CLI Guide

Basic Usage

Detect pockets in a protein structure:

pocketeer protein.pdb  # also works with .cif files

Common Options

• -o DIR or --out-dir DIR : Output directory (default: pockets/)
• --r-min X : Minimum sphere radius (Å, default: 3.0)
• --r-max X : Maximum sphere radius (Å, default: 6.0)
• --min-spheres N : Minimum spheres per pocket (default: 35)
• --merge-distance X : Distance threshold for clustering (Å, default: 2.0)
• --ignore-hetero False : Keep ligands/ions (default: True)
• --no-summary : Skip summary file generation

Examples

Custom Output Directory

pocketeer protein.pdb -o results/

Custom Parameters

pocketeer protein.pdb --r-min 2.5 --r-max 7.0 --min-spheres 25

Batch Processing

for pdb in *.pdb; do
    pocketeer "$pdb" -o "results/${pdb%.pdb}"
done

Output Files

The CLI generates these output files in the specified output directory:

• pockets.json - All pocket descriptors in JSON format
• json/ - Subdirectory with individual JSON files for each pocket (pocket_0.json, pocket_1.json, etc.)
• alphaspheres.pdb - Alpha-spheres as PDB file for visualization in PyMOL or ChimeraX
• summary.txt - Human-readable summary (unless --no-summary is used)

Getting Help

For help and all available options:

pocketeer --help

Open alphaspheres.pdb in PyMOL or ChimeraX to visualize detected pockets.