Collection of scripts for usage, collation and analysis of the IRidium Off-equilibrium Chemical Structures (IROCS) dataset.
NOTE: This repository does not contain the published dataset. The IROCS dataset is available free of charge at DOI:
The exploration of chemical space has traditionally been limited by the focus on small molecules and equilibrium structures in existing datasets. However, understanding chemical reactions and transformation pathways requires access to high-energy, off-equilibrium structures that capture the dynamic nature of chemical processes.
The IROCS (IRidium Off-equilibrium Chemical Structures) dataset addresses this critical gap by providing a comprehensive collection of iridium-containing molecular structures that exist away from their equilibrium configurations. These structures are essential for:
- Reaction mechanism studies: Understanding transition states and intermediate structures
- Catalysis research: Investigating iridium-based catalytic processes and their energy landscapes
- Machine learning model training: Developing ML models that can handle the full spectrum of chemical configurations
- High-energy chemical space exploration: Accessing regions of chemical space typically unavailable in equilibrium-focused datasets
This dataset enables researchers to move beyond the limitations of traditional structure databases and explore the rich chemical space associated with reaction transformations, particularly those involving iridium complexes which are crucial in modern catalysis.
This repository contains Python scripts designed to facilitate the usage, processing, and analysis of the IROCS dataset:
Dataset_utils.py: Extracts molecular structures from .h5 (HDF5) dataset and facilitates conversion between different molecule formats (.xyz, .pdb, etc.).Es_histograms.py: Reads the dataset and plots histograms of the relative energies of all conformer sets compared to the lowest energy conformer of each set.BondEnvironments_all_confs.py: Iterates over all structures in the dataset and retrieves information on every bond. Saves to a JSON file.AngularEnvironments_all_confs.py: Iterates over all strctures and calculates all angles for all molecules. Plots information for each distinct angle as a polar plot.
- Clone this repository
git clone https://github.com/Tuttlelab/IROCS-Usage-Scripts.git cd IROCS-Usage-Scripts
- Install required dependencies
pip install -r requirements.txt