├── README.md ├── inputs.dat ├── models ├── bestmodel_cpu.pth ├── figure1.png └── r6-r1_0.3-2.0nm_train_mean_std.csv ├── retrain ├── generate_features.py ├── inputs.dat ├── samples │ ├── 1bcu │ │ ├── 1bcu_decoys.pdbqt │ │ ├── 1bcu_ligand.mol2 │ │ ├── 1bcu_ligand.sdf │ │ ├── 1bcu_protein.pdb │ │ └── 1bcu_protein_noHETATM.pdb │ ├── 1pxn │ │ ├── 1pxn_decoys.pdbqt │ │ ├── 1pxn_ligand.mol2 │ │ ├── 1pxn_ligand.sdf │ │ ├── 1pxn_protein.pdb │ │ └── 1pxn_protein_noHETATM.pdb │ ├── 3dd0 │ │ ├── 3dd0_decoys.pdbqt │ │ ├── 3dd0_ligand.mol2 │ │ ├── 3dd0_ligand.sdf │ │ ├── 3dd0_protein.pdb │ │ └── 3dd0_protein_noHETATM.pdb │ └── 3ueu │ │ ├── 3ueu_decoys.pdbqt │ │ ├── 3ueu_ligand.mol2 │ │ ├── 3ueu_ligand.sdf │ │ ├── 3ueu_protein.pdb │ │ └── 3ueu_protein_noHETATM.pdb ├── train.py └── utils.py ├── run_pose_optimization.sh ├── samples ├── 1gpn │ ├── 1gpn_protein_atom_noHETATM.pdbqt │ └── decoys │ │ ├── 1gpn_404.pdbqt │ │ ├── 1gpn_483.pdbqt │ │ ├── 1gpn_553.pdbqt │ │ └── 1gpn_617.pdbqt ├── 1syi │ ├── 1syi_protein_atom_noHETATM.pdbqt │ └── decoys │ │ ├── 1syi_562.pdbqt │ │ ├── 1syi_570.pdbqt │ │ ├── 1syi_573.pdbqt │ │ └── 1syi_637.pdbqt ├── 2vw5 │ ├── 2vw5_protein_atom_noHETATM.pdbqt │ └── decoys │ │ ├── 2vw5_415.pdbqt │ │ ├── 2vw5_434.pdbqt │ │ ├── 2vw5_537.pdbqt │ │ └── 2vw5_687.pdbqt ├── 3aru │ ├── 3aru_protein_atom_noHETATM.pdbqt │ └── decoys │ │ ├── 3aru_482.pdbqt │ │ ├── 3aru_533.pdbqt │ │ ├── 3aru_686.pdbqt │ │ └── 3aru_99.pdbqt ├── 3n86 │ ├── 3n86_protein_atom_noHETATM.pdbqt │ └── decoys │ │ ├── 3n86_404.pdbqt │ │ ├── 3n86_412.pdbqt │ │ ├── 3n86_451.pdbqt │ │ └── 3n86_472.pdbqt └── 4ddk │ ├── 4ddk_protein_atom_noHETATM.pdbqt │ └── decoys │ └── 4ddk_515.pdbqt ├── scoring ├── out.csv ├── run_scoring.sh ├── samples │ ├── 1bcu_decoys.pdbqt │ └── 1bcu_protein_noHETATM.pdbqt └── scripts │ ├── __pycache__ │ ├── argparse_utils.cpython-38.pyc │ ├── model.cpython-38.pyc │ ├── parse_ligand.cpython-38.pyc │ ├── parse_receptor.cpython-38.pyc │ ├── scoring_function.cpython-38.pyc │ └── utils.cpython-38.pyc │ ├── argparse_utils.py │ ├── atomtype_mapping.json │ ├── covalent_radii_dict.json │ ├── model.py │ ├── parse_ligand.py │ ├── parse_receptor.py │ ├── run.py │ ├── scoring_function.py │ └── vdw_radii_dict.json ├── scripts ├── __pycache__ │ ├── argparse_utils.cpython-38.pyc │ ├── argparse_utils.cpython-39.pyc │ ├── conformation_to_xyz.cpython-38.pyc │ ├── conformation_to_xyz.cpython-39.pyc │ ├── model.cpython-38.pyc │ ├── model.cpython-39.pyc │ ├── optimization.cpython-38.pyc │ ├── optimization.cpython-39.pyc │ ├── parse_ligand.cpython-38.pyc │ ├── parse_ligand.cpython-39.pyc │ ├── parse_receptor.cpython-38.pyc │ ├── parse_receptor.cpython-39.pyc │ ├── scoring_function.cpython-38.pyc │ ├── scoring_function.cpython-39.pyc │ ├── utils.cpython-38.pyc │ └── utils.cpython-39.pyc ├── argparse_utils.py ├── atomtype_mapping.json ├── conformation_to_xyz.py ├── covalent_radii_dict.json ├── model.py ├── optimization.py ├── parse_ligand.py ├── parse_receptor.py ├── run.py ├── scoring_function.py ├── test_ligand.py ├── utils.py └── vdw_radii_dict.json ├── test_output ├── 1gpn │ ├── 1gpn_404 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 1gpn_483 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 1gpn_553 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ └── 1gpn_617 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb ├── 1syi │ ├── 1syi_562 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 1syi_570 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 1syi_573 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ └── 1syi_637 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb ├── 2vw5 │ ├── 2vw5_415 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 2vw5_434 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 2vw5_537 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ └── 2vw5_687 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb ├── 3aru │ ├── 3aru_482 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 3aru_533 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 3aru_686 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ └── 3aru_99 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb ├── 3n86 │ ├── 3n86_404 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 3n86_412 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ ├── 3n86_451 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb │ └── 3n86_472 │ │ ├── current_pose.pdb │ │ ├── final_optimized_cnfr.pdb │ │ ├── final_score.csv │ │ ├── opt_data.csv │ │ └── optimized_traj.pdb └── 4ddk │ └── 4ddk_515 │ ├── current_pose.pdb │ ├── opt_data.csv │ └── optimized_traj.pdb └── write_inputs.py /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/README.md -------------------------------------------------------------------------------- /inputs.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/inputs.dat -------------------------------------------------------------------------------- /models/bestmodel_cpu.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/models/bestmodel_cpu.pth -------------------------------------------------------------------------------- /models/figure1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/models/figure1.png -------------------------------------------------------------------------------- /models/r6-r1_0.3-2.0nm_train_mean_std.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/models/r6-r1_0.3-2.0nm_train_mean_std.csv -------------------------------------------------------------------------------- /retrain/generate_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/generate_features.py -------------------------------------------------------------------------------- /retrain/inputs.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/inputs.dat -------------------------------------------------------------------------------- /retrain/samples/1bcu/1bcu_decoys.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1bcu/1bcu_decoys.pdbqt -------------------------------------------------------------------------------- /retrain/samples/1bcu/1bcu_ligand.mol2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1bcu/1bcu_ligand.mol2 -------------------------------------------------------------------------------- /retrain/samples/1bcu/1bcu_ligand.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1bcu/1bcu_ligand.sdf -------------------------------------------------------------------------------- /retrain/samples/1bcu/1bcu_protein.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1bcu/1bcu_protein.pdb -------------------------------------------------------------------------------- /retrain/samples/1bcu/1bcu_protein_noHETATM.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1bcu/1bcu_protein_noHETATM.pdb -------------------------------------------------------------------------------- /retrain/samples/1pxn/1pxn_decoys.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1pxn/1pxn_decoys.pdbqt -------------------------------------------------------------------------------- /retrain/samples/1pxn/1pxn_ligand.mol2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1pxn/1pxn_ligand.mol2 -------------------------------------------------------------------------------- /retrain/samples/1pxn/1pxn_ligand.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1pxn/1pxn_ligand.sdf -------------------------------------------------------------------------------- /retrain/samples/1pxn/1pxn_protein.