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arXiv · 2507.08852

Open, Reproducible Calculation of Assembly Indices

Devansh Vimal·Garrett Parzych·Olivia M. Smith·Devendra Parkar·Sean Bergen·Joshua J. Daymude·Cole Mathis
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Abstract

We present assembly-theory, a Rust package for computing assembly indices of covalently bonded molecular structures. This is a key complexity measure of assembly theory, a recent theoretical framework quantifying selection across diverse systems, most importantly chemistry. assembly-theory is designed for researchers and practitioners alike, providing (i) extensible, high-performance implementations of assembly index calculation algorithms, (ii) comprehensive benchmarks against which current and future algorithmic improvements can be tested, and (iii) Python bindings and RDKit-compatible data loaders to support integration with existing computational pipelines.

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Devansh Vimal, Garrett Parzych, Olivia M. Smith, Devendra Parkar, Sean Bergen, Joshua J. Daymude, Cole Mathis. 2025-07-08. Open, Reproducible Calculation of Assembly Indices. https://doi.org/10.21105/joss.09318

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