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

dasmy/Smiles-TO-iUpac-Translator