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1pxn/1pxn_protein.pdb -------------------------------------------------------------------------------- /retrain/samples/1pxn/1pxn_protein_noHETATM.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/1pxn/1pxn_protein_noHETATM.pdb -------------------------------------------------------------------------------- /retrain/samples/3dd0/3dd0_decoys.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3dd0/3dd0_decoys.pdbqt -------------------------------------------------------------------------------- /retrain/samples/3dd0/3dd0_ligand.mol2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3dd0/3dd0_ligand.mol2 -------------------------------------------------------------------------------- /retrain/samples/3dd0/3dd0_ligand.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3dd0/3dd0_ligand.sdf -------------------------------------------------------------------------------- /retrain/samples/3dd0/3dd0_protein.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3dd0/3dd0_protein.pdb -------------------------------------------------------------------------------- /retrain/samples/3dd0/3dd0_protein_noHETATM.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3dd0/3dd0_protein_noHETATM.pdb -------------------------------------------------------------------------------- /retrain/samples/3ueu/3ueu_decoys.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3ueu/3ueu_decoys.pdbqt -------------------------------------------------------------------------------- /retrain/samples/3ueu/3ueu_ligand.mol2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3ueu/3ueu_ligand.mol2 -------------------------------------------------------------------------------- /retrain/samples/3ueu/3ueu_ligand.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3ueu/3ueu_ligand.sdf -------------------------------------------------------------------------------- /retrain/samples/3ueu/3ueu_protein.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3ueu/3ueu_protein.pdb -------------------------------------------------------------------------------- /retrain/samples/3ueu/3ueu_protein_noHETATM.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/samples/3ueu/3ueu_protein_noHETATM.pdb -------------------------------------------------------------------------------- /retrain/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/train.py -------------------------------------------------------------------------------- /retrain/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/retrain/utils.py -------------------------------------------------------------------------------- /run_pose_optimization.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/run_pose_optimization.sh -------------------------------------------------------------------------------- /samples/1gpn/1gpn_protein_atom_noHETATM.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1gpn/1gpn_protein_atom_noHETATM.pdbqt -------------------------------------------------------------------------------- /samples/1gpn/decoys/1gpn_404.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1gpn/decoys/1gpn_404.pdbqt -------------------------------------------------------------------------------- /samples/1gpn/decoys/1gpn_483.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1gpn/decoys/1gpn_483.pdbqt -------------------------------------------------------------------------------- /samples/1gpn/decoys/1gpn_553.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1gpn/decoys/1gpn_553.pdbqt -------------------------------------------------------------------------------- /samples/1gpn/decoys/1gpn_617.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1gpn/decoys/1gpn_617.pdbqt -------------------------------------------------------------------------------- /samples/1syi/1syi_protein_atom_noHETATM.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1syi/1syi_protein_atom_noHETATM.pdbqt -------------------------------------------------------------------------------- /samples/1syi/decoys/1syi_562.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1syi/decoys/1syi_562.pdbqt -------------------------------------------------------------------------------- /samples/1syi/decoys/1syi_570.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1syi/decoys/1syi_570.pdbqt -------------------------------------------------------------------------------- /samples/1syi/decoys/1syi_573.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1syi/decoys/1syi_573.pdbqt -------------------------------------------------------------------------------- /samples/1syi/decoys/1syi_637.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/1syi/decoys/1syi_637.pdbqt -------------------------------------------------------------------------------- /samples/2vw5/2vw5_protein_atom_noHETATM.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/2vw5/2vw5_protein_atom_noHETATM.pdbqt -------------------------------------------------------------------------------- /samples/2vw5/decoys/2vw5_415.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/2vw5/decoys/2vw5_415.pdbqt -------------------------------------------------------------------------------- /samples/2vw5/decoys/2vw5_434.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/2vw5/decoys/2vw5_434.pdbqt -------------------------------------------------------------------------------- /samples/2vw5/decoys/2vw5_537.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/2vw5/decoys/2vw5_537.pdbqt -------------------------------------------------------------------------------- /samples/2vw5/decoys/2vw5_687.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/2vw5/decoys/2vw5_687.pdbqt -------------------------------------------------------------------------------- /samples/3aru/3aru_protein_atom_noHETATM.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3aru/3aru_protein_atom_noHETATM.pdbqt -------------------------------------------------------------------------------- /samples/3aru/decoys/3aru_482.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3aru/decoys/3aru_482.pdbqt -------------------------------------------------------------------------------- /samples/3aru/decoys/3aru_533.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3aru/decoys/3aru_533.pdbqt -------------------------------------------------------------------------------- /samples/3aru/decoys/3aru_686.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3aru/decoys/3aru_686.pdbqt -------------------------------------------------------------------------------- /samples/3aru/decoys/3aru_99.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3aru/decoys/3aru_99.pdbqt -------------------------------------------------------------------------------- /samples/3n86/3n86_protein_atom_noHETATM.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3n86/3n86_protein_atom_noHETATM.pdbqt -------------------------------------------------------------------------------- /samples/3n86/decoys/3n86_404.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3n86/decoys/3n86_404.pdbqt -------------------------------------------------------------------------------- /samples/3n86/decoys/3n86_412.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3n86/decoys/3n86_412.pdbqt -------------------------------------------------------------------------------- /samples/3n86/decoys/3n86_451.