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MolPy

Python License Documentation

A fast, clean, and composable toolkit for molecular modeling

Quick Start GitHub

Features

  • 🤖 LLM-Friendly

    Clean APIs, explicit typing, no hidden magic

  • 🏗️ Extensible

    Composition-based design for easy customization

  • 🔗 Interoperable

    Works smoothly with AmberTools, LAMMPS, OpenMM, Packmol, RDKit

  • ⚙️ Modular Architecture

    Clear, composable modules built around a unified data model

  • 📊 Flexible Structures

    Frame/Block system and memory-mapped Trajectory support

  • 🔧 Force-Field System

    SMARTS/SMIRKS typing and structured parameter management

Getting Started

New to MolPy? Start with our Quick Start Guide to learn the basics.

Documentation

Explore comprehensive guides in our User Guide and Tutorials.

API Reference

Detailed API documentation is available in the API Reference section.

Need Help?

Check out our FAQ or open an issue on GitHub.

Roadmap

Core Foundations

  • Stabilize core data structures (Frame, Block, Box, Trajectory)
  • Unify topology representation (bonds/angles/dihedrals)
  • Improve I/O layer (XYZ, PDB, LAMMPS DATA)
  • Strengthen typing, doctests, and basic documentation

Modeling & Construction

  • General lattice + crystal builder (SC/BCC/FCC/HCP + regions)
  • Basic molecular builders (monomers, ports, polymer assembly)
  • System assembly utilities (packing, placement, initialization)
  • Core editing tools (add/remove atoms, merge fragments, simple reactions)

Force Fields & Typing

  • Force field container (atom types + bonded parameters)
  • Typifier system (rule-based SMARTS-style typing)
  • Parameter assignment and export for external engines
  • Validation / consistency tools for typed systems

Compute & Analysis

  • Unified Compute + Result abstraction
  • Common analysis functions (RDF, MSD, basic time series)
  • Optional shared context (neighbor lists, box info)
  • Export analysis results to arrays / DataFrames

Performance & User Experience

  • Rust backend for performance-critical operations
  • Visualization integration with molvis

Ecosystem

MolVis — Production-level visualization with WebGL acceleration and real-time manipulation MolRS — Rust backend for performance-critical operations

Dependencies

License

This project is licensed under the BSD-3-Clause License. See LICENSE for details.