Command Line

Top-level shortcut (single file)

autofragment --input water64.xyz --output partitioned.json --n-fragments 4

Fragment a single XYZ

autofragment single --input water64.xyz --output partitioned.json --n-fragments 4

Batch mode (consistent labeling)

autofragment batch --reference ref.xyz --input-dir ./trajectory/ --output-dir ./partitioned/ --n-fragments 4

Biological systems (mmCIF)

autofragment bio --input protein.cif --output partitioned.json

Geometric tiling mode

autofragment geometric --input water64.xyz --output tiled.json --tiling-shape cube --n-fragments 8

Tiered (hierarchical) partitioning

# 2-tier: 4 primary x 4 secondary
autofragment single --input water64.xyz --output tiered.json \
    --tiers 2 --n-primary 4 --n-secondary 4 --method kmeans

# 3-tier: 2 primary x 2 secondary x 2 tertiary
autofragment single --input water64.xyz --output tiered.json \
    --tiers 3 --n-primary 2 --n-secondary 2 --n-tertiary 2

# With seeding strategy
autofragment single --input water64.xyz --output tiered.json \
    --tiers 2 --n-primary 4 --n-secondary 4 --init-strategy pca

# Batch mode with tiered partitioning
autofragment batch --reference ref.xyz --input-dir ./trajectory/ --output-dir ./partitioned/ \
    --tiers 2 --n-primary 4 --n-secondary 4

Show version and optional features

autofragment info
autofragment --version