Ring_Atlas

This repository contains the public code and data for the paper "Ring strain energy prediction with machine learning and the application in strain-promoted reactions". Specifically, it contains the following components:

• The AIMNet2 RSE Workflow for ring strain energy (RSE) computation
• The link to Ring Atlas

RSE prediction methods

Please note that the above methods only apply to single-ring molecules

Installation

To run the above methods, the following packages are required:

1. Python >= 3.7
2. PyTorch >= 2.1.0
3. Auto3D >= 2.2.11

The code can be installed following the steps below:

git clone https://github.com/isayevlab/RSE_Atlas.git
cd Ring_Atlas
pip install .

Compute RSE using the workflow

Open any command line interface and run the following command:

compute_rse "path_to_smiles_file.smi" --gpu_idx=0

This will run the workflow on the SMILES file and output the computed RSE to the same directory in a CSV file. The workflow also outputs the final conformers for the rings and broken rings (methyl groups attached to each end) in the .sdf file. The CSV and SDF file have the same file name as the input smi file., but different extensions

• 📗 Here is also an example using Colab.

Ring Atlas

A interactive visualization for the Ring Atlas is available at https://rseatlas.isayevlab.org. This website visualzies about 10% of the Ring Atlas, and provides a search bar for querying the database. The full dataset can be downloaded as a CSV file here.