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3n86/decoys/3n86_451.pdbqt -------------------------------------------------------------------------------- /samples/3n86/decoys/3n86_472.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/3n86/decoys/3n86_472.pdbqt -------------------------------------------------------------------------------- /samples/4ddk/4ddk_protein_atom_noHETATM.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/4ddk/4ddk_protein_atom_noHETATM.pdbqt -------------------------------------------------------------------------------- /samples/4ddk/decoys/4ddk_515.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/samples/4ddk/decoys/4ddk_515.pdbqt -------------------------------------------------------------------------------- /scoring/out.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/out.csv -------------------------------------------------------------------------------- /scoring/run_scoring.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/run_scoring.sh -------------------------------------------------------------------------------- /scoring/samples/1bcu_decoys.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/samples/1bcu_decoys.pdbqt -------------------------------------------------------------------------------- /scoring/samples/1bcu_protein_noHETATM.pdbqt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/samples/1bcu_protein_noHETATM.pdbqt -------------------------------------------------------------------------------- /scoring/scripts/__pycache__/argparse_utils.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/__pycache__/argparse_utils.cpython-38.pyc -------------------------------------------------------------------------------- /scoring/scripts/__pycache__/model.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/__pycache__/model.cpython-38.pyc -------------------------------------------------------------------------------- /scoring/scripts/__pycache__/parse_ligand.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/__pycache__/parse_ligand.cpython-38.pyc -------------------------------------------------------------------------------- /scoring/scripts/__pycache__/parse_receptor.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/__pycache__/parse_receptor.cpython-38.pyc -------------------------------------------------------------------------------- /scoring/scripts/__pycache__/scoring_function.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/__pycache__/scoring_function.cpython-38.pyc -------------------------------------------------------------------------------- /scoring/scripts/__pycache__/utils.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/__pycache__/utils.cpython-38.pyc -------------------------------------------------------------------------------- /scoring/scripts/argparse_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/argparse_utils.py -------------------------------------------------------------------------------- /scoring/scripts/atomtype_mapping.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/atomtype_mapping.json -------------------------------------------------------------------------------- /scoring/scripts/covalent_radii_dict.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/covalent_radii_dict.json -------------------------------------------------------------------------------- /scoring/scripts/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/model.py -------------------------------------------------------------------------------- /scoring/scripts/parse_ligand.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/parse_ligand.py -------------------------------------------------------------------------------- /scoring/scripts/parse_receptor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/parse_receptor.py -------------------------------------------------------------------------------- /scoring/scripts/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/run.py -------------------------------------------------------------------------------- /scoring/scripts/scoring_function.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/scoring_function.py -------------------------------------------------------------------------------- /scoring/scripts/vdw_radii_dict.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scoring/scripts/vdw_radii_dict.json -------------------------------------------------------------------------------- /scripts/__pycache__/argparse_utils.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/argparse_utils.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/argparse_utils.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/argparse_utils.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/conformation_to_xyz.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/conformation_to_xyz.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/conformation_to_xyz.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/conformation_to_xyz.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/model.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/model.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/model.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/model.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/optimization.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/optimization.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/optimization.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/optimization.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/parse_ligand.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/parse_ligand.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/parse_ligand.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/parse_ligand.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/parse_receptor.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/parse_receptor.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/parse_receptor.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/parse_receptor.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/scoring_function.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/scoring_function.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/scoring_function.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/scoring_function.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/utils.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/utils.cpython-38.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/utils.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/__pycache__/utils.cpython-39.pyc -------------------------------------------------------------------------------- /scripts/argparse_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/argparse_utils.py -------------------------------------------------------------------------------- /scripts/atomtype_mapping.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/atomtype_mapping.json -------------------------------------------------------------------------------- /scripts/conformation_to_xyz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/conformation_to_xyz.py -------------------------------------------------------------------------------- /scripts/covalent_radii_dict.