autofragment

Getting Started

  • Quickstart Guide
  • AutoFragment Examples
  • Installation
  • Command Line

Tutorials

  • Water Cluster Fragmentation Tutorial
  • Protein Fragmentation Guide
  • Materials Science Guide
  • Custom Rules Authoring Guide
  • Output Formats Guide
  • Geometric Tiling Partitioning

User Guide

  • Python API
  • I/O Formats Guide
  • Fragmentation Rules
  • Fragmentation Algorithms Guide
  • Biological System Support
  • Materials Science Fragmentation
  • Multi-Level Methods & QM/MM Partitioning
  • Core Concepts
  • Migration Guide
  • Output format

Theory

  • Clustering Algorithms for Molecular Fragmentation
  • Graph Partitioning for Molecular Fragmentation
  • Fragmentation Scoring Functions
  • Many-Body Expansion (MBE) Theory
  • QM/MM and Embedding Theory

API Reference

  • API Reference

Development

  • Development
  • Performance Profiling
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© Copyright 2026, Bryce M. Westheimer.

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