├── .github └── workflows │ ├── publish-pypi.yml │ └── python-package.yml ├── .gitignore ├── .readthedocs.yaml ├── ALGORITHMS.md ├── CONTRIBUTING.md ├── CUDA_ERROR_DIAGNOSIS.md ├── Documentations ├── COMPREHENSIVE_TESTING_README.md ├── ENHANCED_HIERARCHICAL_GPU_FIXES.md ├── GPU_ALGORITHM_FIX_SUMMARY.md ├── GPU_FIXES_APPLIED.md ├── GPU_FIXES_COMPLETE.md ├── GPU_SETUP.md ├── GPU_SPEED_FIXES.md ├── Implementation_algorithms.txt ├── Metal_ions_parameter.txt └── README_ML.md ├── INSTALL.md ├── LICENSE ├── PandaDock.png ├── Paper ├── ENHANCED_HIERARCHICAL_PERFORMANCE_FIX.md ├── PandaDock_Academic_Paper.md ├── PandaDock_Algorithm_Comparison.png ├── PandaDock_Algorithm_Flowchart.png ├── PandaDock_Energy_Decomposition.png ├── PandaDock_LaTeX_Template.tex ├── PandaDock_Performance_Comparison.png ├── PandaDock_Supplementary_Tables.md ├── create_paper_figures.py └── create_simple_figures.py ├── README.md ├── READTHEDOCS_SETUP.md ├── benchmarking ├── README.md ├── analyze_binding_affinity_correlation.py ├── analyze_pdbbind_results.py ├── analyze_results.py ├── compare_affinity_methods.py ├── comprehensive_benchmark │ ├── algorithm_summary.csv │ ├── analysis │ │ ├── figures │ │ │ ├── fig1_success_rates.pdf │ │ │ ├── fig1_success_rates.png │ │ │ ├── fig2_rmsd_distribution.pdf │ │ │ ├── fig2_rmsd_distribution.png │ │ │ ├── fig3_rmsd_boxplot.pdf │ │ │ ├── fig3_rmsd_boxplot.png │ │ │ ├── fig4_runtime_comparison.pdf │ │ │ ├── fig4_runtime_comparison.png │ │ │ ├── fig5_success_vs_runtime.pdf │ │ │ └── fig5_success_vs_runtime.png │ │ └── tables │ │ │ ├── statistical_tests.csv │ │ │ └── summary_statistics.csv │ ├── benchmark_results.csv │ ├── benchmark_results.json │ ├── benchmark_results_intermediate.csv │ ├── binding_affinity_analysis │ │ ├── BINDING_AFFINITY_CORRELATION_REPORT.md │ │ ├── correlation_heatmap.pdf │ │ ├── correlation_heatmap.png │ │ ├── correlation_scatter_plots.pdf │ │ ├── correlation_scatter_plots.png │ │ ├── correlation_statistics.csv │ │ ├── merged_data.csv │ │ ├── performance_by_affinity_range.pdf │ │ └── performance_by_affinity_range.png │ ├── method_comparison │ │ ├── AFFINITY_METHOD_COMPARISON_REPORT.md │ │ ├── method_comparison_literature.pdf │ │ └── method_comparison_literature.png │ └── progress.json ├── full_benchmark │ ├── PDBbind_v2020 │ │ ├── INDEX_refined_set.2020 │ │ ├── extract_grid.py │ │ ├── index │ │ │ ├── 2020_index.lst │ │ │ ├── INDEX_general_NL.2020 │ │ │ ├── INDEX_general_PL.2020 │ │ │ ├── INDEX_general_PL_data.2020 │ │ │ ├── INDEX_general_PL_name.2020 │ │ │ ├── INDEX_general_PN.2020 │ │ │ ├── INDEX_general_PP.2020 │ │ │ ├── INDEX_refined_data.2020 │ │ │ ├── INDEX_refined_name.2020 │ │ │ ├── INDEX_refined_set.2020 │ │ │ └── INDEX_structure.2020 │ │ └── readme │ │ │ ├── PDBbind-101.txt │ │ │ └── pdbbind_2020_intro.pdf │ ├── PDBbind_v2020_prepared │ │ └── preparation_summary.csv │ ├── grid_centers.csv │ └── grid_centers_prepared_150.csv ├── monitor_benchmark.py ├── prepare_benchmark_simple.py ├── prepare_ligands_comprehensive.py ├── prepare_pdbbind_core.py ├── quick_test.sh ├── run_benchmark_comparison.py ├── run_comprehensive_benchmark.sh ├── run_flex_mmgbsa_benchmark.py └── run_pdbbind_benchmark.py ├── cpu_comprehensive_test_fixed.sh ├── cpu_comprehensive_testing_fixed ├── cpu_detailed_results.csv ├── cpu_fast_46cores │ ├── crystal_guided_cpu_empirical_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── crystal_guided_cpu_hybrid_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── crystal_guided_cpu_physics_based_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── crystal_guided_cpu_precision_score_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_empirical_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_hybrid_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_physics_based_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_precision_score_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_empirical_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_hybrid_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_physics_based_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_precision_score_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_empirical_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_hybrid_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_physics_based_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_precision_score_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── monte_carlo_cpu_empirical_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── monte_carlo_cpu_hybrid_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── monte_carlo_cpu_physics_based_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ └── monte_carlo_cpu_precision_score_fast │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json ├── cpu_full_46cores │ ├── crystal_guided_cpu_empirical_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── crystal_guided_cpu_hybrid_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── crystal_guided_cpu_physics_based_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── crystal_guided_cpu_precision_score_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_empirical_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_hybrid_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_physics_based_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── enhanced_hierarchical_cpu_precision_score_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_empirical_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_hybrid_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_physics_based_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── genetic_algorithm_cpu_precision_score_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_empirical_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_hybrid_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_physics_based_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── hierarchical_cpu_precision_score_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── monte_carlo_cpu_empirical_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── monte_carlo_cpu_hybrid_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ ├── monte_carlo_cpu_physics_based_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json │ └── monte_carlo_cpu_precision_score_full │ │ ├── binding_affinities.png │ │ ├── etomidate.pdb_poses.json │ │ ├── etomidate.pdb_summary.json │ │ └── interaction_analysis.json └── cpu_publication_reports │ └── cpu_full_report │ ├── pandadock_comprehensive_analysis.pdf │ ├── pandadock_comprehensive_analysis.png │ └── pandadock_detailed_analysis.pdf ├── docs ├── Makefile ├── requirements.txt └── source │ ├── _static │ ├── custom.css │ ├── favicon.png │ └── logo.png │ ├── about │ ├── analysis.rst │ ├── basic_docking.rst │ ├── best_practices.rst │ ├── changelog.rst │ ├── citation.rst │ ├── contributing.rst │ ├── cpu_algorithms.rst │ ├── docking.rst │ ├── empirical.rst │ ├── faq.rst │ ├── flexible_docking.rst │ ├── gpu_acceleration.rst │ ├── gpu_algorithms.rst │ ├── gpu_scoring.rst │ ├── high_accuracy.rst │ ├── hybrid.rst │ ├── license.rst │ ├── metal_coordination.rst │ ├── overview.rst │ ├── pandadock.rst │ ├── pandadock_flex.rst │ ├── pandadock_metal.rst │ ├── pandadock_ml.rst │ ├── pandadock_report.rst │ ├── pandadock_tethered.rst │ ├── performance.rst │ ├── physics_based.rst │ ├── scoring.rst │ ├── selection_guide.rst │ ├── specialized_modes.rst │ ├── troubleshooting.rst │ ├── virtual_screening.rst │ └── visualization.rst │ ├── algorithms │ ├── cpu_algorithms.rst │ ├── gpu_algorithms.rst │ ├── overview.rst │ ├── selection_guide.rst │ └── specialized_modes.rst │ ├── api │ ├── analysis.rst │ ├── basic_docking.rst │ ├── best_practices.rst │ ├── changelog.rst │ ├── citation.rst │ ├── contributing.rst │ ├── cpu_algorithms.rst │ ├── docking.rst │ ├── empirical.rst │ ├── faq.rst │ ├── flexible_docking.rst │ ├── gpu_acceleration.rst │ ├── gpu_algorithms.rst │ ├── gpu_scoring.rst │ ├── high_accuracy.rst │ ├── hybrid.rst │ ├── license.rst │ ├── metal_coordination.rst │ ├── overview.rst │ ├── pandadock.rst │ ├── pandadock_flex.rst │ ├── pandadock_metal.rst │ ├── pandadock_ml.rst │ ├── pandadock_report.rst │ ├── pandadock_tethered.rst │ ├── performance.rst │ ├── physics_based.rst │ ├── scoring.rst │ ├── selection_guide.rst │ ├── specialized_modes.rst │ ├── troubleshooting.rst │ ├── virtual_screening.rst │ └── visualization.rst │ ├── cli │ ├── pandadock.rst │ ├── pandadock_flex.rst │ ├── pandadock_metal.rst │ ├── pandadock_ml.rst │ ├── pandadock_report.rst │ └── pandadock_tethered.rst │ ├── conf.py │ ├── getting_started │ ├── basic_usage.rst │ ├── installation.rst │ └── quickstart.rst │ ├── guide │ ├── analysis.rst │ ├── basic_docking.rst │ ├── best_practices.rst │ ├── changelog.rst │ ├── citation.rst │ ├── contributing.rst │ ├── cpu_algorithms.rst │ ├── docking.rst │ ├── empirical.rst │ ├── faq.rst │ ├── flexible_docking.rst │ ├── gpu_acceleration.rst │ ├── gpu_algorithms.rst │ ├── gpu_scoring.rst │ ├── high_accuracy.rst │ ├── hybrid.rst │ ├── license.rst │ ├── metal_coordination.rst │ ├── overview.rst │ ├── pandadock.rst │ ├── pandadock_flex.rst │ ├── pandadock_metal.rst │ ├── pandadock_ml.rst │ ├── pandadock_report.rst │ ├── pandadock_tethered.rst │ ├── performance.rst │ ├── physics_based.rst │ ├── scoring.rst │ ├── selection_guide.rst │ ├── specialized_modes.rst │ ├── troubleshooting.rst │ ├── virtual_screening.rst │ └── visualization.rst │ ├── index.rst │ ├── scoring │ ├── empirical.rst │ ├── gpu_scoring.rst │ ├── hybrid.rst │ ├── overview.rst │ └── physics_based.rst │ └── tutorials │ ├── analysis.rst │ ├── basic_docking.rst │ ├── best_practices.rst │ ├── changelog.rst │ ├── citation.rst │ ├── contributing.rst │ ├── cpu_algorithms.rst │ ├── docking.rst │ ├── empirical.rst │ ├── faq.rst │ ├── flexible_docking.rst │ ├── gpu_acceleration.rst │ ├── gpu_algorithms.rst │ ├── gpu_scoring.rst │ ├── high_accuracy.rst │ ├── hybrid.rst │ ├── license.rst │ ├── metal_coordination.rst │ ├── overview.rst │ ├── pandadock.rst │ ├── pandadock_flex.rst │ ├── pandadock_metal.rst │ ├── pandadock_ml.rst │ ├── pandadock_report.rst │ ├── pandadock_tethered.rst │ ├── performance.rst │ ├── physics_based.rst │ ├── scoring.rst │ ├── selection_guide.rst │ ├── specialized_modes.rst │ ├── troubleshooting.rst │ ├── virtual_screening.rst │ └── visualization.rst ├── gpu_comprehensive_test.sh ├── pandadock ├── __init__.py ├── ai │ ├── __init__.py │ └── binding_site_prediction.py ├── analysis │ ├── __init__.py │ └── scoring_analysis.py ├── cli.py ├── docking │ ├── __init__.py │ ├── algorithms │ │ ├── __init__.py │ │ ├── crystal_guided_cpu.py │ │ ├── enhanced_common.py │ │ ├── enhanced_hierarchical_cpu.py │ │ ├── enhanced_hierarchical_gpu.py │ │ ├── genetic_algorithm_cpu.py │ │ ├── genetic_algorithm_gpu.py │ │ ├── hierarchical_cpu.py │ │ ├── monte_carlo_cpu.py │ │ └── monte_carlo_gpu.py │ ├── analysis │ │ ├── __init__.py │ │ └── interaction_analysis.py │ ├── core.py │ ├── refinement │ │ ├── __init__.py │ │ ├── ensemble_refinement.py │ │ ├── mmgbsa.py │ │ └── simulated_annealing.py │ ├── scoring │ │ ├── __init__.py │ │ ├── empirical.py │ │ ├── ensemble.py │ │ ├── gpu_scoring.py │ │ ├── hybrid.py │ │ ├── physics_based.py │ │ └── precision_score.py │ └── visualization │ │ ├── __init__.py │ │ ├── analyzer.py │ │ ├── plotter.py │ │ └── visualizer.py ├── docking_cli.py ├── flex_docking │ ├── __init__.py │ ├── core.py │ └── phases.py ├── flex_docking_cli.py ├── gridbox │ ├── __init__.py │ ├── cavity_detection.py │ ├── core.py │ └── ligand_based.py ├── gridbox_cli.py ├── gui │ ├── __init__.py │ └── grid_selector.py ├── metal_docking │ ├── __init__.py │ ├── metal_core.py │ ├── metal_parameters.py │ ├── metal_preparation.py │ └── metal_scoring.py ├── metal_docking_cli.py ├── ml │ ├── __init__.py │ ├── feature_extraction.py │ ├── hybrid_pipeline.py │ ├── models │ │ ├── __init__.py │ │ ├── diffusion.py │ │ ├── energy_prediction.py │ │ └── pose_ranking.py │ └── training │ │ ├── __init__.py │ │ └── trainer.py ├── ml_docking_cli.py ├── preprocessing │ ├── __init__.py │ ├── ligand.py │ └── receptor.py ├── report_cli.py ├── tethered │ ├── __init__.py │ ├── complete_analyzer.py │ ├── ligand_extractor.py │ ├── pose_validator.py │ └── tethered_docker.py ├── tethered_cli.py ├── utils │ ├── __init__.py │ └── io.py └── visualization │ ├── __init__.py │ ├── flex_visualizer.py │ ├── pandamap │ ├── __init__.py │ └── pandamap_integration.py │ ├── publication_plots.py │ └── simple_publication_plots.py ├── preprocessing └── preprocessing.out ├── scripts ├── check_gpu_status.sh ├── comprehensive_algorithms.sh ├── comprehensive_algorithms_office.sh ├── comprehensive_gpu_only.sh ├── diagnose_gpu_office.py ├── pandadock-flex ├── pandadock-ml ├── pandadock-report ├── test_algorithms_full.sh ├── test_all_algorithms.sh ├── test_comprehensive_script.sh ├── test_gpu_speed.sh └── test_pandadock_ml_integration.py ├── setup.py └── tests ├── __init__.py ├── conftest.py └── test_imports.py 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