Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/kohulan/smiles-to-iupac-translator
Transformer based SMILES to IUPAC Translator
https://github.com/kohulan/smiles-to-iupac-translator
iupac-translator neural-machine-translation smiles stout
Last synced: 2 days ago
JSON representation
Transformer based SMILES to IUPAC Translator
- Host: GitHub
- URL: https://github.com/kohulan/smiles-to-iupac-translator
- Owner: Kohulan
- License: mit
- Created: 2020-11-03T10:09:28.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-12-02T03:01:27.000Z (about 1 month ago)
- Last Synced: 2025-01-02T00:49:28.345Z (8 days ago)
- Topics: iupac-translator, neural-machine-translation, smiles, stout
- Language: Python
- Homepage:
- Size: 38 MB
- Stars: 144
- Watchers: 8
- Forks: 30
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
STOUT V2.0
Smiles TO iUpac Translator: Advanced Chemical Nomenclature Translation
Key Features •
Installation •
How To Use •
Training STOUT •
Acknowledgements •
Citation
## Key Features
- 🧪 Translate SMILES to IUPAC names
- 🔬 Convert IUPAC names back to valid SMILES strings
- 🤖 Powered by advanced transformer models
- 💻 Cross-platform support (Linux, macOS, Windows via Ubuntu shell)
- 🚀 High-performance chemical nomenclature translation
- 🧠 Training code available for custom model development
## Installation
Choose your preferred installation method:
📦 PyPI Installation
```bash
pip install STOUT-pypi
```
🐍 Conda Environment Setup
```bash
conda create --name STOUT python=3.10
conda activate STOUT
conda install -c decimer stout-pypi
```
📥 Direct Repository Installation
```bash
pip install git+https://github.com/Kohulan/Smiles-TO-iUpac-Translator.git
```
## How To Use
```python
from STOUT import translate_forward, translate_reverse
# SMILES to IUPAC name translation
SMILES = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
IUPAC_name = translate_forward(SMILES)
print(f"🧪 IUPAC name of {SMILES} is: {IUPAC_name}")
# IUPAC name to SMILES translation
IUPAC_name = "1,3,7-trimethylpurine-2,6-dione"
SMILES = translate_reverse(IUPAC_name)
print(f"🔬 SMILES of {IUPAC_name} is: {SMILES}")
```
## Training STOUT
For researchers interested in training their own STOUT models or understanding the training process, we provide the training code in a separate repository:
[STOUT Training Repository](https://github.com/Kohulan/IWOMI_Tutorials/tree/IWOMI_2024/STOUT_Training)
This repository contains the necessary scripts and instructions for training STOUT models. Please note that training requires significant computational resources and a large dataset. Refer to the README in the training repository for detailed instructions.
## Model Card
> Rajan, K., Steinbeck, C., & Zielesny, A. (2024). STOUT V2 - Model library (Version v3). Zenodo. https://doi.org/10.5281/zenodo.13318286
### Model Use
- Primary intended uses: Translation between SMILES and IUPAC names for chemical compounds
- Primary intended users: Chemists, researchers, and developers in the field of cheminformatics
- Out-of-scope use cases: Not intended for critical applications where 100% accuracy is required
## Acknowledgements
Research supported with Cloud TPUs from Google's TPU Research Cloud (TRC)
Part of the DECIMER Project
About Us
## Citation
1. Rajan, K., Zielesny, A. & Steinbeck, C. STOUT: SMILES to IUPAC names using neural machine translation. J Cheminform 13, 34 (2021). https://doi.org/10.1186/s13321-021-00512-4
2. Rajan K, Zielesny A, Steinbeck C. STOUT V2.0: SMILES to IUPAC name conversion using transformer models. ChemRxiv. 2024; https://doi.org/10.26434/chemrxiv-2024-089vs
## Repository Analytics
---
Made with ❤️ by the Steinbeck Group