AutoFragment Examples

This directory contains examples and test data for autofragment.

Notebooks

Interactive Jupyter notebooks demonstrating core features:

  1. Quickstart: A 5-minute introduction to fragmentation concepts.

  2. Water Cluster MBE: Many-Body Expansion (MBE) fragmentation of water clusters.

  3. Protein EFMO: Fragmenting proteins for GAMESS EFMO calculations.

  4. Algorithm Comparison: Benchmarking different partitioning algorithms.

  5. Custom Scoring: Implementing custom partitioning logic.

  6. Zeolite Fragmentation: Dealing with periodic systems and CIF files.

  7. QM/MM Setup: Defining QM and MM regions.

Data

Test data files used in the examples:

  • 1l2y.pdb: Trp-cage protein structure (20 residues).

  • 1l2y.cif: Trp-cage protein structure (mmCIF format).

  • sodalite.cif: Sodalite zeolite unit cell.

  • aspirin.xyz: Aspirin molecule.

  • caffeine.xyz: Caffeine molecule.

  • dna_hairpin.pdb: DNA hairpin structure.

  • water_64.xyz: Cluster of 64 water molecules.

Usage

To run the notebooks, ensure you have jupyter installed:

pip install jupyter

Then start the notebook server:

jupyter notebook examples/notebooks/