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/covalent_radii_dict.json -------------------------------------------------------------------------------- /scripts/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/model.py -------------------------------------------------------------------------------- /scripts/optimization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/optimization.py -------------------------------------------------------------------------------- /scripts/parse_ligand.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/parse_ligand.py -------------------------------------------------------------------------------- /scripts/parse_receptor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/parse_receptor.py -------------------------------------------------------------------------------- /scripts/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/run.py -------------------------------------------------------------------------------- /scripts/scoring_function.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/scoring_function.py -------------------------------------------------------------------------------- /scripts/test_ligand.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/test_ligand.py -------------------------------------------------------------------------------- /scripts/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/utils.py -------------------------------------------------------------------------------- /scripts/vdw_radii_dict.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/scripts/vdw_radii_dict.json -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_404/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_404/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_404/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_404/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_404/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_404/final_score.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_404/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_404/opt_data.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_404/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_404/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_483/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_483/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_483/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_483/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_483/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_483/final_score.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_483/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_483/opt_data.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_483/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_483/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_553/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_553/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_553/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_553/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_553/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_553/final_score.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_553/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_553/opt_data.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_553/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_553/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_617/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_617/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_617/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_617/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_617/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_617/final_score.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_617/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_617/opt_data.csv -------------------------------------------------------------------------------- /test_output/1gpn/1gpn_617/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1gpn/1gpn_617/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_562/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_562/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_562/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_562/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_562/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_562/final_score.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_562/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_562/opt_data.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_562/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_562/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_570/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_570/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_570/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_570/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_570/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_570/final_score.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_570/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_570/opt_data.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_570/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_570/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_573/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_573/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_573/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_573/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_573/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_573/final_score.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_573/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_573/opt_data.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_573/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_573/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_637/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_637/current_pose.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_637/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_637/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/1syi/1syi_637/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_637/final_score.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_637/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_637/opt_data.csv -------------------------------------------------------------------------------- /test_output/1syi/1syi_637/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/1syi/1syi_637/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_415/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_415/current_pose.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_415/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_415/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_415/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_415/final_score.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_415/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_415/opt_data.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_415/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_415/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_434/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_434/current_pose.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_434/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_434/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_434/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_434/final_score.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_434/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_434/opt_data.