{ "run_id": "reference_sample_full", "created_at": "2026-06-14T19:21:57.883976+00:00", "engine": "real-rdock", "n_runs": 50, "jobs": 11, "input_hashes": { "ligands_sdf": "2a3f3ae8b7cd8f9496b6e1540a06bde78a1409aac77dff6ec36f50dcb65c497a", "dock_prm": "5c8dac7b2bc7df707cf9f9b077dc8d5824e7b15dd59c0fba76d9a11dd2790cfb", "receptor_prm": "201d2bb6f0bfde45152afb559ea064b1e2e587c89653ecad6d1a8b5a524b071d", "cavity_as": "df88c2e520f8c7ea40db272badfed9178cf64de4709539f37bd799e7b3368a92" }, "rdock_versions": { "rbdock": "The rDock program is\u00a0licensed under GNU-LGPLv3.0. http://rdock.sourceforge.net/", "rbcavity": "The rDock program is\u00a0licensed under GNU-LGPLv3.0. http://rdock.sourceforge.net/" }, "target_config": { "receptor": "/Users/makardorohuntsev/docking_project/data/datasets/rdock_3PTB_25k_pubchem_local/target/rdock_prm/target_raw.pdb", "reference_ligand": "/Users/makardorohuntsev/docking_project/data/datasets/rdock_3PTB_25k_pubchem_local/target/rdock_prm/reference_ligand.sdf", "target_dir": "/Users/makardorohuntsev/Docking_project/data/datasets/rdock_3PTB_25k_pubchem_local/target/rdock_prm", "receptor_mol2": "/Users/makardorohuntsev/docking_project/data/datasets/rdock_3PTB_25k_pubchem_local/target/rdock_prm/receptor.mol2", "receptor_prm": "/Users/makardorohuntsev/docking_project/data/datasets/rdock_3PTB_25k_pubchem_local/target/rdock_prm/receptor.prm", "cavity_as": "/Users/makardorohuntsev/docking_project/data/datasets/rdock_3PTB_25k_pubchem_local/target/rdock_prm/receptor.as", "pocket_center": [ -1.7591111111111113, 14.461, 16.915777777777777 ], "pocket_radius": 6.0, "diagnostics": { "receptor_atom_count": 1629, "reference_ligand_atom_count": 9, "reference_ligand_centroid": [ -1.7591111111111113, 14.461, 16.915777777777777 ], "reference_ligand_radius": 2.647231878261507, "min_receptor_ligand_distance": 2.8153411871387823, "reference_centroid_to_nearest_receptor_atom": 3.8328772127991604, "severe_clash_pairs_lt_1A": 0 } }, "commands": [ { "stage": "rbdock_chunk_003", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_003.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_003_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.425607+00:00", "end_time": "2026-06-14T19:21:15.991230+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_003.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_003.stderr.log" }, { "stage": "rbdock_chunk_010", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_010.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_010_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.484261+00:00", "end_time": "2026-06-14T19:21:24.863380+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_010.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_010.stderr.log" }, { "stage": "rbdock_chunk_007", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_007.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_007_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.436900+00:00", "end_time": "2026-06-14T19:21:28.202709+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_007.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_007.stderr.log" }, { "stage": "rbdock_chunk_005", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_005.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_005_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.472506+00:00", "end_time": "2026-06-14T19:21:37.228152+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_005.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_005.stderr.log" }, { "stage": "rbdock_chunk_002", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_002.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_002_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.436818+00:00", "end_time": "2026-06-14T19:21:38.099933+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_002.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_002.stderr.log" }, { "stage": "rbdock_chunk_006", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_006.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_006_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.464847+00:00", "end_time": "2026-06-14T19:21:40.036567+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_006.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_006.stderr.log" }, { "stage": "rbdock_chunk_009", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_009.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_009_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.436336+00:00", "end_time": "2026-06-14T19:21:40.505081+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_009.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_009.stderr.log" }, { "stage": "rbdock_chunk_004", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_004.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_004_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.426128+00:00", "end_time": "2026-06-14T19:21:42.834640+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_004.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_004.stderr.log" }, { "stage": "rbdock_chunk_008", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_008.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_008_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.455039+00:00", "end_time": "2026-06-14T19:21:43.297182+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_008.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_008.stderr.log" }, { "stage": "rbdock_chunk_001", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_001.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_001_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.454622+00:00", "end_time": "2026-06-14T19:21:51.256582+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_001.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_001.stderr.log" }, { "stage": "rbdock_chunk_000", "command": [ "/opt/homebrew/bin/rbdock", "-r", "receptor.prm", "-p", "/opt/homebrew/Cellar/rdock/24.04.204/share/data/scripts/dock.prm", "-n", "50", "-i", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunks/chunk_000.sdf", "-o", "/Users/makardorohuntsev/Docking_project/results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_000_out" ], "cwd": "results/benchmark_fixes/reference_sample/full_docking/target", "start_time": "2026-06-14T19:18:32.416364+00:00", "end_time": "2026-06-14T19:21:57.012419+00:00", "exit_code": 0, "stdout_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_000.stdout.log", "stderr_log": "results/benchmark_fixes/reference_sample/full_docking/rdock/chunk_000.stderr.log" } ], "artifacts": { "all_poses_sdf": "results/benchmark_fixes/reference_sample/full_docking/poses/all_poses.sdf", "best_per_ligand_sdf": "results/benchmark_fixes/reference_sample/full_docking/poses/best_per_ligand.sdf", "best_ligand_poses_sdf": "results/benchmark_fixes/reference_sample/full_docking/poses/best_ligand_50.sdf", "scores_long_csv": "results/benchmark_fixes/reference_sample/full_docking/tables/scores_long.csv", "best_per_ligand_csv": "results/benchmark_fixes/reference_sample/full_docking/tables/best_per_ligand.csv", "failed_chunks_csv": "results/benchmark_fixes/reference_sample/full_docking/tables/failed_chunks.csv", "failed_ligands_csv": "results/benchmark_fixes/reference_sample/full_docking/tables/failed_ligands.csv", "rdock_failure_summary_json": "results/benchmark_fixes/reference_sample/full_docking/metrics/rdock_failure_summary.json", "commands_log": "results/benchmark_fixes/reference_sample/full_docking/commands.log" }, "pose_count": 14900, "docked_ligand_count": 298, "rdock_failure_summary": { "failure_policy": "mark_failed", "total_chunks": 11, "successful_chunks": 11, "failed_chunks": 0, "failed_ligands": 0, "records_without_score_dropped": 50 } }