LICENSE
README.md
setup.py
pandadock/__init__.py
pandadock/cli.py
pandadock/docking_cli.py
pandadock/flex_docking_cli.py
pandadock/gridbox_cli.py
pandadock/metal_docking_cli.py
pandadock/ml_docking_cli.py
pandadock/report_cli.py
pandadock/tethered_cli.py
pandadock.egg-info/PKG-INFO
pandadock.egg-info/SOURCES.txt
pandadock.egg-info/dependency_links.txt
pandadock.egg-info/entry_points.txt
pandadock.egg-info/requires.txt
pandadock.egg-info/top_level.txt
pandadock/ai/__init__.py
pandadock/ai/binding_site_prediction.py
pandadock/analysis/__init__.py
pandadock/analysis/scoring_analysis.py
pandadock/docking/__init__.py
pandadock/docking/algorithm_selector.py
pandadock/docking/core.py
pandadock/docking/algorithms/__init__.py
pandadock/docking/algorithms/crystal_guided_cpu.py
pandadock/docking/algorithms/enhanced_common.py
pandadock/docking/algorithms/enhanced_hierarchical_cpu.py
pandadock/docking/algorithms/enhanced_hierarchical_gpu.py
pandadock/docking/algorithms/genetic_algorithm_cpu.py
pandadock/docking/algorithms/genetic_algorithm_gpu.py
pandadock/docking/algorithms/hierarchical_cpu.py
pandadock/docking/algorithms/monte_carlo_cpu.py
pandadock/docking/algorithms/monte_carlo_gpu.py
pandadock/docking/analysis/__init__.py
pandadock/docking/analysis/interaction_analysis.py
pandadock/docking/refinement/__init__.py
pandadock/docking/refinement/ensemble_refinement.py
pandadock/docking/refinement/mmgbsa.py
pandadock/docking/refinement/simulated_annealing.py
pandadock/docking/scoring/__init__.py
pandadock/docking/scoring/empirical.py
pandadock/docking/scoring/ensemble.py
pandadock/docking/scoring/gpu_scoring.py
pandadock/docking/scoring/hybrid.py
pandadock/docking/scoring/physics_based.py
pandadock/docking/scoring/precision_score.py
pandadock/docking/scoring/vina_scoring.py
pandadock/docking/visualization/__init__.py
pandadock/docking/visualization/analyzer.py
pandadock/docking/visualization/plotter.py
pandadock/docking/visualization/visualizer.py
pandadock/flex_docking/__init__.py
pandadock/flex_docking/core.py
pandadock/flex_docking/phases.py
pandadock/gnn/__init__.py
pandadock/gnn/cli.py
pandadock/gnn/scoring.py
pandadock/gnn/data/__init__.py
pandadock/gnn/data/dataset.py
pandadock/gnn/data/featurizer.py
pandadock/gnn/data/graph_builder.py
pandadock/gnn/data/mol2_parser.py
pandadock/gnn/data/pdbbind_dataset.py
pandadock/gnn/models/__init__.py
pandadock/gnn/models/layers.py
pandadock/gnn/models/pandadock_gnn.py
pandadock/gnn/models/pooling.py
pandadock/gnn/tests/__init__.py
pandadock/gnn/tests/test_gnn.py
pandadock/gnn/training/__init__.py
pandadock/gnn/training/losses.py
pandadock/gnn/training/metrics.py
pandadock/gnn/training/trainer.py
pandadock/gridbox/__init__.py
pandadock/gridbox/cavity_detection.py
pandadock/gridbox/core.py
pandadock/gridbox/ligand_based.py
pandadock/gui/__init__.py
pandadock/gui/grid_selector.py
pandadock/metal_docking/__init__.py
pandadock/metal_docking/metal_core.py
pandadock/metal_docking/metal_parameters.py
pandadock/metal_docking/metal_preparation.py
pandadock/metal_docking/metal_scoring.py
pandadock/ml/__init__.py
pandadock/ml/feature_extraction.py
pandadock/ml/hybrid_pipeline.py
pandadock/ml/models/__init__.py
pandadock/ml/models/diffusion.py
pandadock/ml/models/energy_prediction.py
pandadock/ml/models/pose_ranking.py
pandadock/ml/training/__init__.py
pandadock/ml/training/trainer.py
pandadock/preprocessing/__init__.py
pandadock/preprocessing/ligand.py
pandadock/preprocessing/receptor.py
pandadock/tethered/__init__.py
pandadock/tethered/complete_analyzer.py
pandadock/tethered/ligand_extractor.py
pandadock/tethered/pose_validator.py
pandadock/tethered/tethered_docker.py
pandadock/utils/__init__.py
pandadock/utils/io.py
pandadock/visualization/__init__.py
pandadock/visualization/flex_visualizer.py
pandadock/visualization/publication_plots.py
pandadock/visualization/simple_publication_plots.py
pandadock/visualization/pandamap/__init__.py
pandadock/visualization/pandamap/pandamap_integration.py
tests/__init__.py
tests/conftest.py
tests/test_gnn.py
tests/test_imports.py