement No 101072930 ([TACsy](https://tacsy.eu/) -- Training Alliance for Computational)

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