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
- autofragment API
  - Top-level
  - Submodules

Development

Development
Performance Profiling

autofragment

API Reference
autofragment API
autofragment.core
autofragment.core.atom
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autofragment.core.atom

Memory-efficient atom storage utilities.

Classes

CompactAtomArray(n_atoms)

Memory-efficient atom storage using structured numpy arrays.

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