randatoms 0.0.2

A random atoms package for atomistic scientists: easily generate, filter, and manage atomic datasets.

randatoms

A random atoms package for atomistic scientists: easily sample random structures from existing datasets, filter, and manage atomic datasets.

Overview

randatoms provides tools for sampling random atomic structures from pre-existing datasets, as well as utilities for filtering, merging, and loading these structures. The package is designed to help researchers in computational chemistry and materials science efficiently retrieve random structures, apply various filters, and manage large collections of atomic data.

Installation

You can install randatoms using pip:

pip install randatoms

Usage

💬 Conversational AI Docs	🔗 Try it on Google Colab

Loading Random Structures

from randatoms import randomatoms

# Get a single random structure
atoms = randomatoms()

# Get multiple random structures with filters
atoms_list = randomatoms(5, seed=42, include_elements=['C', 'H'], max_atoms=50)

Advanced Data Loading

from randatoms import DataLoader

# Initialize loader
loader = DataLoader()

# filter query
filter = dict(
    include_elements=['C', 'H', 'O'],
    has_metals=True,
    is_periodic=True
    )

# Get random structures
atoms = loader.get_random_structures(**filter)

# View statistics
loader.print_statistics(**filter)

Unit test

wget -O randatoms-main.zip https://github.com/kangmg/randatoms/archive/refs/heads/main.zip

unzip randatoms-main.zip "randatoms-main/test/*" && mv randatoms-main/test ./test && rm -rf randatoms-main randatoms-main.zip


python3 -m unittest discover test -v

Dataset References

• [OMOL25 set]
  Levine, D.S. et al. (2025). The Open Molecules 2025 (OMol25) Dataset, Evaluations, and Models.
  arXiv preprint arXiv:2505.08762

• [OMAT24 set]
  Barroso-Luque, L. et al. (2024). Open Materials 2024 (OMat24) Inorganic Materials Dataset and Models.
  arXiv preprint arXiv:2410.12771

• [peptide set]
  Řezáč, J. et al. (2018). Journal of Chemical Theory and Computation, 14(3), 1254–1266.
  DOI: 10.1021/acs.jctc.7b01074

• [X23b set]
  Zhugayevych, A. et al. (2023). Journal of Chemical Theory and Computation, 19(22), 8481–8490.
  DOI: 10.1021/acs.jctc.3c00861

• [ODAC23 set]
  Sriram, A. et al. (2024). ACS Central Science, 10(5), 923–941.
  DOI: 10.1021/acscentsci.3c01629