├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── docker_install_script.sh ├── run_model ├── .gitignore ├── change_b_factor_from_dict.py ├── cluster_trajectory.py ├── get_all_ca_pos.py ├── get_concavity_score.py ├── get_confidence_score.py ├── get_dock_score.py ├── get_list_of_segids.py ├── input_data │ └── .gitkeep ├── ligands │ ├── 2F2_ideal.pdbqt │ ├── 2F2_ideal.sdf │ ├── ACE_ideal.pdbqt │ ├── ACE_ideal.sdf │ ├── ACM_ideal.pdbqt │ ├── ACM_ideal.sdf │ ├── ACN_ideal.pdbqt │ ├── ACN_ideal.sdf │ ├── BNZ_ideal.pdbqt │ ├── BNZ_ideal.sdf │ ├── CCN_ideal.pdbqt │ ├── CCN_ideal.sdf │ ├── CHX_ideal.pdbqt │ ├── CHX_ideal.sdf │ ├── DMF_ideal.pdbqt │ ├── DMF_ideal.sdf │ ├── EOH_ideal.pdbqt │ ├── EOH_ideal.sdf │ ├── HBX_ideal.pdbqt │ ├── HBX_ideal.sdf │ ├── IPA_ideal.pdbqt │ ├── IPA_ideal.sdf │ ├── IPH_ideal.pdbqt │ ├── IPH_ideal.sdf │ ├── NME_ideal.pdbqt │ ├── NME_ideal.sdf │ ├── TBU_ideal.pdbqt │ ├── TBU_ideal.sdf │ ├── URE_ideal.pdbqt │ ├── URE_ideal.sdf │ ├── convert.sh │ ├── ethane.pdb │ ├── ethane_ideal.pdbqt │ └── ligand_codes.txt ├── output_data │ └── .gitkeep ├── run_tactics.py ├── run_tactics_alt_cluster.py ├── run_tactics_pdb.py └── tactics.py └── train_model ├── README.txt ├── generate_training_database ├── README.txt ├── ext_crypto_database │ ├── README.txt │ ├── align.py │ ├── check_if_site_unbound.py │ ├── get_extended_site.py │ ├── get_pdbs.py │ ├── run_check_pdb.py │ └── run_get_pdbs.py └── gen_crypto_database │ ├── README.txt │ ├── apo_ids_unformatted.txt │ ├── apo_pdb_and_chain.csv │ ├── apo_pdbs_formatted_for_downloader.txt │ ├── combine_all_data.py │ ├── combine_apo_holo_ligand.py │ ├── cryptic_site_locations.csv │ ├── cryptosite_database.csv │ ├── find_cryptic_site.py │ ├── holo_ids_unformatted.txt │ ├── holo_pdb_and_chain.csv │ ├── holo_pdbs_formatted_for_downloader.txt │ ├── ligands.csv │ ├── match_numbering.py │ ├── pdbs_and_ligands.csv │ ├── reformat_names.py │ ├── residue_codes.json │ └── split_pdb_and_chain.py └── ml ├── README.txt 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