├── .gitignore ├── LICENSE ├── README.md ├── dataset ├── README.md ├── amberlib │ ├── protein.ff14SB.xml │ └── tip3p_standard.xml ├── create_custom_set.py ├── environment.yml ├── main.py ├── posex │ ├── align.py │ ├── ccd.py │ ├── data.py │ ├── mmcif.py │ ├── preprocess.py │ └── utils.py ├── template │ ├── ccd_query.txt │ ├── cross_dock.txt │ ├── self_dock.txt │ └── vs_query.txt └── utils │ ├── __init__.py │ ├── common_helper.py │ ├── mol_correct_helper.py │ ├── openmm_helper.py │ ├── pdb_helper.py │ ├── pdb_process.py │ └── repair_pdb.py ├── environments ├── base.yaml ├── boltz-1.txt ├── boltz-1x.txt ├── chai-1.txt ├── relax.yaml └── rfaa.yaml ├── figures ├── logo.png ├── posex_cross_dock.png └── posex_self_dock.png ├── scripts ├── calculate_benchmark_result.py ├── calculate_benchmark_result.sh ├── complex_structure_alignment.py ├── complex_structure_alignment.sh ├── convert_to_model_input.py ├── convert_to_model_input.sh ├── extract_model_output.py ├── extract_model_output.sh ├── generate_docking_benchmark.py ├── generate_docking_benchmark.sh ├── relax_model_outputs.py ├── run_alphafold3 │ └── run_alphafold3.sh ├── run_boltz │ └── run_boltz.sh ├── run_boltz1x │ └── run_boltz1x.sh ├── run_chai │ ├── run_chai.py │ └── run_chai.sh ├── run_deepdock │ ├── evaluate.py │ ├── prepare.py │ ├── run_deepdock.py │ └── run_deepdock.sh ├── run_diffdock │ ├── run_diffdock.py │ └── run_diffdock.sh ├── run_diffdock_l │ ├── run_diffdock_l.py │ └── run_diffdock_l.sh ├── run_diffdock_pocket │ └── run_diffdock_pocket.sh ├── run_dynamicbind │ ├── run_dynamicbind.py │ └── run_dynamicbind.sh ├── run_equibind │ ├── run_equibind.py │ └── run_equibind.sh ├── run_fabind │ ├── run_fabind.py │ └── run_fabind.sh ├── run_gnina │ ├── run_gnina.sh │ └── run_gnina_help.sh ├── run_interformer │ ├── run_interformer.py │ └── run_interformer.sh ├── run_neuralplexer │ ├── run_neuralplexer.py │ └── run_neuralplexer.sh ├── run_protenix │ └── run_protenix.sh ├── run_rfaa │ └── run_rfaa.sh ├── run_surfdock │ ├── run_surfdock.sh │ └── run_surfdock_help.sh ├── run_tankbind │ ├── run_tankbind.py │ └── run_tankbind.sh └── run_unimol │ ├── run_unimol.py │ └── run_unimol.sh └── tests ├── s1_download_mmcif.py └── s2_prepare_and_post_relax.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CataAI/PoseX/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CataAI/PoseX/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CataAI/PoseX/HEAD/README.md -------------------------------------------------------------------------------- /dataset/README.md: 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