pyar-chem 1.2.0

PyAR: Python program for Aggregation and Reaction

PyAR

PyAR is a chemistry-focused structure-search package for aggregation, reaction discovery, solvation growth, and bond scans.

Install

python -m pip install pyar-chem

Quick Start

pyar-cli --help
pyar-cli -a C H -as 1 4 -N 8
pyar-cli react A.xyz B.xyz -N 8 -gmin 100 -gmax 1000 --software xtb
pyar-cli solvate solute.xyz solvent.xyz --software xtb -ss 10 -N 16

Supported Workflows

• aggregate for clusters, aggregates, and noncovalent complexes
• react for AFIR-style reaction searches between two reactants
• solvate for microsolvation, ligand addition, and growth around a core
• scan-bond for a simple bond-distance probe
• pyar-reaction-trace for reaction-trace analysis

External Program Requirements

Some workflows rely on external executables such as xTB, ORCA, Gaussian, Psi4, MOPAC, Turbomole, OpenBabel, MLatom, and DFT-D4. The optional extras install Python dependencies only; they do not bundle large model or vendor files into the main pyar-chem wheel. AIMNet2 .jpt models, AIQM1 .pt models, and vendored MLatom binaries must come from the upstream project or another separate model/package source. See docs/external_programs.rst for the official project websites and installation notes.

Documentation

Full documentation: docs/ and https://pyar.readthedocs.io/ Changelog: CHANGELOG.md

Citation

If you use PyAR, cite the paper that matches your chemistry problem. See docs/publications.rst for the current publication map. For general cluster-building use, start with:

• Nandi et al., Computational and Theoretical Chemistry 1111, 69-81 (2017)
• Khatun et al., Frontiers in Chemistry 7:644 (2019)