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_434/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_434/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_537/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_537/current_pose.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_537/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_537/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_537/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_537/final_score.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_537/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_537/opt_data.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_537/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_537/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_687/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_687/current_pose.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_687/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_687/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_687/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_687/final_score.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_687/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_687/opt_data.csv -------------------------------------------------------------------------------- /test_output/2vw5/2vw5_687/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/2vw5/2vw5_687/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_482/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_482/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_482/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_482/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_482/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_482/final_score.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_482/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_482/opt_data.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_482/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_482/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_533/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_533/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_533/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_533/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_533/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_533/final_score.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_533/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_533/opt_data.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_533/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_533/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_686/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_686/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_686/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_686/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_686/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_686/final_score.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_686/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_686/opt_data.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_686/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_686/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_99/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_99/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_99/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_99/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3aru/3aru_99/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_99/final_score.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_99/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_99/opt_data.csv -------------------------------------------------------------------------------- /test_output/3aru/3aru_99/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3aru/3aru_99/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_404/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_404/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_404/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_404/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_404/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_404/final_score.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_404/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_404/opt_data.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_404/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_404/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_412/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_412/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_412/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_412/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_412/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_412/final_score.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_412/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_412/opt_data.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_412/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_412/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_451/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_451/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_451/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_451/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_451/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_451/final_score.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_451/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_451/opt_data.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_451/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_451/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_472/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_472/current_pose.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_472/final_optimized_cnfr.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_472/final_optimized_cnfr.pdb -------------------------------------------------------------------------------- /test_output/3n86/3n86_472/final_score.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_472/final_score.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_472/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_472/opt_data.csv -------------------------------------------------------------------------------- /test_output/3n86/3n86_472/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/3n86/3n86_472/optimized_traj.pdb -------------------------------------------------------------------------------- /test_output/4ddk/4ddk_515/current_pose.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/4ddk/4ddk_515/current_pose.pdb -------------------------------------------------------------------------------- /test_output/4ddk/4ddk_515/opt_data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/4ddk/4ddk_515/opt_data.csv -------------------------------------------------------------------------------- /test_output/4ddk/4ddk_515/optimized_traj.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/test_output/4ddk/4ddk_515/optimized_traj.pdb -------------------------------------------------------------------------------- /write_inputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zchwang/DeepRMSD-Vina_Optimization/HEAD/write_inputs.py --------------------------------------------------------------------------------