scalachina/smiles-to-iupac-translator

Transformer based SMILES to IUPAC Translator

STOUT V2.0 - Smiles TO iUpac Translator Version 2.0

This repository contains STOUT-V2, SMILES to IUPAC name translator using transformers. STOUT-V2 can translate SMILES to IUPAC names and IUPAC names back to a valid SMILES string. STOUT-V1 is already published and for more details check here

OS-Support: Linux, MACOS and Windows (On Windows you can run STOUT inside the Ubuntu shell). But It is highly recommended to use a Linux system.

Usage

We suggest to use STOUT inside a Conda environment, which makes the dependencies to install easily.

• Conda can be downloaded as part of the Anaconda or the Miniconda plattforms (Python 3.7). We recommend to install miniconda3. Using Linux you can get it with:

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

How to install STOUT

Install directly using PyPi

pip install STOUT-pypi

In a conda environment

conda create --name STOUT python=3.8 
conda activate STOUT
conda install -c decimer stout-pypi

Straight from the repository

pip install git+https://github.com/Kohulan/Smiles-TO-iUpac-Translator.git

Simple usage

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("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("SMILES of "+IUPAC_name+" is: "+SMILES)

Happy Brewing... 🍺

How to cite us?

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

Acknowledgement

• Research supported with Cloud TPUs from Google's TPU Research Cloud (TRC)

STOUT-V2 is part of DECIMER project

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