MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations

Molecular modeling of synthetic polymers is today increasingly dependent on automation, high-throughput exploration, and the use of a diverse set of simulation tools. However, despite notable progress in molecular simulation methods, the practical infrastructure for constructing, modifying, and parametrizing polymer systems remains fragmented. Here, we launch a toolkit, MolPy, which aims to bridge this gap by providing an extensible and chemically intuitive platform for building polymer systems and orchestrating simulation workflows. The design philosophy emphasizes a clear separation of responsibilities, a stable and inspectable execution model, and a modular architecture that enables flexible extensions. In practice, the framework supports the introduction of new chemical building blocks and bonding schemes that automatically participate in construction, topology generation, and force-field assignment without requiring modification of existing modules. Interoperability with established simulation tools positions MolPy to support streamlined polymer modeling workflows that remain compatible with emerging large language model (LLM)-driven orchestration and other forms of automated pipeline construction.