autofragment

Molecular fragmentation for computational chemistry.

autofragment partitions molecular systems (water clusters, proteins, etc.) into fragments suitable for many-body expansion calculations. Supports both flat partitioning and tiered hierarchical fragmentation (2-tier and 3-tier).

Getting Started

• Quickstart Guide
  • Installation
  • Your First Fragmentation
  • Export to a Quantum Chemistry Program
  • Command-Line Interface
  • Common Workflows
  • Configuration
  • Next Steps
  • Getting Help
  • Troubleshooting
• AutoFragment Examples
  • Notebooks
  • Data
  • Usage
• Installation
  • Requirements
  • Conda (recommended)
  • Pip (PyPI)
  • Pip fallback (from source)
  • Optional extras
  • Verify installation
  • Coverage workflow
• Command Line
  • Top-level shortcut (single file)
  • Fragment a single XYZ
  • Batch mode (consistent labeling)
  • Biological systems (mmCIF)
  • Geometric tiling mode
  • Tiered (hierarchical) partitioning
  • Show version and optional features

Tutorials

• Water Cluster Fragmentation Tutorial
  • Overview
  • Prerequisites
  • Step 1: Load Water Cluster
  • Step 2: Partition into Fragments
  • Step 3: Write Input Files
  • Step 4: Export and Save Results
  • Step 5: Quick API
  • Complete Example
  • Tips and Best Practices
  • Next Steps
• Protein Fragmentation Guide
  • Overview
  • Prerequisites
  • Step 1: Partition from mmCIF
  • Step 2: Generate FMO Input
  • Step 3: Charge Assignment
  • Complete Example
  • Troubleshooting
  • Next Steps
• Materials Science Guide
  • Prerequisites
  • Loading Periodic Systems
  • Surface Systems
  • Future Work
  • Tips
• Custom Rules Authoring Guide
  • Rule System Overview
  • Rule Actions
  • Base Classes
  • Creating Bond Rules
  • Creating Custom Rule Classes
  • Advanced: SMARTS Patterns
  • Building a RuleSet
  • Using Custom Rules
  • Priority System
  • Example: Polymer Rule Set
  • Debugging Rules
  • Best Practices
• Output Formats Guide
  • Supported Programs
  • GAMESS
  • Psi4
  • Q-Chem
  • ORCA
  • NWChem
  • Molpro
  • Turbomole
  • CFOUR
  • Generic Formats
  • Format Registry
  • Writer Options
  • Batch Writing
  • Custom Writers
• Geometric Tiling Partitioning
  • Available tiling shapes
  • CLI usage
  • Python API
  • Output metadata

User Guide

• Python API
  • Quick API
  • Partitioner objects
  • Tiered (Hierarchical) Partitioning
  • Topology-Aware Selection
  • Molecular Topology Refinement
  • Rules Engine
• I/O Formats Guide
  • Overview
  • Reading Molecular Structures
  • Writing Fragment Files
  • Format Registry
  • Coordinate Units
  • Error Handling
  • Tips for Large Files
  • See Also
• Fragmentation Rules
  • Overview
  • Quick Start
  • Rule Actions
  • Priority System
  • Built-in Rules
  • Creating Custom Rules
  • RuleEngine API
  • Best Practices
  • Example: Protein Fragmentation
  • Example: MOF Fragmentation
• Fragmentation Algorithms Guide
  • Overview
  • Clustering Algorithms
  • K-Means Seeding Strategies
  • Graph Partitioning
  • Scoring
  • Choosing the Right Algorithm
• Biological System Support
  • Amino Acids & Proteins
  • Nucleic Acids (DNA/RNA)
• Materials Science Fragmentation
  • Periodic System Handling
  • Materials Partitioners
  • Material-Specific Rules
  • Usage Example
• Multi-Level Methods & QM/MM Partitioning
  • Overview
  • Quick Start
  • Computational Layers
  • QM Region Selection
  • Link Atoms
  • Point Charge Embedding
  • Layer Assignment Algorithms
  • ONIOM Input Generation
  • Converting Results
  • Serialization
  • API Reference
• Core Concepts
  • Molecular Graph
  • Chemistry Utilities
  • Data Structures
  • Fragmentation Rules
• Migration Guide
  • ChemicalSystem Is the Canonical System Container
  • XYZ Reader Changes
  • Partitioner Inputs
  • Writing XYZ Files
• Output format
  • High-level shape

Theory

• Clustering Algorithms for Molecular Fragmentation
  • Introduction
  • K-Means Clustering
  • Spectral Clustering
  • Hierarchical Clustering
  • Application to Molecular Fragmentation
  • References
• Graph Partitioning for Molecular Fragmentation
  • Introduction
  • Molecular Graph Representation
  • Minimum Cut Problem
  • Balanced Partitioning
  • Community Detection
  • METIS Algorithm
  • k-way Partitioning
  • Application to Molecular Fragmentation
  • References
• Fragmentation Scoring Functions
  • Overview
  • Total Score Formulation
  • Component Scores
  • Weight Selection
  • Multi-Objective Optimization
  • Trade-offs and Considerations
  • Score Normalization
  • Implementation Notes
  • References
• Many-Body Expansion (MBE) Theory
  • Introduction
  • Mathematical Foundation
  • Convergence Properties
  • Computational Scaling
  • Hierarchy of Methods
  • Implementation Notes
  • Basis Set Superposition Error (BSSE)
  • Comparison with Other Fragment Methods
  • Applications
  • References
• QM/MM and Embedding Theory
  • Introduction
  • QM/MM Energy Expression
  • Embedding Schemes
  • Boundary Treatments
  • ONIOM Method
  • Effective Fragment Potential (EFP)
  • Implementation in AutoFragment
  • Best Practices
  • References

API Reference

• API Reference
  • autofragment API

Development

• Development
• Performance Profiling