# Python cache
__pycache__/
*.py[cod]

# Notebook metadata
.ipynb_checkpoints/

# User-provided local input lists
holo_list.p
apo_list.p

# Generated helper outputs
combined.p
combined_prev.p
all_sites_df.p
sites_cluster_*.p
sasa_output.pkl
degenerate_ligands.txt

# Structure exports
*.pse
*.xyz

# Common pipeline output folders
data/
tmp_*/
run_*/
smoke_test/
*/monomer_calcs/
*/xyz_files/
*/xyz_files_local/
*/rejects/
